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This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 978/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.37.1  (landing page)
Jens Reeder
Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: devel
git_last_commit: 3775db8
git_last_commit_date: 2024-12-17 11:20:20 -0500 (Tue, 17 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for HTSeqGenie on kunpeng2

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: HTSeqGenie
Version: 4.37.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.37.1.tar.gz
StartedAt: 2025-01-25 07:55:54 -0000 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 08:11:02 -0000 (Sat, 25 Jan 2025)
EllapsedTime: 907.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HTSeqGenie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

Documented arguments not in \usage in Rd file 'logdebug.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logerror.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'loginfo.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logwarn.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** 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
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
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 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: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Warning message:
In fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:03:27.970702 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:03:27.979874 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:03:27.985333 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-25 08:03:27.988041 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:03:31.498838 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:03:31.500925 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000001/logs/progress.log
2025-01-25 08:03:34.399597 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-25 08:03:34.401589 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000002/logs/progress.log
2025-01-25 08:03:37.275612 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-01-25 08:03:37.277507 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000003/logs/progress.log
2025-01-25 08:03:40.143958 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-01-25 08:03:40.184393 DEBUG::tools.R/processChunks: done
2025-01-25 08:03:40.189489 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:03:40.192768 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.adapter_contaminated_1.RData
2025-01-25 08:03:40.196728 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:03:40.199331 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.adapter_contaminated_2.RData
2025-01-25 08:03:40.212131 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:03:40.215433 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.summary_preprocess.tab
2025-01-25 08:03:40.220175 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:03:40.227005 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:03:40.232857 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/reports/shortReadReport_1 ...
2025-01-25 08:03:42.256989 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/reports/shortReadReport_2 ...
2025-01-25 08:03:45.573195 INFO::preprocessReads.R/preprocessReads: done
2025-01-25 08:03:45.631791 INFO::alignReads.R/alignReads: starting alignment...
2025-01-25 08:03:45.638587 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:03:49.013698 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:03:49.016069 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000001/logs/progress.log
2025-01-25 08:03:52.128568 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-01-25 08:03:52.130892 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:03:54.829832 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-25 08:03:54.83218 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:03:57.505637 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-25 08:03:57.508829 DEBUG::tools.R/processChunks: done
2025-01-25 08:03:57.510639 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:03:57.832456 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-25 08:03:57.843858 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.summary_alignment.tab
2025-01-25 08:03:57.854273 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.summary_analyzed_bamstats.tab
2025-01-25 08:03:57.856636 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-25 08:03:58.13382 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.2e686d14a2922e/results/test_pe.summary_target_lengths.tab
2025-01-25 08:03:58.194429 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-25 08:03:58.195741 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:03:58.496748 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:03:58.500289 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:03:58.580047 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-25 08:03:58.586457 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:03:58.590714 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-25 08:03:58.593377 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:04:02.004848 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:04:02.006895 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/chunks/chunk_000001/logs/progress.log
2025-01-25 08:04:04.840494 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-25 08:04:04.842364 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/chunks/chunk_000002/logs/progress.log
2025-01-25 08:04:07.670908 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-25 08:04:07.672907 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/chunks/chunk_000003/logs/progress.log
2025-01-25 08:04:10.618584 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-01-25 08:04:10.62056 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/chunks/chunk_000004/logs/progress.log
2025-01-25 08:04:13.43111 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-01-25 08:04:13.472015 DEBUG::tools.R/processChunks: done
2025-01-25 08:04:13.476426 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:04:13.479607 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/results/test_pe.adapter_contaminated_1.RData
2025-01-25 08:04:13.483757 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:04:13.486319 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/results/test_pe.adapter_contaminated_2.RData
2025-01-25 08:04:13.500808 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:04:13.504084 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/results/test_pe.summary_preprocess.tab
2025-01-25 08:04:13.509405 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:04:13.516782 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:04:13.522573 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/reports/shortReadReport_1 ...
2025-01-25 08:04:15.426647 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReads.sparsechunks.2e686d51531ae2/reports/shortReadReport_2 ...
2025-01-25 08:04:18.550973 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:04:18.760083 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-25 08:04:18.766193 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -D /home/biocbuild/.local/share/gmap -t 1 -d TP53_demo_3.2.2 --quality-protocol=illumina  -A sam --read-group-id=test_se -m 0 --split-output /home/biocbuild/tmp/RtmpGbTZqA/test.alignReadsOneSingleEnd.2e686d14de0e55/bams/test.alignReads /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-01-25 08:04:18.915223 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-25 08:04:19.043227 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReadsOneSingleEnd.2e686d14de0e55/results/test.alignReads.summary_alignment.tab
2025-01-25 08:04:19.091916 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.alignReadsOneSingleEnd.2e686d14de0e55/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-25 08:04:19.093915 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0.002 0.004
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:04:19.489133 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.genotype.2e686d4c9c6470/results/test_pe.coverage.RData
2025-01-25 08:04:19.491438 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.genotype.2e686d4c9c6470/results/test_pe.coverage.bw
2025-01-25 08:04:19.669123 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.genotype.2e686d4c9c6470/results/test_pe.summary_coverage.tab
2025-01-25 08:04:19.671483 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:04:32.406971 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:04:32.545434 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:04:32.571128 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:04:32.57322 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.genotype.2e686d4c9c6470/results/test_pe.raw_variants.RData
2025-01-25 08:04:32.576327 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.genotype.2e686d4c9c6470/results/test_pe.filtered_variants.RData
2025-01-25 08:04:32.578233 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-25 08:04:32.579942 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:04:33.19209 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-25 08:04:33.193902 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-25 08:06:02.227366 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:06:02.867195 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-25 08:06:02.868498 INFO::analyzeVariants.R/.callGenotypes: done
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
 done successfully.



Executing test function test.wrap.callVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:06:03.48262 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:06:16.523473 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:06:16.64176 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:06:16.667081 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:06:16.669037 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.2e686d111032f3/results/test_pe.raw_variants.RData
2025-01-25 08:06:16.672187 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.2e686d111032f3/results/test_pe.filtered_variants.RData
2025-01-25 08:06:16.674093 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:06:16.862576 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:06:29.881365 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:06:29.967514 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:06:29.992274 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:06:29.994192 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.filters.2e686d767facda/results/test_pe.raw_variants.RData
2025-01-25 08:06:29.997435 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.filters.2e686d767facda/results/test_pe.filtered_variants.RData
2025-01-25 08:06:29.99939 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-25 08:06:30.001343 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:06:42.890816 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:06:42.950616 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:06:42.976755 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:06:42.978758 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.filters.2e686d767facda/results/test_pe.raw_variants.RData
2025-01-25 08:06:42.982065 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.filters.2e686d767facda/results/test_pe.filtered_variants.RData
2025-01-25 08:06:42.984671 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:06:43.296235 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:06:43.298263 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-25 08:06:46.918819 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:06:47.03499 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:06:47.060426 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:06:47.062422 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.which.2e686d3ebeea2d/results/test_pe.raw_variants.RData
2025-01-25 08:06:47.064832 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.wrap.callVariants.which.2e686d3ebeea2d/results/test_pe.filtered_variants.RData
2025-01-25 08:06:47.066673 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:06:47.274858 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:06:47.276762 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:06:47.519565 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:06:47.838361 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.isFirstFragment  ...  done successfully.



Executing test function test.buildCountsGRangesList  ...   403 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
 done successfully.



Executing test function test.generateSingleGeneDERs  ...  done successfully.



Executing test function test.computeCoverage  ...  done successfully.



Executing test function test.isSparse  ...  done successfully.



Executing test function test.mergeCoverage  ... 2025-01-25 08:08:01.883091 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/lymkfgxo/merged/results/bla.coverage.RData
2025-01-25 08:08:01.889112 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpGbTZqA/lymkfgxo/merged/results/bla.coverage.bw
2025-01-25 08:08:02.011066 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/lymkfgxo/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-01-25 08:08:03.381248 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/wyblnzej/merged/results/bla.coverage.RData
2025-01-25 08:08:03.383177 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpGbTZqA/wyblnzej/merged/results/bla.coverage.bw
2025-01-25 08:08:03.398167 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/wyblnzej/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.findTemplate  ...  done successfully.



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.getConfig  ...  done successfully.



Executing test function test.loadConfig  ...  done successfully.



Executing test function test.parseDCF  ...  done successfully.



Executing test function test.updateConfig  ...  done successfully.



Executing test function test.getAdapterSeqs  ...  done successfully.



Executing test function test.isAdapter  ...  done successfully.



Executing test function test.isAdapter3.primeEnd  ...  done successfully.



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:05.039232 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-25 08:08:05.040919 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.2e686d221ccbcf/bams/rRNA_contam/input1.fastq
2025-01-25 08:08:05.045973 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.2e686d221ccbcf/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.2e686d221ccbcf/bams/rRNA_contam/input1.fastq 2>&1
2025-01-25 08:08:05.160316 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-25 08:08:05.161835 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:05.353592 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-25 08:08:05.354974 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.paired_end.2e686d7fa24b34/bams/rRNA_contam/input1.fastq
2025-01-25 08:08:05.357122 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.paired_end.2e686d7fa24b34/bams/rRNA_contam/input2.fastq
2025-01-25 08:08:05.360265 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.paired_end.2e686d7fa24b34/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.paired_end.2e686d7fa24b34/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpGbTZqA/test.detectRRNA.paired_end.2e686d7fa24b34/bams/rRNA_contam/input2.fastq 2>&1
2025-01-25 08:08:05.61329 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-25 08:08:05.614677 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-01-25 08:08:05.643209 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpGbTZqA/test_get_rRNA_idsrgytoiuq/test_pe /home/biocbuild/tmp/RtmpGbTZqA/test_get_rRNA_idsrgytoiuq/1.fastq -a paired /home/biocbuild/tmp/RtmpGbTZqA/test_get_rRNA_idsrgytoiuq/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-01-25 08:08:05.921734 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpGbTZqA/test_get_rRNAIds_randomrbkdqsyt/test_pe /home/biocbuild/tmp/RtmpGbTZqA/test_get_rRNAIds_randomrbkdqsyt/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-01-25 08:08:06.094971 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-25 08:08:06.096928 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-25 08:08:06.098172 INFO::filterQuality.R/filterByLength: done
2025-01-25 08:08:06.166322 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-25 08:08:06.167594 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-25 08:08:06.168844 INFO::filterQuality.R/filterByLength: done
 done successfully.



Executing test function test.isAboveQualityThresh  ...  done successfully.



Executing test function test.trimTailsByQuality  ... 2025-01-25 08:08:06.24319 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-25 08:08:06.25596 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-25 08:08:06.257549 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-25 08:08:06.264249 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-25 08:08:06.265905 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-25 08:08:06.273074 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-25 08:08:06.274726 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-25 08:08:06.281617 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
 done successfully.



Executing test function test.callVariantsGATK.withFiltering  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.checkGATKJar  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



Executing test function test.excludeVariantsByRegion  ...  done successfully.



Executing test function test.gatk  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndels  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("test.realignIndels() tests need gatk.path option set") : 
  test.realignIndels() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK.parallel  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:06.680485 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:06.683963 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:08.148709 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:08.241267 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-25 08:08:08.245287 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:08.248592 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:08.499118 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:08.677244 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:08.844772 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:08.897569 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-25 08:08:08.901205 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:08.90466 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:09.134237 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:09.190583 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-25 08:08:09.194462 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:09.198244 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.createTmpDir  ...  done successfully.



Executing test function test.detectQualityInFASTQFile  ...  done successfully.



Executing test function test.getObjectFilename  ...  done successfully.



Executing test function test.safeUnlink  ...  done successfully.



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:08:09.976169 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:08:09.982451 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:08:09.98679 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-25 08:08:09.989739 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:08:13.400845 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:08:13.402854 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000001/logs/progress.log
2025-01-25 08:08:16.156618 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-25 08:08:16.158597 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000002/logs/progress.log
2025-01-25 08:08:18.861646 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-25 08:08:18.863475 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000003/logs/progress.log
2025-01-25 08:08:21.643565 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-25 08:08:21.694874 DEBUG::tools.R/processChunks: done
2025-01-25 08:08:21.69842 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:08:21.700622 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.adapter_contaminated_1.RData
2025-01-25 08:08:21.703476 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:08:21.705582 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.adapter_contaminated_2.RData
2025-01-25 08:08:21.717014 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:08:21.719635 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_preprocess.tab
2025-01-25 08:08:21.723302 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:08:21.729887 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:08:21.735309 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/reports/shortReadReport_1 ...
2025-01-25 08:08:23.610826 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/reports/shortReadReport_2 ...
2025-01-25 08:08:25.195054 INFO::preprocessReads.R/preprocessReads: done
2025-01-25 08:08:25.267579 INFO::alignReads.R/alignReads: starting alignment...
2025-01-25 08:08:25.272031 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:08:28.645738 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:08:28.64788 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000001/logs/progress.log
2025-01-25 08:08:31.254767 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-25 08:08:31.256876 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:08:33.871989 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-25 08:08:33.874123 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:08:36.497041 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-25 08:08:36.500413 DEBUG::tools.R/processChunks: done
2025-01-25 08:08:36.502419 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:08:36.803438 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-25 08:08:36.814343 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_alignment.tab
2025-01-25 08:08:36.824847 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_analyzed_bamstats.tab
2025-01-25 08:08:36.827608 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-25 08:08:37.087178 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_target_lengths.tab
2025-01-25 08:08:37.148665 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-25 08:08:37.14997 INFO::alignReads.R/alignReads: done
2025-01-25 08:08:37.223427 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-25 08:08:37.244081 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:08:40.770638 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:08:40.772851 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000001/logs/progress.log
2025-01-25 08:08:43.369016 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-25 08:08:43.3713 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000002/logs/progress.log
2025-01-25 08:08:45.939093 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-01-25 08:08:45.941385 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000003/logs/progress.log
2025-01-25 08:08:48.501749 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-25 08:08:48.505151 DEBUG::tools.R/processChunks: done
2025-01-25 08:08:48.507475 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-25 08:08:48.525227 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_exon.tab
2025-01-25 08:08:48.539575 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_exon_disjoint.tab
2025-01-25 08:08:48.549385 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_gene.tab
2025-01-25 08:08:48.557273 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_gene_coding.tab
2025-01-25 08:08:48.565036 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_gene_exonic.tab
2025-01-25 08:08:48.572958 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_intergenic.tab
2025-01-25 08:08:48.585824 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.counts_intron.tab
2025-01-25 08:08:48.589782 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-25 08:08:48.598975 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_counts.tab
2025-01-25 08:08:48.601424 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-25 08:08:48.969576 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-25 08:08:48.970811 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-25 08:08:49.061041 INFO::coverage.R/calculateCoverage: starting...
2025-01-25 08:08:49.065788 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:08:52.759594 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:08:52.76185 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000001/logs/progress.log
2025-01-25 08:08:54.957878 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-01-25 08:08:54.960064 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000002/logs/progress.log
2025-01-25 08:08:57.165029 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-01-25 08:08:57.167261 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/chunks/chunk_000003/logs/progress.log
2025-01-25 08:08:59.382659 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-01-25 08:08:59.38627 DEBUG::tools.R/processChunks: done
2025-01-25 08:09:01.692599 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.coverage.RData
2025-01-25 08:09:01.694643 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.coverage.bw
2025-01-25 08:09:01.712157 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_coverage.tab
2025-01-25 08:09:01.714195 INFO::coverage.R/calculateCoverage: done
2025-01-25 08:09:01.721063 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-25 08:09:01.805446 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:09:05.636694 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:09:05.74714 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:09:05.771482 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:09:05.773372 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.raw_variants.RData
2025-01-25 08:09:05.775653 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.filtered_variants.RData
2025-01-25 08:09:05.777436 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-25 08:09:05.778836 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:09:06.098621 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-25 08:09:06.241454 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/results/test_pe.summary_variants.tab
2025-01-25 08:09:06.244063 INFO::analyzeVariants/analyzeVariants: done
2025-01-25 08:09:06.247901 INFO::Pipeline run successful.
2025-01-25 08:09:06.43312 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-25 08:09:06.438517 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:09:06.441445 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.adapter_contaminated_1.RData
2025-01-25 08:09:06.44526 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:09:06.447986 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.adapter_contaminated_2.RData
2025-01-25 08:09:06.462498 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:09:06.528949 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_preprocess.tab
2025-01-25 08:09:06.531951 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:09:06.855766 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-25 08:09:06.864726 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_alignment.tab
2025-01-25 08:09:06.875115 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-25 08:09:06.877843 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-25 08:09:07.141018 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_target_lengths.tab
2025-01-25 08:09:07.20533 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-25 08:09:07.246695 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-25 08:09:07.270458 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_exon.tab
2025-01-25 08:09:07.285631 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_exon_disjoint.tab
2025-01-25 08:09:07.295058 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_gene.tab
2025-01-25 08:09:07.302927 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_gene_coding.tab
2025-01-25 08:09:07.31076 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_gene_exonic.tab
2025-01-25 08:09:07.318832 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_intergenic.tab
2025-01-25 08:09:07.332947 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.counts_intron.tab
2025-01-25 08:09:07.336697 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-25 08:09:07.345159 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_counts.tab
2025-01-25 08:09:07.35162 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-25 08:09:07.646843 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-25 08:09:10.159335 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.coverage.RData
2025-01-25 08:09:10.161783 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.coverage.bw
2025-01-25 08:09:10.177544 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_coverage.tab
2025-01-25 08:09:10.22088 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-25 08:09:10.301921 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:09:14.033688 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:09:14.147254 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:09:14.172635 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:09:14.174582 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.raw_variants.RData
2025-01-25 08:09:14.176897 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.filtered_variants.RData
2025-01-25 08:09:14.178771 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-25 08:09:14.180197 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:09:14.502623 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-25 08:09:14.645913 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.mergeLanes.2e686d1cf22682/merged/results/merged.summary_variants.tab
2025-01-25 08:09:14.648475 INFO::analyzeVariants/analyzeVariants: done
2025-01-25 08:09:14.651524 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0.031 0.018 0.049
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
 done successfully.



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:09:14.965758 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:09:14.987457 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:09:14.99591 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-25 08:09:14.998809 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:09:18.414295 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:09:18.416346 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/chunks/chunk_000001/logs/progress.log
2025-01-25 08:09:21.205947 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-25 08:09:21.262515 DEBUG::tools.R/processChunks: done
2025-01-25 08:09:21.265588 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:09:21.267672 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/results/test_pe.adapter_contaminated_1.RData
2025-01-25 08:09:21.270007 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:09:21.271925 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/results/test_pe.adapter_contaminated_2.RData
2025-01-25 08:09:21.280357 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:09:21.282924 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/results/test_pe.summary_preprocess.tab
2025-01-25 08:09:21.285912 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:09:21.292187 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:09:21.298055 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/reports/shortReadReport_1 ...
2025-01-25 08:09:23.254724 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.2e686d29fe8fff/reports/shortReadReport_2 ...
2025-01-25 08:09:24.841556 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:09:25.138712 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:09:25.145366 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:09:25.150053 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-25 08:09:25.153125 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:09:28.875487 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:09:28.877937 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/chunks/chunk_000001/logs/progress.log
2025-01-25 08:09:31.623487 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-25 08:09:31.625472 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/chunks/chunk_000002/logs/progress.log
2025-01-25 08:09:34.370091 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-25 08:09:34.37221 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/chunks/chunk_000003/logs/progress.log
2025-01-25 08:09:37.161946 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-25 08:09:37.220001 DEBUG::tools.R/processChunks: done
2025-01-25 08:09:37.223751 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:09:37.226131 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/results/test_pe.adapter_contaminated_1.RData
2025-01-25 08:09:37.229428 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:09:37.231854 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/results/test_pe.adapter_contaminated_2.RData
2025-01-25 08:09:37.244015 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:09:37.246884 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/results/test_pe.summary_preprocess.tab
2025-01-25 08:09:37.250825 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:09:37.258108 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:09:37.264022 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/reports/shortReadReport_1 ...
2025-01-25 08:09:39.072032 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads.minichunks.2e686d20ebb60/reports/shortReadReport_2 ...
2025-01-25 08:09:40.589979 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:09:40.851193 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:09:40.872959 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-25 08:09:40.875866 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:09:44.515851 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:09:44.517922 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads_single_end.2e686d1a03cfbd/chunks/chunk_000001/logs/progress.log
2025-01-25 08:09:46.976115 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-01-25 08:09:47.022713 DEBUG::tools.R/processChunks: done
2025-01-25 08:09:47.025971 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:09:47.028443 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads_single_end.2e686d1a03cfbd/results/test_se.adapter_contaminated_1.RData
2025-01-25 08:09:47.037202 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-25 08:09:47.039722 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads_single_end.2e686d1a03cfbd/results/test_se.summary_preprocess.tab
2025-01-25 08:09:47.042474 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads_single_end.2e686d1a03cfbd/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:09:47.048106 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpGbTZqA/test.preprocessReads_single_end.2e686d1a03cfbd/reports/shortReadReport_1 ...
2025-01-25 08:09:48.999836 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.readRNASeqEnds  ...  done successfully.



Executing test function test.readRNASeqEnds.dupmark  ...  done successfully.



Executing test function test.how_many  ...  done successfully.



Executing test function test.plotDF  ...  done successfully.



Executing test function test.relativeBarPlot  ...  done successfully.



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:09:49.722567 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-25 08:09:49.729741 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-01-25 08:09:49.735748 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-01-25 08:09:49.738695 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:09:53.229575 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:09:53.231644 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-25 08:09:56.276559 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2025-01-25 08:09:56.353873 DEBUG::tools.R/processChunks: done
2025-01-25 08:09:56.35718 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-25 08:09:56.359321 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-01-25 08:09:56.361723 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-25 08:09:56.363767 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-01-25 08:09:56.373042 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2025-01-25 08:09:56.375706 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-01-25 08:09:56.378852 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-01-25 08:09:56.385325 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-01-25 08:09:56.391816 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-01-25 08:09:58.513624 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-01-25 08:10:00.298446 INFO::preprocessReads.R/preprocessReads: done
2025-01-25 08:10:00.37349 INFO::alignReads.R/alignReads: starting alignment...
2025-01-25 08:10:00.378383 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:10:03.970731 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:10:03.973136 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1206:17367:135118" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1304:1838:53573" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2303:2956:116587" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "M" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1206:20028:108227" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1207:19518:143960" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:2207:4065:173048" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-25 08:10:09.845161 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.098 minutes
2025-01-25 08:10:09.8485 DEBUG::tools.R/processChunks: done
2025-01-25 08:10:09.850458 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-01-25 08:10:09.885273 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-25 08:10:09.894182 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-01-25 08:10:09.902093 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-01-25 08:10:09.904861 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-25 08:10:10.110062 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-01-25 08:10:10.17587 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-25 08:10:10.177309 INFO::alignReads.R/alignReads: done
2025-01-25 08:10:10.251977 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-25 08:10:10.268952 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:10:13.637976 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:10:13.640043 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-25 08:10:16.25702 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-25 08:10:16.260283 DEBUG::tools.R/processChunks: done
2025-01-25 08:10:16.262391 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-25 08:10:16.274372 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-01-25 08:10:16.28454 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-01-25 08:10:16.292078 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-01-25 08:10:16.297568 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-01-25 08:10:16.30318 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-01-25 08:10:16.308782 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-01-25 08:10:16.316911 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-01-25 08:10:16.320903 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-25 08:10:16.325851 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-01-25 08:10:16.328157 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-25 08:10:16.611807 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-25 08:10:16.613107 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-25 08:10:16.696769 INFO::coverage.R/calculateCoverage: starting...
2025-01-25 08:10:16.700995 DEBUG::tools.R/processChunks: starting...
2025-01-25 08:10:20.336471 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-25 08:10:20.338768 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-25 08:10:22.726513 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-01-25 08:10:22.729923 DEBUG::tools.R/processChunks: done
2025-01-25 08:10:25.862865 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-01-25 08:10:25.865139 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-01-25 08:10:25.97684 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-01-25 08:10:25.978733 INFO::coverage.R/calculateCoverage: done
2025-01-25 08:10:25.980545 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-25 08:10:26.058106 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-25 08:10:39.01534 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-25 08:10:39.128094 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-25 08:10:39.15259 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-25 08:10:39.154485 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-01-25 08:10:39.157583 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-01-25 08:10:39.159376 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-25 08:10:39.160804 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-25 08:10:39.480359 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-25 08:10:39.628278 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-01-25 08:10:39.631161 INFO::analyzeVariants/analyzeVariants: done
2025-01-25 08:10:39.636527 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpGbTZqA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-25 08:10:39.921863 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpGbTZqA/test.calcTargetLengths.2e686d326912f6/results/test_pe.summary_target_lengths.tab
 done successfully.



Executing test function test.sclapply  ...  done successfully.



Executing test function test.tryKeepTraceback  ...  done successfully.



Executing test function test.truncateReads  ...  done successfully.



Executing test function test.truncateReads.trim5  ...  done successfully.

RUNIT TEST PROTOCOL -- Sat Jan 25 08:10:54 2025 
*********************************************** 
Number of test functions: 61 
Number of deactivated test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: HTSeqGenie unit testing 
Test function regexp: ^test.+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (31.96 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.34 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.54 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (104.19 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.39 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (26.31 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.08 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.21 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.7 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (38.09 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (32.89 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (1.02 seconds)
test.isSparse: (5 checks) ... OK (0.14 seconds)
test.mergeCoverage: (1 checks) ... OK (1.89 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.41 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.2 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.42 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.47 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.05 seconds)
test.isAdapter: (5 checks) ... OK (0.16 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.11 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.31 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.45 seconds)
test.getRRNAIds: (1 checks) ... OK (0.28 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.19 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.gatk.R 
test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set
test.excludeVariantsByRegion: (3 checks) ... OK (0.22 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (1.48 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.33 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.19 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.17 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.58 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.13 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.2 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (65.06 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.picard.R 
test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test
test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (10.11 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.75 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.41 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.12 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.16 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.14 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (50.15 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.29 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (14.43 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.07 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.24 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
322.905  99.170 469.855

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie000
buildGenomicFeaturesFromTxDb0.0000.0000.001
runPipeline0.0000.0000.001