Alex Chit Hei Wong
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: RELEASE_3_20 |
| git_last_commit: 12996a5 |
| git_last_commit_date: 2024-10-29 11:12:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 2039/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.8.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SpliceWiz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.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: SpliceWiz |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.8.0.tar.gz |
| StartedAt: 2024-12-21 10:38:07 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 11:00:29 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 1341.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
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
NxtSE-class 66.196 1.057 67.902
Build-Reference-methods 64.017 1.327 68.031
ASE-methods 35.230 0.278 35.927
covPlotObject-class 21.406 0.521 22.192
plotCoverage 13.771 0.145 13.959
Run_SpliceWiz_Filters 9.470 0.038 9.557
processBAM 4.944 0.656 3.840
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (SpliceWiz)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Dec 21 10:49:01 Converting FASTA to local TwoBitFile...done
Dec 21 10:49:03 Connecting to genome TwoBitFile...done
Dec 21 10:49:03 Making local copy of GTF file...done
Dec 21 10:49:03 Extracting temp genome FASTA from TwoBit file
Dec 21 10:49:04 Generating synthetic reads, saving to /private/tmp/RtmpPNZUk5/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Dec 21 10:49:04 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.20.0
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 41.9GB / 64.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o genome.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=91.9k bps/s ||
|| 16%, 0 mins elapsed, rate=179.2k bps/s ||
|| 24%, 0 mins elapsed, rate=262.5k bps/s ||
|| 33%, 0 mins elapsed, rate=341.3k bps/s ||
|| 41%, 0 mins elapsed, rate=416.6k bps/s ||
|| 49%, 0 mins elapsed, rate=480.6k bps/s ||
|| 58%, 0 mins elapsed, rate=547.3k bps/s ||
|| 66%, 0 mins elapsed, rate=610.4k bps/s ||
|| 74%, 0 mins elapsed, rate=671.9k bps/s ||
|| 83%, 0 mins elapsed, rate=731.0k bps/s ||
|| 91%, 0 mins elapsed, rate=787.0k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=6.9k bps/s ||
|| 16%, 0 mins elapsed, rate=13.8k bps/s ||
|| 24%, 0 mins elapsed, rate=20.6k bps/s ||
|| 33%, 0 mins elapsed, rate=27.3k bps/s ||
|| 41%, 0 mins elapsed, rate=34.0k bps/s ||
|| 49%, 0 mins elapsed, rate=40.6k bps/s ||
|| 58%, 0 mins elapsed, rate=47.1k bps/s ||
|| 66%, 0 mins elapsed, rate=53.5k bps/s ||
|| 74%, 0 mins elapsed, rate=59.9k bps/s ||
|| 83%, 0 mins elapsed, rate=66.3k bps/s ||
|| 91%, 0 mins elapsed, rate=72.6k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.3 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.20.0
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file : Reads.fa ||
|| Output file : AlignedReads.bam (BAM) ||
|| Index name : reference_index ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 1 / 14 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : transcripts.gtf (GTF) ||
|| ||
\\============================================================================//
//================ Running (21-Dec-2024 10:49:23, pid=92602) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 6.2 mins elapsed, rate=31.1k reads per second ||
|| 83% completed, 6.2 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 6.2 mins elapsed, rate=0.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 6.2 minutes ||
|| ||
\\============================================================================//
Dec 21 10:55:37 Calculating Mappability Exclusion regions from: /tmp/RtmpPNZUk5/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpPNZUk5/refWithMapExcl/Mappability/AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
SpliceWiz was compiled without OpenMP
Dec 21 10:55:41 Reference generated without non-polyA reference
Dec 21 10:55:41 Reference generated without Mappability reference
Dec 21 10:55:41 Reference generated without Blacklist exclusion
Dec 21 10:55:41 Converting FASTA to local TwoBitFile...done
Dec 21 10:55:43 Connecting to genome TwoBitFile...done
Dec 21 10:55:43 Making local copy of GTF file...done
Dec 21 10:55:43 Reading source GTF file...done
Dec 21 10:55:43 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Dec 21 10:55:44 Gene ontology not prepared for this reference
Dec 21 10:55:47 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Dec 21 10:55:52 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Dec 21 10:56:00 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Dec 21 10:56:03 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Dec 21 10:56:05 Splice Annotations Filtered
Dec 21 10:56:06 Translating Alternate Splice Peptides...done
Dec 21 10:56:06 Splice Annotations finished
Reference build finished
Dec 21 10:56:08 Running SpliceWiz processBAM
Dec 21 10:56:09 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpPNZUk5/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/private/tmp/RtmpPNZUk5/02H003.bam processed (525 milliseconds)
Dec 21 10:56:10 SpliceWiz processBAM processed RtmpPNZUk5/02H003.bam
Dec 21 10:56:10 Running SpliceWiz processBAM
Dec 21 10:56:11 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpPNZUk5/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/private/tmp/RtmpPNZUk5/02H003.bam processed (580 milliseconds)
Dec 21 10:56:12 SpliceWiz processBAM processed RtmpPNZUk5/02H003.bam
Dec 21 10:56:12 Reference generated without non-polyA reference
Dec 21 10:56:12 Reference generated without Mappability reference
Dec 21 10:56:12 Reference generated without Blacklist exclusion
Dec 21 10:56:12 Converting FASTA to local TwoBitFile...done
Dec 21 10:56:14 Connecting to genome TwoBitFile...done
Dec 21 10:56:14 Making local copy of GTF file...done
Dec 21 10:56:14 Reading source GTF file...done
Dec 21 10:56:14 Processing gtf file...
...genes
...transcripts
...CDS
Dec 21 10:56:14 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped.
...exons
done
Dec 21 10:56:15 Gene ontology not prepared for this reference
Dec 21 10:56:17 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Dec 21 10:56:22 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Dec 21 10:56:29 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Dec 21 10:56:31 Splice Annotations Filtered
Reference build finished
Dec 21 10:56:34 Running SpliceWiz processBAM
Dec 21 10:56:35 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H003.bam processed (523 milliseconds)
Dec 21 10:56:35 SpliceWiz processBAM processed RtmpPNZUk5/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H025.bam processed (428 milliseconds)
Dec 21 10:56:36 SpliceWiz processBAM processed RtmpPNZUk5/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H026.bam processed (632 milliseconds)
Dec 21 10:56:36 SpliceWiz processBAM processed RtmpPNZUk5/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H033.bam processed (634 milliseconds)
Dec 21 10:56:37 SpliceWiz processBAM processed RtmpPNZUk5/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H043.bam processed (407 milliseconds)
Dec 21 10:56:38 SpliceWiz processBAM processed RtmpPNZUk5/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H046.bam processed (588 milliseconds)
Dec 21 10:56:38 SpliceWiz processBAM processed RtmpPNZUk5/02H046.bam
Dec 21 10:56:40 Using MulticoreParam 1 threads
Dec 21 10:56:40 Validating Experiment; checking COV files...
Dec 21 10:56:40 Compiling Sample Stats
Dec 21 10:56:40 Compiling Junction List...merging...done
Dec 21 10:56:41 Compiling Junction Stats...merging...done
Dec 21 10:56:51 Compiling Intron Retention List...done
Dec 21 10:56:52 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Dec 21 10:57:05 Generating NxtSE assays
Dec 21 10:57:07 Using MulticoreParam 1 threads
|
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|
|======================= | 33%
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|
|=============================================== | 67%
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|========================================================== | 83%
|
|======================================================================| 100%
Dec 21 10:57:26 Building Final NxtSE Object
Dec 21 10:57:26 ...consolidating assays to H5 file
Dec 21 10:57:27 ...packaging reference
Dec 21 10:57:28 ...synthesising NxtSE
Dec 21 10:57:28 ...determining how overlapping introns should be removed
Dec 21 10:57:31 SpliceWiz (NxtSE) Collation Finished
Dec 21 10:57:31 Loading NxtSE object from file...
Dec 21 10:57:31 ...loading reference (NxtSE)
Dec 21 10:57:31 ...linking assays
Dec 21 10:57:31 ...linking COV files
Dec 21 10:57:31 ...loading rowData
Dec 21 10:57:32 ...removing overlapping introns...
Dec 21 10:57:32 NxtSE loaded
Dec 21 10:57:32 SpliceWiz reference already exists in given directory
Dec 21 10:57:32 Running SpliceWiz processBAM
Dec 21 10:57:33 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H003.bam processed (519 milliseconds)
Dec 21 10:57:34 SpliceWiz processBAM processed RtmpPNZUk5/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H025.bam processed (424 milliseconds)
Dec 21 10:57:34 SpliceWiz processBAM processed RtmpPNZUk5/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H026.bam processed (635 milliseconds)
Dec 21 10:57:35 SpliceWiz processBAM processed RtmpPNZUk5/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H033.bam processed (630 milliseconds)
Dec 21 10:57:36 SpliceWiz processBAM processed RtmpPNZUk5/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H043.bam processed (409 milliseconds)
Dec 21 10:57:36 SpliceWiz processBAM processed RtmpPNZUk5/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H046.bam processed (595 milliseconds)
Dec 21 10:57:37 SpliceWiz processBAM processed RtmpPNZUk5/02H046.bam
Dec 21 10:57:38 Using MulticoreParam 1 threads
Dec 21 10:57:38 Validating Experiment; checking COV files...
Dec 21 10:57:38 Compiling Sample Stats
Dec 21 10:57:38 Compiling Junction List...merging...done
Dec 21 10:57:40 Compiling Junction Stats...merging...done
Dec 21 10:57:49 Compiling Intron Retention List...done
Dec 21 10:57:51 Compiling Tandem Junction List...merging...done
Dec 21 10:57:52 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Dec 21 10:57:56 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Dec 21 10:58:09 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Dec 21 10:58:19 Generating NxtSE assays
Dec 21 10:58:20 Using MulticoreParam 1 threads
|
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|============ | 17%
|
|======================= | 33%
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|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Dec 21 10:58:40 Building Final NxtSE Object
Dec 21 10:58:40 ...consolidating assays to H5 file
Dec 21 10:58:41 ...packaging reference
Dec 21 10:58:41 ...synthesising NxtSE
Dec 21 10:58:42 ...determining how overlapping introns should be removed
Dec 21 10:58:45 SpliceWiz (NxtSE) Collation Finished
Dec 21 10:58:45 Loading NxtSE object from file...
Dec 21 10:58:45 ...loading reference (NxtSE)
Dec 21 10:58:45 ...linking assays
Dec 21 10:58:45 ...linking COV files
Dec 21 10:58:45 ...loading rowData
Dec 21 10:58:45 ...removing overlapping introns...
Dec 21 10:58:45 NxtSE loaded
Dec 21 10:58:45 SpliceWiz reference already exists in given directory
Dec 21 10:58:45 Running SpliceWiz processBAM
Dec 21 10:58:47 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H003.bam processed (460 milliseconds)
Dec 21 10:58:47 SpliceWiz processBAM processed RtmpPNZUk5/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H025.bam processed (433 milliseconds)
Dec 21 10:58:48 SpliceWiz processBAM processed RtmpPNZUk5/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H026.bam processed (642 milliseconds)
Dec 21 10:58:48 SpliceWiz processBAM processed RtmpPNZUk5/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H033.bam processed (639 milliseconds)
Dec 21 10:58:49 SpliceWiz processBAM processed RtmpPNZUk5/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H043.bam processed (415 milliseconds)
Dec 21 10:58:49 SpliceWiz processBAM processed RtmpPNZUk5/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPNZUk5/02H046.bam processed (591 milliseconds)
Dec 21 10:58:50 SpliceWiz processBAM processed RtmpPNZUk5/02H046.bam
Dec 21 10:58:51 Using MulticoreParam 1 threads
Dec 21 10:58:51 Validating Experiment; checking COV files...
Dec 21 10:58:51 Compiling Sample Stats
Dec 21 10:58:52 Compiling Junction List...merging...done
Dec 21 10:58:53 Compiling Junction Stats...merging...done
Dec 21 10:59:02 Compiling Intron Retention List...done
Dec 21 10:59:04 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Dec 21 10:59:17 Generating NxtSE assays
Dec 21 10:59:19 Using MulticoreParam 1 threads
|
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|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Dec 21 10:59:38 Building Final NxtSE Object
Dec 21 10:59:38 ...consolidating assays to H5 file
Dec 21 10:59:39 ...packaging reference
Dec 21 10:59:40 ...synthesising NxtSE
Dec 21 10:59:40 ...determining how overlapping introns should be removed
Dec 21 10:59:43 SpliceWiz (NxtSE) Collation Finished
Dec 21 10:59:43 Loading NxtSE object from file...
Dec 21 10:59:43 ...loading reference (NxtSE)
Dec 21 10:59:43 ...linking assays
Dec 21 10:59:43 ...linking COV files
Dec 21 10:59:43 ...loading rowData
Dec 21 10:59:43 ...removing overlapping introns...
Dec 21 10:59:43 NxtSE loaded
path paired strand depth mean_frag_size
02H003 ../SpliceWiz_Output/02H003.txt.gz TRUE -1 106256 149.3108
02H025 ../SpliceWiz_Output/02H025.txt.gz TRUE -1 84872 151.5914
02H026 ../SpliceWiz_Output/02H026.txt.gz TRUE -1 131514 150.3238
02H033 ../SpliceWiz_Output/02H033.txt.gz TRUE -1 129013 153.9754
02H043 ../SpliceWiz_Output/02H043.txt.gz TRUE -1 80254 155.4004
02H046 ../SpliceWiz_Output/02H046.txt.gz TRUE -1 120174 151.2840
directionality_strength Intergenic_Fraction rRNA_Fraction
02H003 9850 0 0
02H025 9848 0 0
02H026 9848 0 0
02H033 9855 0 0
02H043 9841 0 0
02H046 9857 0 0
NonPolyA_Fraction Mitochondrial_Fraction Unanno_Jn_Fraction
02H003 0 0 0.013449472
02H025 0 0 0.011203515
02H026 0 0 0.007282382
02H033 0 0 0.006310241
02H043 0 0 0.005871040
02H046 0 0 0.009819533
NMD_Jn_Fraction Fraction_Splice_Reads Fraction_Span_Reads IRBurden_clean
02H003 0.019509970 0.3506908 0.1735243 0.05796583
02H025 0.019360162 0.3712414 0.1591691 0.03963531
02H026 0.004298323 0.3980261 0.1615037 0.02576549
02H033 0.007705562 0.4003550 0.1734089 0.03090263
02H043 0.028069104 0.3671219 0.1807511 0.03762138
02H046 0.010542303 0.3725598 0.1603508 0.05099352
IRBurden_exitrons IRBurden_clean_unstranded IRBurden_exitrons_unstranded
02H003 0.1291810 0.03844293 0.1296020
02H025 0.1192351 0.02730399 0.1194005
02H026 0.1231055 0.02010410 0.1231939
02H033 0.1378958 0.02300500 0.1380215
02H043 0.1392935 0.02286515 0.1397365
02H046 0.1132136 0.03359077 0.1133852
IRBurden_antisense
02H003 0.021393335
02H025 0.013191532
02H026 0.006007119
02H033 0.008453742
02H043 0.015837096
02H046 0.019043703
MD5 is fcdc53e0f7fbd843529077ebd26dd058
Dec 21 10:59:47 Reference generated without non-polyA reference
Dec 21 10:59:47 Reference generated without Mappability reference
Dec 21 10:59:47 Reference generated without Blacklist exclusion
Dec 21 10:59:47 Converting FASTA to local TwoBitFile...done
Dec 21 10:59:48 Connecting to genome TwoBitFile...done
Dec 21 10:59:48 Making local copy of GTF file...done
Dec 21 10:59:49 Reading source GTF file...done
Dec 21 10:59:49 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Dec 21 10:59:50 Gene ontology not prepared for this reference
Dec 21 10:59:52 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Dec 21 10:59:57 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Dec 21 11:00:05 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Dec 21 11:00:08 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Dec 21 11:00:10 Splice Annotations Filtered
Dec 21 11:00:11 Translating Alternate Splice Peptides...done
Dec 21 11:00:12 Splice Annotations finished
Reference build finished
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
447.750 235.059 691.122
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 2.447 | 0.106 | 2.563 | |
| ASE-methods | 35.230 | 0.278 | 35.927 | |
| ASEFilter-class | 0.044 | 0.004 | 0.048 | |
| Build-Reference-methods | 64.017 | 1.327 | 68.031 | |
| Coverage | 0.972 | 0.039 | 1.048 | |
| Gene-ontology-methods | 2.026 | 0.063 | 2.144 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 3.027 | 0.040 | 3.086 | |
| NxtSE-class | 66.196 | 1.057 | 67.902 | |
| Run_SpliceWiz_Filters | 9.470 | 0.038 | 9.557 | |
| STAR-methods | 0.006 | 0.011 | 0.031 | |
| View-Reference-methods | 0.299 | 0.022 | 0.321 | |
| collateData | 3.284 | 0.069 | 3.387 | |
| coord2GR | 0.029 | 0.002 | 0.032 | |
| covDataObject-class | 1.710 | 0.032 | 1.803 | |
| covPlotObject-class | 21.406 | 0.521 | 22.192 | |
| covPlotly-class | 1.084 | 0.022 | 1.109 | |
| example-SpliceWiz-data | 0.017 | 0.003 | 0.020 | |
| findSamples | 0.005 | 0.005 | 0.010 | |
| isCOV | 0.017 | 0.004 | 0.021 | |
| makeSE | 2.155 | 0.106 | 2.276 | |
| make_plot_data | 0.050 | 0.002 | 0.053 | |
| plotCoverage | 13.771 | 0.145 | 13.959 | |
| processBAM | 4.944 | 0.656 | 3.840 | |
| setSWthreads | 0.005 | 0.013 | 0.020 | |
| theme_white | 0.156 | 0.053 | 0.210 | |