Kuan-Hao Chao
| Snapshot Date: 2026-05-22 13:45 -0400 (Fri, 22 May 2026) |
| git_url: https://git.bioconductor.org/packages/sangeranalyseR |
| git_branch: devel |
| git_last_commit: f6375ae |
| git_last_commit_date: 2026-05-05 23:58:14 -0400 (Tue, 05 May 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-23 11:36 -0400 (Sat, 23 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4937 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4639 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1895/2379 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sangeranalyseR 1.23.0 (landing page) Kuan-Hao Chao
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for sangeranalyseR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the sangeranalyseR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangeranalyseR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: sangeranalyseR |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sangeranalyseR_1.23.0.tar.gz |
| StartedAt: 2026-05-22 21:37:17 -0400 (Fri, 22 May 2026) |
| EndedAt: 2026-05-22 21:39:48 -0400 (Fri, 22 May 2026) |
| EllapsedTime: 150.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sangeranalyseR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sangeranalyseR_1.23.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/sangeranalyseR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-23 01:37:17 UTC
* using option ‘--no-vignettes’
* checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sangeranalyseR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... INFO
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 1.0Mb
extdata 5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SangerAlignment-class 12.953 5.16 17.937
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
sangeranalyseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sangeranalyseR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘sangeranalyseR’ ... ** this is package ‘sangeranalyseR’ version ‘1.23.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c peakvalues.cpp -o peakvalues.o clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sangeranalyseR.so RcppExports.o peakvalues.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-sangeranalyseR/00new/sangeranalyseR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '==' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sangeranalyseR)
sangeranalyseR.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(sangeranalyseR)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following object is masked from 'package:utils':
data
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: DECIPHER
Loading required package: sangerseqR
Loading required package: pwalign
Loading required package: stringr
Welcome to sangeranalyseR
>
> test_check("sangeranalyseR")
INFO [2026-05-22 21:38:42] #################################################
INFO [2026-05-22 21:38:42] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:42] #################################################
INFO [2026-05-22 21:38:42] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:42] ========================================================
INFO [2026-05-22 21:38:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:42] ========================================================
INFO [2026-05-22 21:38:42] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:38:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:42] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:42] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:42] >> The number of reads detected: 2
================================================================================
Time difference of 0.02 secs
SUCCESS [2026-05-22 21:38:43] ==========================================================
SUCCESS [2026-05-22 21:38:43] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:43] ==========================================================
INFO [2026-05-22 21:38:43] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:43] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:43] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:43] ========================================================
INFO [2026-05-22 21:38:43] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:43] ========================================================
INFO [2026-05-22 21:38:43] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:38:43] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:43] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:43] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:43] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:43] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:43] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:43] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:43] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:43] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:44] ==========================================================
SUCCESS [2026-05-22 21:38:44] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:44] ==========================================================
INFO [2026-05-22 21:38:44] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:44] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:44] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:44] ========================================================
INFO [2026-05-22 21:38:44] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:44] ========================================================
INFO [2026-05-22 21:38:44] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:38:44] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:44] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:44] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:44] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:44] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:44] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:44] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:45] ==========================================================
SUCCESS [2026-05-22 21:38:45] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:45] ==========================================================
INFO [2026-05-22 21:38:45] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:45] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:45] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:45] ========================================================
INFO [2026-05-22 21:38:45] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:45] ========================================================
INFO [2026-05-22 21:38:45] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:38:45] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:45] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:45] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:45] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:45] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:45] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:45] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:45] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:45] >> The number of reads detected: 2
================================================================================
Time difference of 0.02 secs
SUCCESS [2026-05-22 21:38:46] ==========================================================
SUCCESS [2026-05-22 21:38:46] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:46] ==========================================================
INFO [2026-05-22 21:38:46] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:46] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:46] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:46] Aligning consensus reads ...
SUCCESS [2026-05-22 21:38:46] #############################################################
SUCCESS [2026-05-22 21:38:46] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:46] #############################################################
INFO [2026-05-22 21:38:46] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:46] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:38:46] >> 1 forward reads.
INFO [2026-05-22 21:38:46] >> 1 reverse reads.
INFO [2026-05-22 21:38:46] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:38:46] >> 1 forward reads.
INFO [2026-05-22 21:38:46] >> 1 reverse reads.
INFO [2026-05-22 21:38:46] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:38:46] >> 1 forward reads.
INFO [2026-05-22 21:38:46] >> 1 reverse reads.
INFO [2026-05-22 21:38:46] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:38:46] >> 1 forward reads.
INFO [2026-05-22 21:38:46] >> 1 reverse reads.
INFO [2026-05-22 21:38:46] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:38:46] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:46] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:46] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:46] #################################################
INFO [2026-05-22 21:38:46] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:46] #################################################
INFO [2026-05-22 21:38:46] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:38:46] ========================================================
INFO [2026-05-22 21:38:46] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:46] ========================================================
INFO [2026-05-22 21:38:46] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:38:46] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:46] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:46] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:46] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:47] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:47] ==========================================================
SUCCESS [2026-05-22 21:38:47] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:47] ==========================================================
INFO [2026-05-22 21:38:47] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:47] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:47] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:47] ========================================================
INFO [2026-05-22 21:38:47] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:47] ========================================================
INFO [2026-05-22 21:38:47] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:47] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:47] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:47] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:48] ==========================================================
SUCCESS [2026-05-22 21:38:48] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:48] ==========================================================
INFO [2026-05-22 21:38:48] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:48] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:48] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:48] ========================================================
INFO [2026-05-22 21:38:48] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:48] ========================================================
INFO [2026-05-22 21:38:48] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:38:48] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:48] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:48] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:48] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:48] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:48] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:48] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:49] ==========================================================
SUCCESS [2026-05-22 21:38:49] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:49] ==========================================================
INFO [2026-05-22 21:38:49] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:49] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:49] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:49] ========================================================
INFO [2026-05-22 21:38:49] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:49] ========================================================
INFO [2026-05-22 21:38:49] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:38:49] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:49] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:49] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:49] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:49] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:49] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:49] >> The number of reads detected: 2
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:49] ==========================================================
SUCCESS [2026-05-22 21:38:49] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:49] ==========================================================
INFO [2026-05-22 21:38:49] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:49] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:49] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:49] Aligning consensus reads ...
SUCCESS [2026-05-22 21:38:50] #############################################################
SUCCESS [2026-05-22 21:38:50] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:50] #############################################################
INFO [2026-05-22 21:38:50] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:50] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:38:50] >> 1 forward reads.
INFO [2026-05-22 21:38:50] >> 1 reverse reads.
INFO [2026-05-22 21:38:50] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:38:50] >> 1 forward reads.
INFO [2026-05-22 21:38:50] >> 1 reverse reads.
INFO [2026-05-22 21:38:50] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:38:50] >> 1 forward reads.
INFO [2026-05-22 21:38:50] >> 1 reverse reads.
INFO [2026-05-22 21:38:50] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:38:50] >> 1 forward reads.
INFO [2026-05-22 21:38:50] >> 1 reverse reads.
INFO [2026-05-22 21:38:50] >> 8 reads created from FASTA file.
DEBUG [2026-05-22 21:38:50] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:50] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:50] ========================================================
INFO [2026-05-22 21:38:50] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:50] ========================================================
INFO [2026-05-22 21:38:50] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:38:50] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:50] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:38:50] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:50] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:50] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:50] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:50] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:50] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:50] >> The number of reads detected: 2
INFO [2026-05-22 21:38:50] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:51] ==========================================================
SUCCESS [2026-05-22 21:38:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:51] ==========================================================
INFO [2026-05-22 21:38:51] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:51] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:51] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:51] >> For more information, please run 'object'
DEBUG [2026-05-22 21:38:51] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:51] ========================================================
INFO [2026-05-22 21:38:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:51] ========================================================
INFO [2026-05-22 21:38:51] >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-22 21:38:51] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:51] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-22 21:38:51] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:51] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:51] >> 'Achl_RBNII384-13_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:51] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:51] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:51] >> 'Achl_RBNII384-13_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:51] >> The number of reads detected: 2
INFO [2026-05-22 21:38:51] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.02 secs
SUCCESS [2026-05-22 21:38:52] ==========================================================
SUCCESS [2026-05-22 21:38:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:52] ==========================================================
INFO [2026-05-22 21:38:52] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:52] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:52] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:52] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:52] >> For more information, please run 'object'
DEBUG [2026-05-22 21:38:52] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:52] ========================================================
INFO [2026-05-22 21:38:52] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:52] ========================================================
INFO [2026-05-22 21:38:52] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:38:52] >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:38:52] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:38:52] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:52] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:52] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:52] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:52] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:52] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:52] >> The number of reads detected: 2
INFO [2026-05-22 21:38:52] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.02 secs
SUCCESS [2026-05-22 21:38:53] ==========================================================
SUCCESS [2026-05-22 21:38:53] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:53] ==========================================================
INFO [2026-05-22 21:38:53] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:53] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:53] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-22 21:38:53] >> For more information, please run 'object'
DEBUG [2026-05-22 21:38:53] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:53] ========================================================
INFO [2026-05-22 21:38:53] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:53] ========================================================
INFO [2026-05-22 21:38:53] >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-22 21:38:53] >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-22 21:38:53] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-22 21:38:53] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:53] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:53] >> 'Achl_RBNII384-13_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:38:53] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:53] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:53] >> 'Achl_RBNII384-13_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:53] >> The number of reads detected: 2
INFO [2026-05-22 21:38:53] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.01 secs
SUCCESS [2026-05-22 21:38:54] ==========================================================
SUCCESS [2026-05-22 21:38:54] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:54] ==========================================================
INFO [2026-05-22 21:38:54] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:38:54] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:38:54] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:54] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:54] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:54] * Making basecall !!
INFO [2026-05-22 21:38:54] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:54] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:54] >> Creating Reverse Read raw abif ...
INFO [2026-05-22 21:38:54] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-22 21:38:54] * Making basecall !!
INFO [2026-05-22 21:38:54] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:54] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-22 21:38:54] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:38:54] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-22 21:38:54] FILE_NOT_EXIST_ERROR
'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/TEST_Achl_ACHLO006-09_2_R.ab1' file does not exist.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:54] ------------------------------------------------
INFO [2026-05-22 21:38:54] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:54] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:54] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:54] * Making basecall !!
INFO [2026-05-22 21:38:54] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:54] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:54] ========================================================
INFO [2026-05-22 21:38:54] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:54] ========================================================
INFO [2026-05-22 21:38:54] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:38:54] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:54] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:54] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:54] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:54] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:54] ==========================================================
SUCCESS [2026-05-22 21:38:54] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:54] ==========================================================
INFO [2026-05-22 21:38:54] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:54] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:54] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:54] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:54] >> For more information, please run 'object'
DEBUG [2026-05-22 21:38:54] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:54] #################################################
INFO [2026-05-22 21:38:54] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:54] #################################################
INFO [2026-05-22 21:38:54] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:54] ========================================================
INFO [2026-05-22 21:38:54] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:54] ========================================================
INFO [2026-05-22 21:38:54] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:55] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:55] ==========================================================
SUCCESS [2026-05-22 21:38:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:55] ==========================================================
INFO [2026-05-22 21:38:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:55] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:55] ==========================================================
SUCCESS [2026-05-22 21:38:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:55] ==========================================================
INFO [2026-05-22 21:38:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:55] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:55] ==========================================================
SUCCESS [2026-05-22 21:38:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:55] ==========================================================
INFO [2026-05-22 21:38:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:55] ========================================================
INFO [2026-05-22 21:38:55] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:55] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:55] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:55] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:55] ==========================================================
SUCCESS [2026-05-22 21:38:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:55] ==========================================================
INFO [2026-05-22 21:38:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:55] Aligning consensus reads ...
INFO [2026-05-22 21:38:55] Before building!!
INFO [2026-05-22 21:38:55] After building!!
SUCCESS [2026-05-22 21:38:55] #############################################################
SUCCESS [2026-05-22 21:38:55] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:55] #############################################################
INFO [2026-05-22 21:38:55] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:55] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:38:55] >> 1 forward reads.
INFO [2026-05-22 21:38:55] >> 1 reverse reads.
INFO [2026-05-22 21:38:55] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:38:55] >> 1 forward reads.
INFO [2026-05-22 21:38:55] >> 1 reverse reads.
INFO [2026-05-22 21:38:55] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:38:55] >> 1 forward reads.
INFO [2026-05-22 21:38:55] >> 1 reverse reads.
INFO [2026-05-22 21:38:55] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:38:55] >> 1 forward reads.
INFO [2026-05-22 21:38:55] >> 1 reverse reads.
INFO [2026-05-22 21:38:55] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:38:55] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:55] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:55] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:55] * Making basecall !!
INFO [2026-05-22 21:38:55] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:38:56] ********************************************
INFO [2026-05-22 21:38:56] ******** SangerRead readTable print ********
INFO [2026-05-22 21:38:56] ********************************************
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Forward Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1
Read fileName (base) : Achl_ACHLO006-09_1_F.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 16
Trimming finish base pair : 477
Read length before trimming : 702
Read length after trimming : 461
Read quality before trimming : 52.87607
Read quality after trimming : 58.21041
Secondary peak cutoff : 0.33
Primary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
Secondary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
INFO [2026-05-22 21:38:56] **********************************************
INFO [2026-05-22 21:38:56] ******** SangerContig readTable print ********
INFO [2026-05-22 21:38:56] **********************************************
================================
=== SangerContig S4 instance ===
================================
Input source : ABIF
Names conversion CSV file :
Contig name : Achl_ACHLO006-09
Suffix forward regex : _[0-9]*_F.ab1$
Suffix reverse regex : _[0-9]*_R.ab1$
Minimum reads number : 2
Minimum read length : 20
Minimum fraction call : 0.5
Reference amino acid sequence : SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN
Maximum fraction lost : 0.5
Accept stop codons : TRUE
Reading frame : 1
Contig sequence : TTATATTTTATTCTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGGATTACGTCTTGAACGAATTCCCCTGTTTGTCTGAGCTGTGCTAATTACAGTTGTTCTTCTACTTCTATCTTTACCAGTGCTAGCAGGTGCCATTACCATACTTCTTACCGACCGAAACCTCAATACTTCATTCTTTGATCCTGCCGGTGGTGGAGACCCCATCCTC
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Forward Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1
Read fileName (base) : Achl_ACHLO006-09_1_F.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 16
Trimming finish base pair : 477
Read length before trimming : 702
Read length after trimming : 461
Read quality before trimming : 52.87607
Read quality after trimming : 58.21041
Secondary peak cutoff : 0.33
Primary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
Secondary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Reverse Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_2_R.ab1
Read fileName (base) : Achl_ACHLO006-09_2_R.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 18
Trimming finish base pair : 658
Read length before trimming : 705
Read length after trimming : 640
Read quality before trimming : 54.85106
Read quality after trimming : 57.29531
Secondary peak cutoff : 0.33
Primary Sequence : GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGAGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA
Secondary Sequence : GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGCGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA
INFO [2026-05-22 21:38:56] Your input is 'SangerRead' S4 instance
INFO [2026-05-22 21:38:56] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb1b4047a8
INFO [2026-05-22 21:38:56] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-22 21:38:56] >> '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb1b4047a8/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-22 21:38:56] Your input is 'SangerContig' S4 instance
INFO [2026-05-22 21:38:56] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb1b4047a8
INFO [2026-05-22 21:38:56] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-22 21:38:56] >> Writing alignment to FASTA ...
INFO [2026-05-22 21:38:56] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:38:56] >> Writing consensus read to FASTA ...
INFO [2026-05-22 21:38:56] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-22 21:38:56] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-22 21:38:56] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb1b4047a8
INFO [2026-05-22 21:38:56] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-22 21:38:56] >> Writing 'alignment' to FASTA ...
INFO [2026-05-22 21:38:56] >> Writing 'contigs' to FASTA ...
INFO [2026-05-22 21:38:56] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:38:56] Finish writing 'SangerAlignment' to FASTA format
INFO [2026-05-22 21:38:56] #################################################
INFO [2026-05-22 21:38:56] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:56] #################################################
INFO [2026-05-22 21:38:56] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] >> Contig Name: 'Top'
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:56] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:56] ==========================================================
SUCCESS [2026-05-22 21:38:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:56] ==========================================================
INFO [2026-05-22 21:38:56] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] >> Contig Name: 'Nested'
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:56] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:56] ==========================================================
SUCCESS [2026-05-22 21:38:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:56] ==========================================================
INFO [2026-05-22 21:38:56] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] Aligning consensus reads ...
INFO [2026-05-22 21:38:56] Before building!!
INFO [2026-05-22 21:38:56] After building!!
INFO [2026-05-22 21:38:56] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-22 21:38:56] #############################################################
SUCCESS [2026-05-22 21:38:56] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:56] #############################################################
INFO [2026-05-22 21:38:56] >> 2 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:56] >> Contig 'Top':
INFO [2026-05-22 21:38:56] >> 1 forward reads.
INFO [2026-05-22 21:38:56] >> 1 reverse reads.
INFO [2026-05-22 21:38:56] >> Contig 'Nested':
INFO [2026-05-22 21:38:56] >> 1 forward reads.
INFO [2026-05-22 21:38:56] >> 1 reverse reads.
INFO [2026-05-22 21:38:56] >> 4 reads created from ABIF file.
INFO [2026-05-22 21:38:56] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:56] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:56] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:56] #################################################
INFO [2026-05-22 21:38:56] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:56] #################################################
INFO [2026-05-22 21:38:56] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] >> Contig Name: 'Top'
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:56] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:56] >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:56] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:56] ==========================================================
SUCCESS [2026-05-22 21:38:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:56] ==========================================================
INFO [2026-05-22 21:38:56] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:56] ========================================================
INFO [2026-05-22 21:38:56] >> Contig Name: 'Nested'
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:57] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:57] ==========================================================
SUCCESS [2026-05-22 21:38:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:57] ==========================================================
INFO [2026-05-22 21:38:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] Aligning consensus reads ...
INFO [2026-05-22 21:38:57] Before building!!
INFO [2026-05-22 21:38:57] After building!!
INFO [2026-05-22 21:38:57] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-22 21:38:57] #############################################################
SUCCESS [2026-05-22 21:38:57] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:57] #############################################################
INFO [2026-05-22 21:38:57] >> 2 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:57] >> Contig 'Top':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> Contig 'Nested':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> 4 reads created from ABIF file.
INFO [2026-05-22 21:38:57] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:57] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:57] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:57] #################################################
INFO [2026-05-22 21:38:57] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:57] #################################################
INFO [2026-05-22 21:38:57] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:57] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:57] ==========================================================
SUCCESS [2026-05-22 21:38:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:57] ==========================================================
INFO [2026-05-22 21:38:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:57] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:57] ==========================================================
SUCCESS [2026-05-22 21:38:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:57] ==========================================================
INFO [2026-05-22 21:38:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:57] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:57] ==========================================================
SUCCESS [2026-05-22 21:38:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:57] ==========================================================
INFO [2026-05-22 21:38:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:57] ========================================================
INFO [2026-05-22 21:38:57] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:57] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:57] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:57] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:57] ==========================================================
SUCCESS [2026-05-22 21:38:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:57] ==========================================================
INFO [2026-05-22 21:38:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:57] Aligning consensus reads ...
INFO [2026-05-22 21:38:57] Before building!!
INFO [2026-05-22 21:38:57] After building!!
SUCCESS [2026-05-22 21:38:57] #############################################################
SUCCESS [2026-05-22 21:38:57] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:57] #############################################################
INFO [2026-05-22 21:38:57] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:57] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:38:57] >> 1 forward reads.
INFO [2026-05-22 21:38:57] >> 1 reverse reads.
INFO [2026-05-22 21:38:57] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:38:57] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:57] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:57] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:58] * Making basecall !!
INFO [2026-05-22 21:38:58] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:58] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:58] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:58] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:58] * Making basecall !!
INFO [2026-05-22 21:38:58] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:58] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:58] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:58] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:58] * Making basecall !!
INFO [2026-05-22 21:38:58] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:58] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:58] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:58] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:58] * Making basecall !!
INFO [2026-05-22 21:38:58] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:58] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:58] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:58] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:38:58] ------------------------------------------------
INFO [2026-05-22 21:38:58] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:38:58] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:38:58] * Making basecall !!
INFO [2026-05-22 21:38:58] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:58] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:38:58] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:58] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:58] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:38:59] #################################################
INFO [2026-05-22 21:38:59] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:38:59] #################################################
INFO [2026-05-22 21:38:59] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:59] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:59] ==========================================================
SUCCESS [2026-05-22 21:38:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:59] ==========================================================
INFO [2026-05-22 21:38:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:59] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:59] ==========================================================
SUCCESS [2026-05-22 21:38:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:59] ==========================================================
INFO [2026-05-22 21:38:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:59] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:59] ==========================================================
SUCCESS [2026-05-22 21:38:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:59] ==========================================================
INFO [2026-05-22 21:38:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:38:59] ========================================================
INFO [2026-05-22 21:38:59] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:38:59] --------------------------------------------------------
SUCCESS [2026-05-22 21:38:59] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:38:59] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:38:59] ==========================================================
SUCCESS [2026-05-22 21:38:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:38:59] ==========================================================
INFO [2026-05-22 21:38:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:38:59] Aligning consensus reads ...
INFO [2026-05-22 21:38:59] Before building!!
INFO [2026-05-22 21:38:59] After building!!
SUCCESS [2026-05-22 21:38:59] #############################################################
SUCCESS [2026-05-22 21:38:59] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:38:59] #############################################################
INFO [2026-05-22 21:38:59] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:38:59] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:38:59] >> 1 forward reads.
INFO [2026-05-22 21:38:59] >> 1 reverse reads.
INFO [2026-05-22 21:38:59] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:38:59] >> 1 forward reads.
INFO [2026-05-22 21:38:59] >> 1 reverse reads.
INFO [2026-05-22 21:38:59] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:38:59] >> 1 forward reads.
INFO [2026-05-22 21:38:59] >> 1 reverse reads.
INFO [2026-05-22 21:38:59] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:38:59] >> 1 forward reads.
INFO [2026-05-22 21:38:59] >> 1 reverse reads.
INFO [2026-05-22 21:38:59] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:38:59] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:38:59] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:38:59] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:00] #################################################
INFO [2026-05-22 21:39:00] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:00] #################################################
INFO [2026-05-22 21:39:00] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:00] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:00] ==========================================================
SUCCESS [2026-05-22 21:39:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:00] ==========================================================
INFO [2026-05-22 21:39:00] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:00] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:00] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] >> Contig Name: 'Achl_ACHLO007-09'
INFO [2026-05-22 21:39:00] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:00] ==========================================================
SUCCESS [2026-05-22 21:39:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:00] ==========================================================
INFO [2026-05-22 21:39:00] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:00] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:00] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:00] ========================================================
INFO [2026-05-22 21:39:00] >> Contig Name: 'Achl_ACHLO040-09'
INFO [2026-05-22 21:39:00] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:01] ==========================================================
SUCCESS [2026-05-22 21:39:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:01] ==========================================================
INFO [2026-05-22 21:39:01] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] >> Contig Name: 'Achl_ACHLO041-09'
INFO [2026-05-22 21:39:01] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:01] ==========================================================
SUCCESS [2026-05-22 21:39:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:01] ==========================================================
INFO [2026-05-22 21:39:01] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] Aligning consensus reads ...
INFO [2026-05-22 21:39:01] Before building!!
INFO [2026-05-22 21:39:01] After building!!
SUCCESS [2026-05-22 21:39:01] #############################################################
SUCCESS [2026-05-22 21:39:01] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:01] #############################################################
INFO [2026-05-22 21:39:01] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:01] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:01] >> 1 forward reads.
INFO [2026-05-22 21:39:01] >> 1 reverse reads.
INFO [2026-05-22 21:39:01] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:01] >> 1 forward reads.
INFO [2026-05-22 21:39:01] >> 1 reverse reads.
INFO [2026-05-22 21:39:01] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:01] >> 1 forward reads.
INFO [2026-05-22 21:39:01] >> 1 reverse reads.
INFO [2026-05-22 21:39:01] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:01] >> 1 forward reads.
INFO [2026-05-22 21:39:01] >> 1 reverse reads.
INFO [2026-05-22 21:39:01] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:01] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:01] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:01] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:01] #################################################
INFO [2026-05-22 21:39:01] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:01] #################################################
INFO [2026-05-22 21:39:01] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:01] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:01] ==========================================================
SUCCESS [2026-05-22 21:39:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:01] ==========================================================
INFO [2026-05-22 21:39:01] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:01] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:01] ==========================================================
SUCCESS [2026-05-22 21:39:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:01] ==========================================================
INFO [2026-05-22 21:39:01] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:01] ========================================================
INFO [2026-05-22 21:39:01] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:01] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:01] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:02] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:02] ==========================================================
SUCCESS [2026-05-22 21:39:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:02] ==========================================================
INFO [2026-05-22 21:39:02] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:02] ========================================================
INFO [2026-05-22 21:39:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:02] ========================================================
INFO [2026-05-22 21:39:02] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:02] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:02] ==========================================================
SUCCESS [2026-05-22 21:39:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:02] ==========================================================
INFO [2026-05-22 21:39:02] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:02] Aligning consensus reads ...
INFO [2026-05-22 21:39:02] Before building!!
INFO [2026-05-22 21:39:02] After building!!
SUCCESS [2026-05-22 21:39:02] #############################################################
SUCCESS [2026-05-22 21:39:02] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:02] #############################################################
INFO [2026-05-22 21:39:02] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:02] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:02] >> 1 forward reads.
INFO [2026-05-22 21:39:02] >> 1 reverse reads.
INFO [2026-05-22 21:39:02] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:02] >> 1 forward reads.
INFO [2026-05-22 21:39:02] >> 1 reverse reads.
INFO [2026-05-22 21:39:02] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:02] >> 1 forward reads.
INFO [2026-05-22 21:39:02] >> 1 reverse reads.
INFO [2026-05-22 21:39:02] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:02] >> 1 forward reads.
INFO [2026-05-22 21:39:02] >> 1 reverse reads.
INFO [2026-05-22 21:39:02] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:02] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:02] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:02] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:02] * Making basecall !!
INFO [2026-05-22 21:39:02] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:02] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:02] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:02] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:02] * Making basecall !!
INFO [2026-05-22 21:39:02] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:02] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:02] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:02] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:02] * Making basecall !!
INFO [2026-05-22 21:39:02] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:02] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:02] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:02] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:02] ------------------------------------------------
INFO [2026-05-22 21:39:02] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:02] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:02] * Making basecall !!
INFO [2026-05-22 21:39:02] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:02] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:02] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:02] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:02] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:02] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:03] #################################################
INFO [2026-05-22 21:39:03] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:03] #################################################
INFO [2026-05-22 21:39:03] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:03] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:03] ==========================================================
SUCCESS [2026-05-22 21:39:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:03] ==========================================================
INFO [2026-05-22 21:39:03] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:03] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:03] ==========================================================
SUCCESS [2026-05-22 21:39:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:03] ==========================================================
INFO [2026-05-22 21:39:03] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:03] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:03] ==========================================================
SUCCESS [2026-05-22 21:39:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:03] ==========================================================
INFO [2026-05-22 21:39:03] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:03] ========================================================
INFO [2026-05-22 21:39:03] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:03] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:03] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:04] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:04] ==========================================================
SUCCESS [2026-05-22 21:39:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:04] ==========================================================
INFO [2026-05-22 21:39:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] Aligning consensus reads ...
INFO [2026-05-22 21:39:04] Before building!!
INFO [2026-05-22 21:39:04] After building!!
SUCCESS [2026-05-22 21:39:04] #############################################################
SUCCESS [2026-05-22 21:39:04] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:04] #############################################################
INFO [2026-05-22 21:39:04] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:04] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:04] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:04] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:04] #################################################
INFO [2026-05-22 21:39:04] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:04] #################################################
INFO [2026-05-22 21:39:04] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:04] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:04] ==========================================================
SUCCESS [2026-05-22 21:39:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:04] ==========================================================
INFO [2026-05-22 21:39:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:04] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:04] ==========================================================
SUCCESS [2026-05-22 21:39:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:04] ==========================================================
INFO [2026-05-22 21:39:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:04] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:04] ==========================================================
SUCCESS [2026-05-22 21:39:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:04] ==========================================================
INFO [2026-05-22 21:39:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:04] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:04] ==========================================================
SUCCESS [2026-05-22 21:39:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:04] ==========================================================
INFO [2026-05-22 21:39:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:04] Aligning consensus reads ...
INFO [2026-05-22 21:39:04] Before building!!
INFO [2026-05-22 21:39:04] After building!!
SUCCESS [2026-05-22 21:39:04] #############################################################
SUCCESS [2026-05-22 21:39:04] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:04] #############################################################
INFO [2026-05-22 21:39:04] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:04] >> 1 forward reads.
INFO [2026-05-22 21:39:04] >> 1 reverse reads.
INFO [2026-05-22 21:39:04] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:04] >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-22 21:39:04] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:04] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:04] #################################################
INFO [2026-05-22 21:39:04] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:04] #################################################
INFO [2026-05-22 21:39:04] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-22 21:39:04] **** Contig number in your Csv file is 4
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:04] ========================================================
INFO [2026-05-22 21:39:04] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:04] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:04] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:05] ==========================================================
SUCCESS [2026-05-22 21:39:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:05] ==========================================================
INFO [2026-05-22 21:39:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:05] ==========================================================
SUCCESS [2026-05-22 21:39:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:05] ==========================================================
INFO [2026-05-22 21:39:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:05] ==========================================================
SUCCESS [2026-05-22 21:39:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:05] ==========================================================
INFO [2026-05-22 21:39:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:05] ==========================================================
SUCCESS [2026-05-22 21:39:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:05] ==========================================================
INFO [2026-05-22 21:39:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] Aligning consensus reads ...
INFO [2026-05-22 21:39:05] Before building!!
INFO [2026-05-22 21:39:05] After building!!
SUCCESS [2026-05-22 21:39:05] #############################################################
SUCCESS [2026-05-22 21:39:05] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:05] #############################################################
INFO [2026-05-22 21:39:05] >> 4 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:05] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:05] >> 1 forward reads.
INFO [2026-05-22 21:39:05] >> 1 reverse reads.
INFO [2026-05-22 21:39:05] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:05] >> 1 forward reads.
INFO [2026-05-22 21:39:05] >> 1 reverse reads.
INFO [2026-05-22 21:39:05] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:05] >> 1 forward reads.
INFO [2026-05-22 21:39:05] >> 1 reverse reads.
INFO [2026-05-22 21:39:05] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:05] >> 1 forward reads.
INFO [2026-05-22 21:39:05] >> 1 reverse reads.
INFO [2026-05-22 21:39:05] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:05] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:05] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:05] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:05] #################################################
INFO [2026-05-22 21:39:05] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:05] #################################################
INFO [2026-05-22 21:39:05] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-22 21:39:05] **** Contig number in your Csv file is 4
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:05] ==========================================================
SUCCESS [2026-05-22 21:39:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:05] ==========================================================
INFO [2026-05-22 21:39:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:05] ========================================================
INFO [2026-05-22 21:39:05] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:05] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:05] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:05] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] Aligning consensus reads ...
INFO [2026-05-22 21:39:06] Before building!!
INFO [2026-05-22 21:39:06] After building!!
SUCCESS [2026-05-22 21:39:06] #############################################################
SUCCESS [2026-05-22 21:39:06] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:06] #############################################################
INFO [2026-05-22 21:39:06] >> 4 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:06] >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-22 21:39:06] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:06] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:06] #################################################
INFO [2026-05-22 21:39:06] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:06] #################################################
INFO [2026-05-22 21:39:06] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:06] Aligning consensus reads ...
INFO [2026-05-22 21:39:06] Before building!!
INFO [2026-05-22 21:39:06] After building!!
SUCCESS [2026-05-22 21:39:06] #############################################################
SUCCESS [2026-05-22 21:39:06] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:06] #############################################################
INFO [2026-05-22 21:39:06] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:06] >> 1 forward reads.
INFO [2026-05-22 21:39:06] >> 1 reverse reads.
INFO [2026-05-22 21:39:06] >> 8 reads created from FASTA file.
DEBUG [2026-05-22 21:39:06] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:06] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:06] #################################################
INFO [2026-05-22 21:39:06] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:06] #################################################
INFO [2026-05-22 21:39:06] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:06] ==========================================================
SUCCESS [2026-05-22 21:39:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:06] ==========================================================
INFO [2026-05-22 21:39:06] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:06] ========================================================
INFO [2026-05-22 21:39:06] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:06] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:06] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:06] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:07] ==========================================================
SUCCESS [2026-05-22 21:39:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:07] ==========================================================
INFO [2026-05-22 21:39:07] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] ========================================================
INFO [2026-05-22 21:39:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:07] ========================================================
INFO [2026-05-22 21:39:07] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:07] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:07] ==========================================================
SUCCESS [2026-05-22 21:39:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:07] ==========================================================
INFO [2026-05-22 21:39:07] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] ========================================================
INFO [2026-05-22 21:39:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:07] ========================================================
INFO [2026-05-22 21:39:07] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:07] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:07] ==========================================================
SUCCESS [2026-05-22 21:39:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:07] ==========================================================
INFO [2026-05-22 21:39:07] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:07] Aligning consensus reads ...
INFO [2026-05-22 21:39:07] Before building!!
INFO [2026-05-22 21:39:07] After building!!
SUCCESS [2026-05-22 21:39:07] #############################################################
SUCCESS [2026-05-22 21:39:07] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:07] #############################################################
INFO [2026-05-22 21:39:07] >> 4 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:07] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:07] >> 1 forward reads.
INFO [2026-05-22 21:39:07] >> 1 reverse reads.
INFO [2026-05-22 21:39:07] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:07] >> 1 forward reads.
INFO [2026-05-22 21:39:07] >> 1 reverse reads.
INFO [2026-05-22 21:39:07] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:07] >> 1 forward reads.
INFO [2026-05-22 21:39:07] >> 1 reverse reads.
INFO [2026-05-22 21:39:07] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:07] >> 1 forward reads.
INFO [2026-05-22 21:39:07] >> 1 reverse reads.
INFO [2026-05-22 21:39:07] >> 8 reads created from FASTA file.
DEBUG [2026-05-22 21:39:07] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:07] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
SUCCESS [2026-05-22 21:39:07] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
SUCCESS [2026-05-22 21:39:07] 'Achl_ACHLO006-09' is successfully created!
SUCCESS [2026-05-22 21:39:07] 'SangerAlignment' is successfully created!
ERROR [2026-05-22 21:39:07] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
DEBUG [2026-05-22 21:39:07] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:07] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-22 21:39:07] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
INFO [2026-05-22 21:39:07] ------------------------------------------------
INFO [2026-05-22 21:39:07] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:07] ------------------------------------------------
INFO [2026-05-22 21:39:07] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:07] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:07] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:07] * Making basecall !!
INFO [2026-05-22 21:39:07] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:07] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:07] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:07] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-22 21:39:07] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
INFO [2026-05-22 21:39:07] ------------------------------------------------
INFO [2026-05-22 21:39:07] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:07] ------------------------------------------------
INFO [2026-05-22 21:39:07] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:07] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:07] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-22 21:39:07] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:07] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:07] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-22 21:39:07] 'Achl_ACHLO006-09_1_F.fa' is successfully created!
ERROR [2026-05-22 21:39:07] 'object' must be S4 instance!
ERROR [2026-05-22 21:39:07] 'object' must be 'SangerAlignment' or 'SangerContig' S4 instance!
INFO [2026-05-22 21:39:07] Your input is 'SangerRead' S4 instance
INFO [2026-05-22 21:39:07] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb78eb651b
INFO [2026-05-22 21:39:07] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-22 21:39:07] >> '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb78eb651b/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-22 21:39:07] Your input is 'SangerContig' S4 instance
INFO [2026-05-22 21:39:07] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb78eb651b
INFO [2026-05-22 21:39:07] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-22 21:39:07] >> Writing alignment to FASTA ...
INFO [2026-05-22 21:39:07] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:39:07] >> Writing consensus read to FASTA ...
INFO [2026-05-22 21:39:07] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-22 21:39:07] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-22 21:39:07] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb78eb651b
INFO [2026-05-22 21:39:07] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-22 21:39:07] >> Writing 'alignment' to FASTA ...
INFO [2026-05-22 21:39:07] >> Writing 'contigs' to FASTA ...
INFO [2026-05-22 21:39:07] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:39:07] Finish writing 'SangerAlignment' to FASTA format
ERROR [2026-05-22 21:39:07] 'object' must be S4 instance!
ERROR [2026-05-22 21:39:07] 'object' must be S4 instance!
INFO [2026-05-22 21:39:08] * Making basecall !!
INFO [2026-05-22 21:39:08] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:08] #################################################
INFO [2026-05-22 21:39:08] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:08] #################################################
INFO [2026-05-22 21:39:08] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:08] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:08] ==========================================================
SUCCESS [2026-05-22 21:39:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:08] ==========================================================
INFO [2026-05-22 21:39:08] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:08] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:08] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:08] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:08] ==========================================================
SUCCESS [2026-05-22 21:39:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:08] ==========================================================
INFO [2026-05-22 21:39:08] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:08] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:08] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:08] ========================================================
INFO [2026-05-22 21:39:08] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:08] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:09] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:09] ==========================================================
SUCCESS [2026-05-22 21:39:09] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:09] ==========================================================
INFO [2026-05-22 21:39:09] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:09] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:09] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:09] ========================================================
INFO [2026-05-22 21:39:09] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:09] ========================================================
INFO [2026-05-22 21:39:09] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:09] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:09] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:09] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:09] ==========================================================
SUCCESS [2026-05-22 21:39:09] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:09] ==========================================================
INFO [2026-05-22 21:39:09] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:09] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:09] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:09] Aligning consensus reads ...
INFO [2026-05-22 21:39:09] Before building!!
INFO [2026-05-22 21:39:09] After building!!
SUCCESS [2026-05-22 21:39:09] #############################################################
SUCCESS [2026-05-22 21:39:09] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:09] #############################################################
INFO [2026-05-22 21:39:09] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:09] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:09] >> 1 forward reads.
INFO [2026-05-22 21:39:09] >> 1 reverse reads.
INFO [2026-05-22 21:39:09] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:09] >> 1 forward reads.
INFO [2026-05-22 21:39:09] >> 1 reverse reads.
INFO [2026-05-22 21:39:09] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:09] >> 1 forward reads.
INFO [2026-05-22 21:39:09] >> 1 reverse reads.
INFO [2026-05-22 21:39:09] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:09] >> 1 forward reads.
INFO [2026-05-22 21:39:09] >> 1 reverse reads.
INFO [2026-05-22 21:39:09] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:09] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:09] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:09] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:11] Aligning consensus reads ...
INFO [2026-05-22 21:39:11] Before building!!
INFO [2026-05-22 21:39:11] After building!!
INFO [2026-05-22 21:39:12] Aligning consensus reads ...
INFO [2026-05-22 21:39:12] Before building!!
INFO [2026-05-22 21:39:12] After building!!
INFO [2026-05-22 21:39:12] #################################################
INFO [2026-05-22 21:39:12] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:12] #################################################
INFO [2026-05-22 21:39:12] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:39:12] ========================================================
INFO [2026-05-22 21:39:12] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:12] ========================================================
INFO [2026-05-22 21:39:12] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:12] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:12] ==========================================================
SUCCESS [2026-05-22 21:39:12] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:12] ==========================================================
INFO [2026-05-22 21:39:12] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:12] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:12] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:12] ========================================================
INFO [2026-05-22 21:39:12] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:12] ========================================================
INFO [2026-05-22 21:39:12] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:12] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:12] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:12] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:13] ==========================================================
SUCCESS [2026-05-22 21:39:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:13] ==========================================================
INFO [2026-05-22 21:39:13] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] ========================================================
INFO [2026-05-22 21:39:13] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:13] ========================================================
INFO [2026-05-22 21:39:13] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:13] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:13] ==========================================================
SUCCESS [2026-05-22 21:39:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:13] ==========================================================
INFO [2026-05-22 21:39:13] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] ========================================================
INFO [2026-05-22 21:39:13] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:13] ========================================================
INFO [2026-05-22 21:39:13] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:13] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:13] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:13] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:13] ==========================================================
SUCCESS [2026-05-22 21:39:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:13] ==========================================================
INFO [2026-05-22 21:39:13] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:13] Aligning consensus reads ...
INFO [2026-05-22 21:39:13] Before building!!
INFO [2026-05-22 21:39:13] After building!!
SUCCESS [2026-05-22 21:39:13] #############################################################
SUCCESS [2026-05-22 21:39:13] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:13] #############################################################
INFO [2026-05-22 21:39:13] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:13] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:13] >> 1 forward reads.
INFO [2026-05-22 21:39:13] >> 1 reverse reads.
INFO [2026-05-22 21:39:13] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:13] >> 1 forward reads.
INFO [2026-05-22 21:39:13] >> 1 reverse reads.
INFO [2026-05-22 21:39:13] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:13] >> 1 forward reads.
INFO [2026-05-22 21:39:13] >> 1 reverse reads.
INFO [2026-05-22 21:39:13] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:13] >> 1 forward reads.
INFO [2026-05-22 21:39:13] >> 1 reverse reads.
INFO [2026-05-22 21:39:13] >> 8 reads created from FASTA file.
DEBUG [2026-05-22 21:39:13] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:13] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:13] SangerAlignment with 'FASTA' inputSource cannot update quality parameters
ERROR [2026-05-22 21:39:13] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
ERROR [2026-05-22 21:39:13] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
INFO [2026-05-22 21:39:13] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb67359e32
INFO [2026-05-22 21:39:13] * Making basecall !!
INFO [2026-05-22 21:39:13] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:13] Chromatogram saved to /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb67359e32/Achl_ACHLO006-09_1_F/Chromatogram.pdf in the current working directory
/usr/local/bin/pandoc +RTS -K512m -RTS SangerRead_Report_ab1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb67359e32/Achl_ACHLO006-09_1_F/SangerRead_Report_ab1.html --lua-filter /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/rmarkdown-strdaeb7e538cc0.html
[WARNING] Div at SangerRead_Report_ab1.knit.md line 153 column 1 unclosed at SangerRead_Report_ab1.knit.md line 229 column 1, closing implicitly.
[WARNING] Div at SangerRead_Report_ab1.knit.md line 147 column 1 unclosed at SangerRead_Report_ab1.knit.md line 229 column 1, closing implicitly.
INFO [2026-05-22 21:39:15] ------------------------------------------------
INFO [2026-05-22 21:39:15] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:15] ------------------------------------------------
INFO [2026-05-22 21:39:15] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:15] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:15] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:15] * Making basecall !!
INFO [2026-05-22 21:39:15] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:15] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:15] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:15] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:15] ------------------------------------------------
INFO [2026-05-22 21:39:15] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:15] ------------------------------------------------
INFO [2026-05-22 21:39:15] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:15] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:15] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:15] * Making basecall !!
INFO [2026-05-22 21:39:15] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:15] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:15] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:15] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:15] ========================================================
INFO [2026-05-22 21:39:15] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:15] ========================================================
INFO [2026-05-22 21:39:15] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:15] >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:39:15] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:15] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:15] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:16] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:16] ==========================================================
SUCCESS [2026-05-22 21:39:16] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:16] ==========================================================
INFO [2026-05-22 21:39:16] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:16] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:16] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-22 21:39:16] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:16] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:16] >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-22 21:39:16] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:16] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:16] ==========================================================
SUCCESS [2026-05-22 21:39:16] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:16] ==========================================================
INFO [2026-05-22 21:39:16] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:16] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:16] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-22 21:39:16] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:16] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:16] #################################################
INFO [2026-05-22 21:39:16] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:16] #################################################
INFO [2026-05-22 21:39:16] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-22 21:39:16] **** Contig number in your Csv file is 2
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] >> Contig Name: 'rbcL2'
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:16] >> The number of reads detected: 4
SUCCESS [2026-05-22 21:39:16] ==========================================================
SUCCESS [2026-05-22 21:39:16] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:16] ==========================================================
INFO [2026-05-22 21:39:16] >> 4 read(s) created from ABIF file.
INFO [2026-05-22 21:39:16] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:16] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] >> Contig Name: 'ITS5'
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:16] >> The number of reads detected: 4
SUCCESS [2026-05-22 21:39:16] ==========================================================
SUCCESS [2026-05-22 21:39:16] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:16] ==========================================================
INFO [2026-05-22 21:39:16] >> 4 read(s) created from ABIF file.
INFO [2026-05-22 21:39:16] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:16] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:16] Aligning consensus reads ...
INFO [2026-05-22 21:39:16] Before building!!
INFO [2026-05-22 21:39:16] After building!!
INFO [2026-05-22 21:39:16] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-22 21:39:16] #############################################################
SUCCESS [2026-05-22 21:39:16] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:16] #############################################################
INFO [2026-05-22 21:39:16] >> 2 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:16] >> Contig 'rbcL2':
INFO [2026-05-22 21:39:16] >> 2 forward reads.
INFO [2026-05-22 21:39:16] >> 2 reverse reads.
INFO [2026-05-22 21:39:16] >> Contig 'ITS5':
INFO [2026-05-22 21:39:16] >> 2 forward reads.
INFO [2026-05-22 21:39:16] >> 2 reverse reads.
INFO [2026-05-22 21:39:16] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:16] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:16] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:16] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:16] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb10f2845b/names_conversion.csv)
WARN [2026-05-22 21:39:16] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb10f2845b/names_conversion.csv)
WARN [2026-05-22 21:39:16] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb10f2845b/names_conversion.csv)
WARN [2026-05-22 21:39:16] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb10f2845b/names_conversion.csv)
WARN [2026-05-22 21:39:16] 'NONEXISTENT_F.ab1' is not in the parent directory.
WARN [2026-05-22 21:39:16] 'NONEXISTENT_R.ab1' is not in the parent directory.
INFO [2026-05-22 21:39:16] #################################################
INFO [2026-05-22 21:39:16] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:16] #################################################
INFO [2026-05-22 21:39:16] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-22 21:39:16] **** Contig number in your Csv file is 2
WARN [2026-05-22 21:39:16] >> Contig 'ghost' has no reads matching any file under ABIF_Directory; skipping.
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:16] ========================================================
INFO [2026-05-22 21:39:16] >> Contig Name: 'good'
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:16] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:16] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 4
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 4 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:17] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
SUCCESS [2026-05-22 21:39:17] #############################################################
SUCCESS [2026-05-22 21:39:17] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:17] #############################################################
INFO [2026-05-22 21:39:17] >> 1 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:17] >> Contig 'good':
INFO [2026-05-22 21:39:17] >> 2 forward reads.
INFO [2026-05-22 21:39:17] >> 2 reverse reads.
INFO [2026-05-22 21:39:17] >> 4 reads created from ABIF file.
INFO [2026-05-22 21:39:17] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:17] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-22 21:39:17] #################################################
INFO [2026-05-22 21:39:17] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:17] #################################################
INFO [2026-05-22 21:39:17] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] Aligning consensus reads ...
INFO [2026-05-22 21:39:17] Before building!!
INFO [2026-05-22 21:39:17] After building!!
SUCCESS [2026-05-22 21:39:17] #############################################################
SUCCESS [2026-05-22 21:39:17] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:17] #############################################################
INFO [2026-05-22 21:39:17] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> 4 reads created from ABIF file.
INFO [2026-05-22 21:39:17] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:17] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-22 21:39:17] #################################################
INFO [2026-05-22 21:39:17] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:17] #################################################
INFO [2026-05-22 21:39:17] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-22 21:39:17] Aligning consensus reads ...
INFO [2026-05-22 21:39:17] Before building!!
INFO [2026-05-22 21:39:17] After building!!
SUCCESS [2026-05-22 21:39:17] #############################################################
SUCCESS [2026-05-22 21:39:17] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:17] #############################################################
INFO [2026-05-22 21:39:17] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:17] >> 1 forward reads.
INFO [2026-05-22 21:39:17] >> 0 reverse reads.
INFO [2026-05-22 21:39:17] >> 4 reads created from ABIF file.
INFO [2026-05-22 21:39:17] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:17] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:17] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:17] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:17] ==========================================================
SUCCESS [2026-05-22 21:39:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:17] ==========================================================
INFO [2026-05-22 21:39:17] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:17] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:17] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:17] >> There is only one read in your SangerContig.
INFO [2026-05-22 21:39:17] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-22 21:39:17] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:17] ------------------------------------------------
INFO [2026-05-22 21:39:17] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:17] ------------------------------------------------
INFO [2026-05-22 21:39:17] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:17] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:17] >> Creating Forward Read raw sangerseq ...
WARN [2026-05-22 21:39:17] >> ABIF 'Achl_ACHLO006-09_1_F.ab1' has no PCON.2 quality block; synthesising flat Phred 30 (MISSING_QUALITY_SCORES_WARN).
INFO [2026-05-22 21:39:17] * Making basecall !!
INFO [2026-05-22 21:39:17] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:17] ------------------------------------------------
INFO [2026-05-22 21:39:17] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:17] ------------------------------------------------
INFO [2026-05-22 21:39:17] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:17] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:17] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:17] * Making basecall !!
INFO [2026-05-22 21:39:17] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:17] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:17] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:17] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
WARN [2026-05-22 21:39:17] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:17] ========================================================
INFO [2026-05-22 21:39:17] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:17] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:17] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:17] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:18] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:18] ==========================================================
SUCCESS [2026-05-22 21:39:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:18] ==========================================================
INFO [2026-05-22 21:39:18] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:18] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:18] >> There is only one read in your SangerContig.
INFO [2026-05-22 21:39:18] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-22 21:39:18] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:18] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb4f7136ba
INFO [2026-05-22 21:39:18] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-22 21:39:18] >> Writing alignment to FASTA ...
INFO [2026-05-22 21:39:18] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:39:18] >> Writing consensus read to FASTA ...
INFO [2026-05-22 21:39:18] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-22 21:39:18] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:18] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:18] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:18] >> The number of reads detected: 1
SUCCESS [2026-05-22 21:39:18] ==========================================================
SUCCESS [2026-05-22 21:39:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:18] ==========================================================
INFO [2026-05-22 21:39:18] >> 1 read(s) created from ABIF file.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-22 21:39:18] >> No 'reverse read' is detected!
WARN [2026-05-22 21:39:18] >> There is only one read in your SangerContig.
INFO [2026-05-22 21:39:18] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-22 21:39:18] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:18] Your input is 'SangerContig' S4 instance
INFO [2026-05-22 21:39:18] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/filedaeb51155cf4
INFO [2026-05-22 21:39:18] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-22 21:39:18] >> Writing alignment to FASTA ...
INFO [2026-05-22 21:39:18] >> Writing all single reads to FASTA ...
INFO [2026-05-22 21:39:18] >> Writing consensus read to FASTA ...
INFO [2026-05-22 21:39:18] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-22 21:39:18] >> Dropping 1 read(s) with trimmed length < 2 bp (MIN_READ_LENGTH_DEFENSIVE_DROP).
WARN [2026-05-22 21:39:18] >> Fewer than 2 usable reads after defensive filter; returning empty consensus.
INFO [2026-05-22 21:39:18] ------------------------------------------------
INFO [2026-05-22 21:39:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:18] ------------------------------------------------
INFO [2026-05-22 21:39:18] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-22 21:39:18] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:18] ------------------------------------------------
INFO [2026-05-22 21:39:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:18] ------------------------------------------------
INFO [2026-05-22 21:39:18] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:18] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:18] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:18] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:18] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:18] ==========================================================
SUCCESS [2026-05-22 21:39:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:18] ==========================================================
INFO [2026-05-22 21:39:18] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:18] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig.
WARN [2026-05-22 21:39:18] 'Achl_ACHLO007-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb228f889/names_conversion.csv)
WARN [2026-05-22 21:39:18] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb228f889/names_conversion.csv)
WARN [2026-05-22 21:39:18] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb228f889/names_conversion.csv)
WARN [2026-05-22 21:39:18] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb228f889/names_conversion.csv)
WARN [2026-05-22 21:39:18] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb228f889/names_conversion.csv)
WARN [2026-05-22 21:39:18] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig. (READ_ASSIGNED_MULTIPLE_CONTIGS_WARN)
[[1]]
character(0)
[[2]]
character(0)
[[1]]
character(0)
[[2]]
character(0)
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:18] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:18] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:18] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:18] ==========================================================
SUCCESS [2026-05-22 21:39:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:18] ==========================================================
INFO [2026-05-22 21:39:18] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:18] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:18] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:18] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:18] ========================================================
INFO [2026-05-22 21:39:18] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:18] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:18] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:18] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:18] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:18] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:19] ==========================================================
SUCCESS [2026-05-22 21:39:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:19] ==========================================================
INFO [2026-05-22 21:39:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:19] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:19] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:19] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:19] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:19] ==========================================================
SUCCESS [2026-05-22 21:39:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:19] ==========================================================
INFO [2026-05-22 21:39:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:19] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-22 21:39:19] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:19] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:19] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:19] ==========================================================
SUCCESS [2026-05-22 21:39:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:19] ==========================================================
INFO [2026-05-22 21:39:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:19] >> For more information, please run 'object'
DEBUG [2026-05-22 21:39:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:19] #################################################
INFO [2026-05-22 21:39:19] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:19] #################################################
INFO [2026-05-22 21:39:19] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:19] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:19] ==========================================================
SUCCESS [2026-05-22 21:39:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:19] ==========================================================
INFO [2026-05-22 21:39:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:19] ========================================================
INFO [2026-05-22 21:39:19] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:19] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:19] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:19] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] Aligning consensus reads ...
INFO [2026-05-22 21:39:20] Before building!!
INFO [2026-05-22 21:39:20] After building!!
SUCCESS [2026-05-22 21:39:20] #############################################################
SUCCESS [2026-05-22 21:39:20] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:20] #############################################################
INFO [2026-05-22 21:39:20] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:20] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:20] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:20] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:20] #################################################
INFO [2026-05-22 21:39:20] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:20] #################################################
INFO [2026-05-22 21:39:20] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:20] ==========================================================
SUCCESS [2026-05-22 21:39:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:20] ==========================================================
INFO [2026-05-22 21:39:20] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:20] Aligning consensus reads ...
INFO [2026-05-22 21:39:20] Before building!!
INFO [2026-05-22 21:39:20] After building!!
SUCCESS [2026-05-22 21:39:20] #############################################################
SUCCESS [2026-05-22 21:39:20] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:20] #############################################################
INFO [2026-05-22 21:39:20] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:20] >> 1 forward reads.
INFO [2026-05-22 21:39:20] >> 1 reverse reads.
INFO [2026-05-22 21:39:20] >> 8 reads created from FASTA file.
DEBUG [2026-05-22 21:39:20] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:20] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:20] #################################################
INFO [2026-05-22 21:39:20] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:20] #################################################
INFO [2026-05-22 21:39:20] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:20] ========================================================
INFO [2026-05-22 21:39:20] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:20] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:20] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:20] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:21] ==========================================================
SUCCESS [2026-05-22 21:39:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:21] ==========================================================
INFO [2026-05-22 21:39:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:21] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:21] ==========================================================
SUCCESS [2026-05-22 21:39:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:21] ==========================================================
INFO [2026-05-22 21:39:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:21] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:21] ==========================================================
SUCCESS [2026-05-22 21:39:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:21] ==========================================================
INFO [2026-05-22 21:39:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:21] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:21] ==========================================================
SUCCESS [2026-05-22 21:39:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:21] ==========================================================
INFO [2026-05-22 21:39:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:21] Aligning consensus reads ...
INFO [2026-05-22 21:39:21] Before building!!
INFO [2026-05-22 21:39:21] After building!!
SUCCESS [2026-05-22 21:39:21] #############################################################
SUCCESS [2026-05-22 21:39:21] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:21] #############################################################
INFO [2026-05-22 21:39:21] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:21] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:21] >> 1 forward reads.
INFO [2026-05-22 21:39:21] >> 1 reverse reads.
INFO [2026-05-22 21:39:21] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:21] >> 1 forward reads.
INFO [2026-05-22 21:39:21] >> 1 reverse reads.
INFO [2026-05-22 21:39:21] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:21] >> 1 forward reads.
INFO [2026-05-22 21:39:21] >> 1 reverse reads.
INFO [2026-05-22 21:39:21] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:21] >> 1 forward reads.
INFO [2026-05-22 21:39:21] >> 1 reverse reads.
INFO [2026-05-22 21:39:21] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:21] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:21] * Making basecall !!
INFO [2026-05-22 21:39:21] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:21] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:21] * Making basecall !!
INFO [2026-05-22 21:39:21] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:21] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:21] * Making basecall !!
INFO [2026-05-22 21:39:21] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:21] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:21] * Making basecall !!
INFO [2026-05-22 21:39:21] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:21] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:21] ------------------------------------------------
INFO [2026-05-22 21:39:21] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:21] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:21] * Making basecall !!
INFO [2026-05-22 21:39:21] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:21] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:21] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:21] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:21] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:21] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:21] #################################################
INFO [2026-05-22 21:39:21] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:21] #################################################
INFO [2026-05-22 21:39:21] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:21] ========================================================
INFO [2026-05-22 21:39:21] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:22] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:22] ==========================================================
SUCCESS [2026-05-22 21:39:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:22] ==========================================================
INFO [2026-05-22 21:39:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:22] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:22] ==========================================================
SUCCESS [2026-05-22 21:39:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:22] ==========================================================
INFO [2026-05-22 21:39:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:22] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:22] ==========================================================
SUCCESS [2026-05-22 21:39:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:22] ==========================================================
INFO [2026-05-22 21:39:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:22] ========================================================
INFO [2026-05-22 21:39:22] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:22] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:22] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:22] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:22] ==========================================================
SUCCESS [2026-05-22 21:39:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:22] ==========================================================
INFO [2026-05-22 21:39:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:22] Aligning consensus reads ...
INFO [2026-05-22 21:39:22] Before building!!
INFO [2026-05-22 21:39:22] After building!!
SUCCESS [2026-05-22 21:39:22] #############################################################
SUCCESS [2026-05-22 21:39:22] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:22] #############################################################
INFO [2026-05-22 21:39:22] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:22] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:22] >> 1 forward reads.
INFO [2026-05-22 21:39:22] >> 1 reverse reads.
INFO [2026-05-22 21:39:22] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:22] >> 1 forward reads.
INFO [2026-05-22 21:39:22] >> 1 reverse reads.
INFO [2026-05-22 21:39:22] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:22] >> 1 forward reads.
INFO [2026-05-22 21:39:22] >> 1 reverse reads.
INFO [2026-05-22 21:39:22] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:22] >> 1 forward reads.
INFO [2026-05-22 21:39:22] >> 1 reverse reads.
INFO [2026-05-22 21:39:22] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:22] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:22] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:24] Aligning consensus reads ...
INFO [2026-05-22 21:39:24] Before building!!
INFO [2026-05-22 21:39:24] After building!!
INFO [2026-05-22 21:39:26] Aligning consensus reads ...
INFO [2026-05-22 21:39:26] Before building!!
INFO [2026-05-22 21:39:26] After building!!
INFO [2026-05-22 21:39:27] Aligning consensus reads ...
INFO [2026-05-22 21:39:27] Before building!!
INFO [2026-05-22 21:39:27] After building!!
INFO [2026-05-22 21:39:29] Aligning consensus reads ...
INFO [2026-05-22 21:39:29] Before building!!
INFO [2026-05-22 21:39:29] After building!!
INFO [2026-05-22 21:39:31] Aligning consensus reads ...
INFO [2026-05-22 21:39:31] Before building!!
INFO [2026-05-22 21:39:31] After building!!
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:31] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:31] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:31] * Making basecall !!
INFO [2026-05-22 21:39:31] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:31] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:31] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:31] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:31] >> Creating Reverse Read raw abif ...
INFO [2026-05-22 21:39:31] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-22 21:39:31] * Making basecall !!
INFO [2026-05-22 21:39:31] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:31] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:31] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:31] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:31] ------------------------------------------------
INFO [2026-05-22 21:39:31] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:31] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:31] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:31] * Making basecall !!
INFO [2026-05-22 21:39:31] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:31] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:31] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:31] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:31] #################################################
INFO [2026-05-22 21:39:31] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:31] #################################################
INFO [2026-05-22 21:39:31] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:31] ========================================================
INFO [2026-05-22 21:39:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:31] ========================================================
INFO [2026-05-22 21:39:31] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:31] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:31] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:31] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:31] ==========================================================
SUCCESS [2026-05-22 21:39:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:31] ==========================================================
INFO [2026-05-22 21:39:31] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:31] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:31] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:31] ========================================================
INFO [2026-05-22 21:39:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:31] ========================================================
INFO [2026-05-22 21:39:31] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:32] ==========================================================
SUCCESS [2026-05-22 21:39:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:32] ==========================================================
INFO [2026-05-22 21:39:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:32] ==========================================================
SUCCESS [2026-05-22 21:39:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:32] ==========================================================
INFO [2026-05-22 21:39:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:32] ==========================================================
SUCCESS [2026-05-22 21:39:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:32] ==========================================================
INFO [2026-05-22 21:39:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] Aligning consensus reads ...
INFO [2026-05-22 21:39:32] Before building!!
INFO [2026-05-22 21:39:32] After building!!
SUCCESS [2026-05-22 21:39:32] #############################################################
SUCCESS [2026-05-22 21:39:32] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:32] #############################################################
INFO [2026-05-22 21:39:32] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:32] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:32] >> 1 forward reads.
INFO [2026-05-22 21:39:32] >> 1 reverse reads.
INFO [2026-05-22 21:39:32] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:32] >> 1 forward reads.
INFO [2026-05-22 21:39:32] >> 1 reverse reads.
INFO [2026-05-22 21:39:32] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:32] >> 1 forward reads.
INFO [2026-05-22 21:39:32] >> 1 reverse reads.
INFO [2026-05-22 21:39:32] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:32] >> 1 forward reads.
INFO [2026-05-22 21:39:32] >> 1 reverse reads.
INFO [2026-05-22 21:39:32] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:32] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:32] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:32] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:32] #################################################
INFO [2026-05-22 21:39:32] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:32] #################################################
INFO [2026-05-22 21:39:32] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:32] ==========================================================
SUCCESS [2026-05-22 21:39:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:32] ==========================================================
INFO [2026-05-22 21:39:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:32] ==========================================================
SUCCESS [2026-05-22 21:39:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:32] ==========================================================
INFO [2026-05-22 21:39:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:32] ========================================================
INFO [2026-05-22 21:39:32] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:32] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:32] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:32] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:33] ==========================================================
SUCCESS [2026-05-22 21:39:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:33] ==========================================================
INFO [2026-05-22 21:39:33] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:33] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:33] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:33] ========================================================
INFO [2026-05-22 21:39:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:33] ========================================================
INFO [2026-05-22 21:39:33] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:33] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:33] ==========================================================
SUCCESS [2026-05-22 21:39:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:33] ==========================================================
INFO [2026-05-22 21:39:33] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:33] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-22 21:39:33] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-22 21:39:33] Aligning consensus reads ...
INFO [2026-05-22 21:39:33] Before building!!
INFO [2026-05-22 21:39:33] After building!!
SUCCESS [2026-05-22 21:39:33] #############################################################
SUCCESS [2026-05-22 21:39:33] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:33] #############################################################
INFO [2026-05-22 21:39:33] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-22 21:39:33] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-22 21:39:33] >> 1 forward reads.
INFO [2026-05-22 21:39:33] >> 1 reverse reads.
INFO [2026-05-22 21:39:33] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:33] >> 1 forward reads.
INFO [2026-05-22 21:39:33] >> 1 reverse reads.
INFO [2026-05-22 21:39:33] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:33] >> 1 forward reads.
INFO [2026-05-22 21:39:33] >> 1 reverse reads.
INFO [2026-05-22 21:39:33] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:33] >> 1 forward reads.
INFO [2026-05-22 21:39:33] >> 1 reverse reads.
INFO [2026-05-22 21:39:33] >> 8 reads created from ABIF file.
INFO [2026-05-22 21:39:33] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:33] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:33] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:33] ------------------------------------------------
INFO [2026-05-22 21:39:33] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:33] ------------------------------------------------
INFO [2026-05-22 21:39:33] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:33] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:33] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:33] * Making basecall !!
INFO [2026-05-22 21:39:33] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:33] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:33] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:33] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:33] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:33] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
INFO [2026-05-22 21:39:36] Aligning consensus reads ...
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
INFO [2026-05-22 21:39:38] Aligning consensus reads ...
================================================================================
Time difference of 0.01 secs
================================================================================
Time difference of 0.01 secs
INFO [2026-05-22 21:39:40] * Making basecall !!
INFO [2026-05-22 21:39:40] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:40] * Making basecall !!
INFO [2026-05-22 21:39:40] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:40] * Making basecall !!
INFO [2026-05-22 21:39:40] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:40] * Making basecall !!
INFO [2026-05-22 21:39:40] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:40] * Making basecall !!
INFO [2026-05-22 21:39:40] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:41] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ
INFO [2026-05-22 21:39:41] Start writing '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-22 21:39:41] >> '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-22 21:39:41] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ
INFO [2026-05-22 21:39:41] Start writing '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2026-05-22 21:39:41] >> '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-22 21:39:41] >>> outputDir : /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ
INFO [2026-05-22 21:39:41] Start writing '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2026-05-22 21:39:41] >> '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpug8pfQ/Achl_ACHLO006-09_2_R.fa' is written
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:41] * Making basecall !!
INFO [2026-05-22 21:39:41] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:41] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Reverse Read raw abif ...
INFO [2026-05-22 21:39:41] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-22 21:39:41] * Making basecall !!
INFO [2026-05-22 21:39:41] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:41] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:41] * Making basecall !!
INFO [2026-05-22 21:39:41] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:41] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-22 21:39:41] * Making basecall !!
INFO [2026-05-22 21:39:41] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:41] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:41] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-22 21:39:41] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-22 21:39:41] FILE_TYPE_ERROR
'/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb17ea9cf/Sanger_all_reads.Xfa' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:41] FILE_TYPE_ERROR
'/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb302d193b/Achl_ACHLO006-09_1_F.Xab1' file extension must be '.ab1'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-22 21:39:41] FILE_TYPE_ERROR
'/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaebc77387d/Achl_ACHLO006-09_1_F.ab2' file extension must be '.ab1'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-22 21:39:41] FILE_TYPE_ERROR
'/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb2ef420af/Sanger_all_reads.fast' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:41] FILE_NOT_EXIST_ERROR
'/no/such/file_1_F.ab1' file does not exist.
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] -------- Creating 'SangerRead' instance --------
INFO [2026-05-22 21:39:41] ------------------------------------------------
INFO [2026-05-22 21:39:41] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw abif ...
INFO [2026-05-22 21:39:41] >> Creating Forward Read raw sangerseq ...
ERROR [2026-05-22 21:39:41] CSV_MISMATCH_ERROR
'contig' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb578aa91d/missing_contig.csv)
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:41] CSV_MISMATCH_ERROR
'direction' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb467c1381/missing_direction.csv)
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:41] CSV_MISMATCH_ERROR
'reads' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb3657e343/missing_reads.csv)
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:41] CSV_VALUE_ERROR
In the 'direction' column of your CSV file, you can only have 'F' and 'R'
DEBUG [2026-05-22 21:39:41] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:41] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:41] 'Achl_ACHLO006-09_1_F.ab1' is not in the csv file (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpug8pfQ/filedaeb1725e8c2/mismatched_names_conversion.csv)
WARN [2026-05-22 21:39:41] 'DOES_NOT_EXIST.ab1' is not in the parent directory.
INFO [2026-05-22 21:39:41] #################################################
INFO [2026-05-22 21:39:41] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:41] #################################################
INFO [2026-05-22 21:39:41] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-22 21:39:41] **** Contig number in your Csv file is 4
INFO [2026-05-22 21:39:41] ========================================================
INFO [2026-05-22 21:39:41] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:41] ========================================================
INFO [2026-05-22 21:39:41] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 1
WARN [2026-05-22 21:39:42] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-22 21:39:42] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from ABIF file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] Aligning consensus reads ...
INFO [2026-05-22 21:39:42] Before building!!
INFO [2026-05-22 21:39:42] After building!!
SUCCESS [2026-05-22 21:39:42] #############################################################
SUCCESS [2026-05-22 21:39:42] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:42] #############################################################
INFO [2026-05-22 21:39:42] >> 3 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> 6 reads created from ABIF file.
INFO [2026-05-22 21:39:42] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-22 21:39:42] 'Achl_ACHLO006-09_1_F' is not in the parent directory.
INFO [2026-05-22 21:39:42] #################################################
INFO [2026-05-22 21:39:42] #### Start creating SangerAlignment instance ####
INFO [2026-05-22 21:39:42] #################################################
INFO [2026-05-22 21:39:42] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 1
WARN [2026-05-22 21:39:42] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-22 21:39:42] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-22 21:39:42] ========================================================
INFO [2026-05-22 21:39:42] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-22 21:39:42] --------------------------------------------------------
SUCCESS [2026-05-22 21:39:42] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-22 21:39:42] >> The number of reads detected: 2
SUCCESS [2026-05-22 21:39:42] ==========================================================
SUCCESS [2026-05-22 21:39:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-22 21:39:42] ==========================================================
INFO [2026-05-22 21:39:42] >> 2 read(s) created from FASTA file.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-22 21:39:42] Aligning consensus reads ...
INFO [2026-05-22 21:39:42] Before building!!
INFO [2026-05-22 21:39:42] After building!!
SUCCESS [2026-05-22 21:39:42] #############################################################
SUCCESS [2026-05-22 21:39:42] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-22 21:39:42] #############################################################
INFO [2026-05-22 21:39:42] >> 3 contigs detected from 'csv file'.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-22 21:39:42] >> 1 forward reads.
INFO [2026-05-22 21:39:42] >> 1 reverse reads.
INFO [2026-05-22 21:39:42] >> 6 reads created from FASTA file.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_RANGE_ERROR
'M1TrimmingCutoff' must be between 0 and 1.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'TrimmingMethod' must be 'M1' or 'M2'.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_TYPE_ERROR
'processorsNum' must be numeric
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_RANGE_ERROR
'signalRatioCutoff' must be between 0 and 1.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'inputSource' must be one of: 'ABIF', 'FASTA'.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'processMethod' must be one of: 'REGEX', 'CSV'.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'acceptStopCodons' must be 'TRUE' or 'FALSE'
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'readingFrame' must be 1, 2, or 3.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_RANGE_ERROR
'minFractionCall' must be between 0 and 1.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-22 21:39:42] PARAMETER_VALUE_ERROR
'minReadsNum' cannot be zero.
DEBUG [2026-05-22 21:39:42] >> For more information, please run 'object'.
DEBUG [2026-05-22 21:39:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-22 21:39:43] Aligning consensus reads ...
================================================================================
Time difference of 0.02 secs
INFO [2026-05-22 21:39:43] * Making basecall !!
INFO [2026-05-22 21:39:43] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-22 21:39:43] * Making basecall !!
INFO [2026-05-22 21:39:43] * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-LazyAA-Reports.R:65:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]
>
> proc.time()
user system elapsed
57.325 5.495 63.855
sangeranalyseR.Rcheck/sangeranalyseR-Ex.timings
| name | user | system | elapsed | |
| ChromatogramParam-class | 0.002 | 0.000 | 0.002 | |
| MakeBaseCalls-methods | 0.152 | 0.003 | 0.155 | |
| ObjectResults-class | 0.000 | 0.000 | 0.001 | |
| QualityReport-class-qualityBasePlot | 0.000 | 0.001 | 0.001 | |
| QualityReport-class-updateQualityParam | 0.002 | 0.003 | 0.005 | |
| QualityReport-class | 0.070 | 0.004 | 0.074 | |
| SangerAlignment-class-generateReportSA | 0.053 | 0.002 | 0.054 | |
| SangerAlignment-class-launchAppSA | 0.062 | 0.002 | 0.064 | |
| SangerAlignment-class-updateQualityParam | 0.054 | 0.001 | 0.054 | |
| SangerAlignment-class-writeFastaSA | 0.061 | 0.002 | 0.064 | |
| SangerAlignment-class | 12.953 | 5.160 | 17.937 | |
| SangerAlignment | 2.827 | 1.447 | 4.183 | |
| SangerContig-class-generateReportSC | 0.020 | 0.001 | 0.022 | |
| SangerContig-class-launchAppSC | 0.025 | 0.002 | 0.027 | |
| SangerContig-class-readTable | 0.036 | 0.002 | 0.038 | |
| SangerContig-class-updateQualityParam | 0.021 | 0.001 | 0.022 | |
| SangerContig-class-writeFastaSC | 0.032 | 0.002 | 0.034 | |
| SangerContig-class | 3.090 | 1.315 | 4.301 | |
| SangerContig | 0.184 | 0.031 | 0.215 | |
| SangerRead-class-MakeBaseCalls | 0.104 | 0.004 | 0.109 | |
| SangerRead-class-generateReportSR | 0.016 | 0.001 | 0.016 | |
| SangerRead-class-qualityBasePlot | 0.015 | 0.001 | 0.016 | |
| SangerRead-class-readTable | 0.036 | 0.003 | 0.039 | |
| SangerRead-class-updateQualityParam | 0.093 | 0.004 | 0.097 | |
| SangerRead-class-writeFastaSR | 0.020 | 0.001 | 0.021 | |
| SangerRead-class | 0.183 | 0.013 | 0.196 | |
| SangerRead | 0.054 | 0.004 | 0.058 | |
| chromatogram_overwrite | 0.015 | 0.001 | 0.016 | |
| chromatogram_plotly | 0.015 | 0.001 | 0.016 | |
| generateReport | 0.089 | 0.004 | 0.093 | |
| generateReportSA-methods | 0.052 | 0.002 | 0.055 | |
| generateReportSC-methods | 0.020 | 0.002 | 0.022 | |
| generateReportSR-methods | 0.015 | 0.001 | 0.016 | |
| globalTrimApp | 0 | 0 | 0 | |
| launchApp | 0.080 | 0.002 | 0.083 | |
| launchAppSA-methods | 0.052 | 0.001 | 0.054 | |
| launchAppSC-methods | 0.019 | 0.000 | 0.021 | |
| primaryAASeqS1-methods | 0.016 | 0.001 | 0.018 | |
| primaryAASeqS2-methods | 0.015 | 0.000 | 0.017 | |
| primaryAASeqS3-methods | 0.015 | 0.001 | 0.017 | |
| qualityBasePlot-methods | 0.124 | 0.015 | 0.144 | |
| readTable-methods | 0.036 | 0.001 | 0.038 | |
| updateQualityParam-methods | 0.090 | 0.004 | 0.093 | |
| writeFasta | 0.088 | 0.002 | 0.090 | |
| writeFastaSA-methods | 0.059 | 0.002 | 0.062 | |
| writeFastaSC-methods | 0.031 | 0.002 | 0.034 | |
| writeFastaSR-methods | 0.019 | 0.002 | 0.020 | |