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This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 999/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.38.0  (landing page)
Jens Reeder
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: RELEASE_3_21
git_last_commit: 1638d9f
git_last_commit_date: 2025-04-15 10:16:04 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kjohnson3macOS 13.7.1 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / 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: 4.38.0
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_4.38.0.tar.gz
StartedAt: 2025-04-17 07:39:17 -0000 (Thu, 17 Apr 2025)
EndedAt: 2025-04-17 07:54:19 -0000 (Thu, 17 Apr 2025)
EllapsedTime: 901.9 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_4.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.38.0’
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** this is package ‘HTSeqGenie’ version ‘4.38.0’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:46:41.289295 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:46:41.298254 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:46:41.303694 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-17 07:46:41.306707 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:46:44.587647 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:46:44.589718 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/chunks/chunk_000001/logs/progress.log
2025-04-17 07:46:47.475218 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-04-17 07:46:47.477132 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/chunks/chunk_000002/logs/progress.log
2025-04-17 07:46:50.359385 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-04-17 07:46:50.361223 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/chunks/chunk_000003/logs/progress.log
2025-04-17 07:46:53.218797 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-04-17 07:46:53.259594 DEBUG::tools.R/processChunks: done
2025-04-17 07:46:53.266069 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:46:53.269233 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.adapter_contaminated_1.RData
2025-04-17 07:46:53.273189 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:46:53.275721 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.adapter_contaminated_2.RData
2025-04-17 07:46:53.289034 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
2025-04-17 07:46:53.292182 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.summary_preprocess.tab
2025-04-17 07:46:53.296757 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:46:53.304661 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:46:53.310631 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/reports/shortReadReport_1 ...
2025-04-17 07:46:55.24272 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/reports/shortReadReport_2 ...
2025-04-17 07:46:58.383993 INFO::preprocessReads.R/preprocessReads: done
2025-04-17 07:46:58.441915 INFO::alignReads.R/alignReads: starting alignment...
2025-04-17 07:46:58.448272 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:47:01.669836 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:47:01.67198 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/chunks/chunk_000001/logs/progress.log
2025-04-17 07:47:04.789478 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-04-17 07:47:04.791687 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/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.
2025-04-17 07:47:07.550515 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-04-17 07:47:07.552919 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/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.
2025-04-17 07:47:10.308909 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-04-17 07:47:10.312355 DEBUG::tools.R/processChunks: done
2025-04-17 07:47:10.314365 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.
2025-04-17 07:47:10.671835 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-17 07:47:10.703854 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.summary_alignment.tab
2025-04-17 07:47:10.718063 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.summary_analyzed_bamstats.tab
2025-04-17 07:47:10.721021 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-17 07:47:11.039454 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.20ace67c3ea546/results/test_pe.summary_target_lengths.tab
2025-04-17 07:47:11.105205 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-17 07:47:11.106566 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:47:11.403581 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:47:11.407082 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:47:11.487029 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-04-17 07:47:11.493319 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:47:11.497463 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-17 07:47:11.499986 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:47:14.760139 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:47:14.762135 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/chunks/chunk_000001/logs/progress.log
2025-04-17 07:47:17.582108 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-04-17 07:47:17.58395 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/chunks/chunk_000002/logs/progress.log
2025-04-17 07:47:20.407261 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-04-17 07:47:20.409317 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/chunks/chunk_000003/logs/progress.log
2025-04-17 07:47:23.341881 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-04-17 07:47:23.34392 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/chunks/chunk_000004/logs/progress.log
2025-04-17 07:47:26.142012 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-04-17 07:47:26.181531 DEBUG::tools.R/processChunks: done
2025-04-17 07:47:26.186042 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:47:26.189243 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/results/test_pe.adapter_contaminated_1.RData
2025-04-17 07:47:26.193346 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:47:26.195828 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/results/test_pe.adapter_contaminated_2.RData
2025-04-17 07:47:26.209439 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
2025-04-17 07:47:26.212467 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/results/test_pe.summary_preprocess.tab
2025-04-17 07:47:26.217337 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:47:26.224232 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:47:26.229686 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/reports/shortReadReport_1 ...
2025-04-17 07:47:28.201593 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReads.sparsechunks.20ace6363cd329/reports/shortReadReport_2 ...
2025-04-17 07:47:31.269571 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:47:31.503046 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-04-17 07:47:31.509865 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/Rtmp2NBZT7/test.alignReadsOneSingleEnd.20ace66178f812/bams/test.alignReads /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-04-17 07:47:31.665432 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-04-17 07:47:31.813102 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReadsOneSingleEnd.20ace66178f812/results/test.alignReads.summary_alignment.tab
2025-04-17 07:47:31.872995 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.alignReadsOneSingleEnd.20ace66178f812/results/test.alignReads.summary_analyzed_bamstats.tab
2025-04-17 07:47:31.875132 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.004 0 0.003
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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:47:32.310208 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.genotype.20ace655aac529/results/test_pe.coverage.RData
2025-04-17 07:47:32.312898 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.genotype.20ace655aac529/results/test_pe.coverage.bw
2025-04-17 07:47:32.502662 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.genotype.20ace655aac529/results/test_pe.summary_coverage.tab
2025-04-17 07:47:32.505149 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:47:44.48411 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:47:44.633086 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:47:44.65894 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:47:44.661126 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.genotype.20ace655aac529/results/test_pe.raw_variants.RData
2025-04-17 07:47:44.66428 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.genotype.20ace655aac529/results/test_pe.filtered_variants.RData
2025-04-17 07:47:44.666382 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-17 07:47:44.668103 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:47:45.255099 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-17 07:47:45.256932 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-04-17 07:49:18.550743 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:49:19.199448 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-17 07:49:19.200714 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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:49:19.794631 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:49:31.725416 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:49:31.851244 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:49:31.880228 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:49:31.882431 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.20ace618db8c08/results/test_pe.raw_variants.RData
2025-04-17 07:49:31.885846 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.20ace618db8c08/results/test_pe.filtered_variants.RData
2025-04-17 07:49:31.887988 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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:49:32.090733 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:49:43.844335 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:49:43.93168 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:49:43.958541 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:49:43.960603 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.filters.20ace65e0cc436/results/test_pe.raw_variants.RData
2025-04-17 07:49:43.963826 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.filters.20ace65e0cc436/results/test_pe.filtered_variants.RData
2025-04-17 07:49:43.965758 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-17 07:49:43.967727 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:49:55.841805 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:49:55.900975 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:49:55.927305 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:49:55.929335 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.filters.20ace65e0cc436/results/test_pe.raw_variants.RData
2025-04-17 07:49:55.93275 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.filters.20ace65e0cc436/results/test_pe.filtered_variants.RData
2025-04-17 07:49:55.935505 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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:49:56.25032 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:49:56.252599 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-04-17 07:49:59.760288 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:49:59.876334 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:49:59.901801 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:49:59.903656 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.which.20ace67749462d/results/test_pe.raw_variants.RData
2025-04-17 07:49:59.905991 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.wrap.callVariants.which.20ace67749462d/results/test_pe.filtered_variants.RData
2025-04-17 07:49:59.907801 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:50:00.090646 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:50:00.092434 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:50:00.334242 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:50:00.652028 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  ... 2025-04-17 07:51:19.198151 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/wrteasgf/merged/results/bla.coverage.RData
2025-04-17 07:51:19.201534 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/wrteasgf/merged/results/bla.coverage.bw
2025-04-17 07:51:19.318331 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/wrteasgf/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-04-17 07:51:20.711436 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/cabitxfo/merged/results/bla.coverage.RData
2025-04-17 07:51:20.718168 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/cabitxfo/merged/results/bla.coverage.bw
2025-04-17 07:51:20.732885 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/cabitxfo/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:22.421432 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-04-17 07:51:22.42299 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.20ace671040ff7/bams/rRNA_contam/input1.fastq
2025-04-17 07:51:22.427481 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/Rtmp2NBZT7/test.detectRRNA.20ace671040ff7/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.20ace671040ff7/bams/rRNA_contam/input1.fastq 2>&1
2025-04-17 07:51:22.539124 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-04-17 07:51:22.540535 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:22.741957 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-04-17 07:51:22.743329 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.paired_end.20ace64994feec/bams/rRNA_contam/input1.fastq
2025-04-17 07:51:22.745497 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.paired_end.20ace64994feec/bams/rRNA_contam/input2.fastq
2025-04-17 07:51:22.74867 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/Rtmp2NBZT7/test.detectRRNA.paired_end.20ace64994feec/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.paired_end.20ace64994feec/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp2NBZT7/test.detectRRNA.paired_end.20ace64994feec/bams/rRNA_contam/input2.fastq 2>&1
2025-04-17 07:51:22.999253 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-04-17 07:51:23.000637 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-04-17 07:51:23.028319 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/Rtmp2NBZT7/test_get_rRNA_idsdimbwraz/test_pe /home/biocbuild/tmp/Rtmp2NBZT7/test_get_rRNA_idsdimbwraz/1.fastq -a paired /home/biocbuild/tmp/Rtmp2NBZT7/test_get_rRNA_idsdimbwraz/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-04-17 07:51:23.325865 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/Rtmp2NBZT7/test_get_rRNAIds_randomeiavrfmd/test_pe /home/biocbuild/tmp/Rtmp2NBZT7/test_get_rRNAIds_randomeiavrfmd/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-04-17 07:51:23.494619 INFO::filterQuality.R/filterQuality: filterByLength...
2025-04-17 07:51:23.496568 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-04-17 07:51:23.497851 INFO::filterQuality.R/filterByLength: done
2025-04-17 07:51:23.566379 INFO::filterQuality.R/filterQuality: filterByLength...
2025-04-17 07:51:23.567669 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-04-17 07:51:23.56893 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-04-17 07:51:23.646036 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-17 07:51:23.659302 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-17 07:51:23.660931 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-17 07:51:23.667714 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-17 07:51:23.669316 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-17 07:51:23.676033 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-17 07:51:23.677631 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-17 07:51:23.684452 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 0 0
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: 0.001 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 0.001
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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:24.101233 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:24.104637 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:24.359304 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:24.422585 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-17 07:51:24.426592 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:24.430096 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:24.776935 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:24.981376 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:25.218421 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:25.290906 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-17 07:51:25.29444 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:25.297786 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:25.561141 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:25.646434 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-17 07:51:25.650108 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:25.653682 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:51:26.627593 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:51:26.634414 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:51:26.639134 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-17 07:51:26.642384 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:51:30.074484 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:51:30.076434 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000001/logs/progress.log
2025-04-17 07:51:32.848784 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-04-17 07:51:32.850801 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000002/logs/progress.log
2025-04-17 07:51:35.572121 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-04-17 07:51:35.574067 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000003/logs/progress.log
2025-04-17 07:51:38.330338 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-04-17 07:51:38.404087 DEBUG::tools.R/processChunks: done
2025-04-17 07:51:38.407779 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:51:38.410216 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.adapter_contaminated_1.RData
2025-04-17 07:51:38.413254 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:51:38.415522 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.adapter_contaminated_2.RData
2025-04-17 07:51:38.426607 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
2025-04-17 07:51:38.429274 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_preprocess.tab
2025-04-17 07:51:38.432718 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:51:38.438726 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:51:38.444142 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/reports/shortReadReport_1 ...
2025-04-17 07:51:40.340951 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/reports/shortReadReport_2 ...
2025-04-17 07:51:41.866728 INFO::preprocessReads.R/preprocessReads: done
2025-04-17 07:51:41.938401 INFO::alignReads.R/alignReads: starting alignment...
2025-04-17 07:51:41.943243 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:51:45.379666 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:51:45.381812 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000001/logs/progress.log
2025-04-17 07:51:48.006498 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-04-17 07:51:48.008709 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/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.
2025-04-17 07:51:50.653992 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-04-17 07:51:50.656057 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/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.
2025-04-17 07:51:53.305439 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-04-17 07:51:53.308943 DEBUG::tools.R/processChunks: done
2025-04-17 07:51:53.311035 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.
2025-04-17 07:51:53.620247 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-17 07:51:53.631253 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_alignment.tab
2025-04-17 07:51:53.641963 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_analyzed_bamstats.tab
2025-04-17 07:51:53.644708 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-17 07:51:53.907589 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_target_lengths.tab
2025-04-17 07:51:53.968712 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-17 07:51:53.970104 INFO::alignReads.R/alignReads: done
2025-04-17 07:51:54.044826 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-04-17 07:51:54.067711 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:51:57.55623 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:51:57.558447 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000001/logs/progress.log
2025-04-17 07:52:00.123766 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-04-17 07:52:00.126145 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000002/logs/progress.log
2025-04-17 07:52:02.691728 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-04-17 07:52:02.693999 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000003/logs/progress.log
2025-04-17 07:52:05.271152 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-04-17 07:52:05.274642 DEBUG::tools.R/processChunks: done
2025-04-17 07:52:05.285027 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-04-17 07:52:05.31184 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_exon.tab
2025-04-17 07:52:05.326509 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_exon_disjoint.tab
2025-04-17 07:52:05.335926 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_gene.tab
2025-04-17 07:52:05.343549 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_gene_coding.tab
2025-04-17 07:52:05.351144 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_gene_exonic.tab
2025-04-17 07:52:05.359114 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_intergenic.tab
2025-04-17 07:52:05.37171 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.counts_intron.tab
2025-04-17 07:52:05.375639 INFO::countGenomicFeatures.R/mergeCounts: done
2025-04-17 07:52:05.384748 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_counts.tab
2025-04-17 07:52:05.387327 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-04-17 07:52:05.757795 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-04-17 07:52:05.759173 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-04-17 07:52:05.858201 INFO::coverage.R/calculateCoverage: starting...
2025-04-17 07:52:05.862692 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:52:09.270951 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:52:09.273121 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000001/logs/progress.log
2025-04-17 07:52:11.46946 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-04-17 07:52:11.471733 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000002/logs/progress.log
2025-04-17 07:52:13.686038 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-04-17 07:52:13.688172 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/chunks/chunk_000003/logs/progress.log
2025-04-17 07:52:15.884938 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-04-17 07:52:15.888259 DEBUG::tools.R/processChunks: done
2025-04-17 07:52:19.228976 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.coverage.RData
2025-04-17 07:52:19.231269 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.coverage.bw
2025-04-17 07:52:19.248258 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_coverage.tab
2025-04-17 07:52:19.250195 INFO::coverage.R/calculateCoverage: done
2025-04-17 07:52:19.258059 INFO::analyzeVariants/analyzeVariants: starting ...
2025-04-17 07:52:19.347032 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:52:23.211003 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:52:23.332075 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:52:23.358995 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:52:23.361137 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.raw_variants.RData
2025-04-17 07:52:23.363767 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.filtered_variants.RData
2025-04-17 07:52:23.365895 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-17 07:52:23.367576 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:52:23.707991 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-17 07:52:23.860295 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/results/test_pe.summary_variants.tab
2025-04-17 07:52:23.863172 INFO::analyzeVariants/analyzeVariants: done
2025-04-17 07:52:23.867166 INFO::Pipeline run successful.
2025-04-17 07:52:24.055957 INFO::mergeLanes.R/doMergeLanes: starting...
2025-04-17 07:52:24.061219 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:52:24.064161 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.adapter_contaminated_1.RData
2025-04-17 07:52:24.068004 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:52:24.070805 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.adapter_contaminated_2.RData
2025-04-17 07:52:24.085104 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
2025-04-17 07:52:24.088455 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_preprocess.tab
2025-04-17 07:52:24.091446 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.
2025-04-17 07:52:24.42416 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-17 07:52:24.433448 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_alignment.tab
2025-04-17 07:52:24.444605 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_analyzed_bamstats.tab
2025-04-17 07:52:24.447601 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-17 07:52:24.716069 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_target_lengths.tab
2025-04-17 07:52:24.780504 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-17 07:52:24.82324 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-04-17 07:52:24.847054 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_exon.tab
2025-04-17 07:52:24.862332 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_exon_disjoint.tab
2025-04-17 07:52:24.871832 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_gene.tab
2025-04-17 07:52:24.87992 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_gene_coding.tab
2025-04-17 07:52:24.888346 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_gene_exonic.tab
2025-04-17 07:52:24.896575 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_intergenic.tab
2025-04-17 07:52:24.9114 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.counts_intron.tab
2025-04-17 07:52:24.915119 INFO::countGenomicFeatures.R/mergeCounts: done
2025-04-17 07:52:24.92348 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_counts.tab
2025-04-17 07:52:24.926078 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-04-17 07:52:25.21517 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-04-17 07:52:27.615418 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.coverage.RData
2025-04-17 07:52:27.618496 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.coverage.bw
2025-04-17 07:52:27.633949 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_coverage.tab
2025-04-17 07:52:27.673048 INFO::analyzeVariants/analyzeVariants: starting ...
2025-04-17 07:52:27.755617 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:52:31.513693 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:52:31.631662 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:52:31.66175 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:52:31.663711 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.raw_variants.RData
2025-04-17 07:52:31.666129 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.filtered_variants.RData
2025-04-17 07:52:31.66802 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-17 07:52:31.669576 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:52:32.015804 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-17 07:52:32.174246 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.mergeLanes.20ace65aec186f/merged/results/merged.summary_variants.tab
2025-04-17 07:52:32.177322 INFO::analyzeVariants/analyzeVariants: done
2025-04-17 07:52:32.18627 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0.001 0 0.001
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/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:52:32.549774 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:52:32.573218 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:52:32.594118 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-17 07:52:32.597158 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:52:36.137893 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:52:36.140059 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/chunks/chunk_000001/logs/progress.log
2025-04-17 07:52:38.896676 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-04-17 07:52:38.963877 DEBUG::tools.R/processChunks: done
2025-04-17 07:52:38.966742 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:52:38.968773 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/results/test_pe.adapter_contaminated_1.RData
2025-04-17 07:52:38.970947 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:52:38.972882 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/results/test_pe.adapter_contaminated_2.RData
2025-04-17 07:52:38.980833 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
2025-04-17 07:52:38.983238 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/results/test_pe.summary_preprocess.tab
2025-04-17 07:52:38.986066 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:52:38.991769 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:52:38.996867 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/reports/shortReadReport_1 ...
2025-04-17 07:52:40.955461 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.20ace62a6f7909/reports/shortReadReport_2 ...
2025-04-17 07:52:42.551689 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:52:42.873536 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:52:42.880182 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:52:42.884783 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-17 07:52:42.887644 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:52:46.420089 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:52:46.422266 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/chunks/chunk_000001/logs/progress.log
2025-04-17 07:52:49.152458 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-04-17 07:52:49.154363 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/chunks/chunk_000002/logs/progress.log
2025-04-17 07:52:51.895624 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-04-17 07:52:51.897552 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/chunks/chunk_000003/logs/progress.log
2025-04-17 07:52:54.668031 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-04-17 07:52:54.740386 DEBUG::tools.R/processChunks: done
2025-04-17 07:52:54.744025 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:52:54.746308 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/results/test_pe.adapter_contaminated_1.RData
2025-04-17 07:52:54.749081 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:52:54.751224 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/results/test_pe.adapter_contaminated_2.RData
2025-04-17 07:52:54.762141 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
2025-04-17 07:52:54.764935 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/results/test_pe.summary_preprocess.tab
2025-04-17 07:52:54.768431 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:52:54.775135 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:52:54.780801 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/reports/shortReadReport_1 ...
2025-04-17 07:52:56.659838 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads.minichunks.20ace6e4281d5/reports/shortReadReport_2 ...
2025-04-17 07:52:58.17482 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:52:58.477225 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:52:58.499422 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-17 07:52:58.502397 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:53:01.989243 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:53:01.991227 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads_single_end.20ace6b2d7ffe/chunks/chunk_000001/logs/progress.log
2025-04-17 07:53:04.450845 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-04-17 07:53:04.515253 DEBUG::tools.R/processChunks: done
2025-04-17 07:53:04.518719 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:53:04.521068 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads_single_end.20ace6b2d7ffe/results/test_se.adapter_contaminated_1.RData
2025-04-17 07:53:04.52949 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
2025-04-17 07:53:04.531889 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads_single_end.20ace6b2d7ffe/results/test_se.summary_preprocess.tab
2025-04-17 07:53:04.534479 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads_single_end.20ace6b2d7ffe/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:53:04.539748 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp2NBZT7/test.preprocessReads_single_end.20ace6b2d7ffe/reports/shortReadReport_1 ...
2025-04-17 07:53:06.484937 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-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:53:07.246227 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-17 07:53:07.271063 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-04-17 07:53:07.294219 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-04-17 07:53:07.297423 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:53:11.536357 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:53:11.538571 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-04-17 07:53:14.587189 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2025-04-17 07:53:14.667319 DEBUG::tools.R/processChunks: done
2025-04-17 07:53:14.670573 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-17 07:53:14.6727 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-04-17 07:53:14.674893 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-17 07:53:14.676826 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-04-17 07:53:14.685117 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
2025-04-17 07:53:14.687618 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-04-17 07:53:14.6909 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-04-17 07:53:14.698091 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-04-17 07:53:14.704276 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-04-17 07:53:16.974036 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-04-17 07:53:18.965717 INFO::preprocessReads.R/preprocessReads: done
2025-04-17 07:53:19.050045 INFO::alignReads.R/alignReads: starting alignment...
2025-04-17 07:53:19.054585 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:53:22.610837 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:53:22.613042 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.
2025-04-17 07:53:28.466565 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.098 minutes
2025-04-17 07:53:28.477317 DEBUG::tools.R/processChunks: done
2025-04-17 07:53:28.48004 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-04-17 07:53:28.518088 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-17 07:53:28.528834 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-04-17 07:53:28.536741 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-04-17 07:53:28.53941 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-17 07:53:28.736828 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-04-17 07:53:28.796568 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-17 07:53:28.797914 INFO::alignReads.R/alignReads: done
2025-04-17 07:53:28.872712 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-04-17 07:53:28.892174 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:53:32.592715 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:53:32.594962 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-04-17 07:53:35.211794 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-04-17 07:53:35.215214 DEBUG::tools.R/processChunks: done
2025-04-17 07:53:35.217405 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-04-17 07:53:35.229481 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-04-17 07:53:35.239413 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-04-17 07:53:35.24679 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-04-17 07:53:35.252116 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-04-17 07:53:35.257374 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-04-17 07:53:35.262601 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-04-17 07:53:35.270457 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-04-17 07:53:35.274531 INFO::countGenomicFeatures.R/mergeCounts: done
2025-04-17 07:53:35.279752 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-04-17 07:53:35.282206 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-04-17 07:53:35.556753 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-04-17 07:53:35.557994 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-04-17 07:53:35.647906 INFO::coverage.R/calculateCoverage: starting...
2025-04-17 07:53:35.652374 DEBUG::tools.R/processChunks: starting...
2025-04-17 07:53:39.081657 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-17 07:53:39.08384 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-04-17 07:53:41.464325 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-04-17 07:53:41.467798 DEBUG::tools.R/processChunks: done
2025-04-17 07:53:43.217557 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-04-17 07:53:43.219596 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-04-17 07:53:43.351944 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-04-17 07:53:43.353904 INFO::coverage.R/calculateCoverage: done
2025-04-17 07:53:43.355769 INFO::analyzeVariants/analyzeVariants: starting ...
2025-04-17 07:53:43.441205 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-17 07:53:55.964994 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-17 07:53:56.085656 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-17 07:53:56.111817 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-17 07:53:56.113841 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-04-17 07:53:56.117173 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-04-17 07:53:56.119313 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-17 07:53:56.120946 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-17 07:53:56.470576 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-17 07:53:56.623244 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-04-17 07:53:56.626122 INFO::analyzeVariants/analyzeVariants: done
2025-04-17 07:53:56.63148 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp2NBZT7/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-04-17 07:53:56.962017 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp2NBZT7/test.calcTargetLengths.20ace67e139898/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 -- Thu Apr 17 07:54:12 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-devel_2025-02-19/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (31.44 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.17 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.59 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (107.74 seconds)
test.wrap.callVariants: (4 checks) ... OK (12.26 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (24.05 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (3.97 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.18 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.72 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (40 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (35.75 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (0.97 seconds)
test.isSparse: (5 checks) ... OK (0.13 seconds)
test.mergeCoverage: (1 checks) ... OK (1.66 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.44 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.41 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.48 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-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.06 seconds)
test.isAdapter: (5 checks) ... OK (0.17 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.12 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.32 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.46 seconds)
test.getRRNAIds: (1 checks) ... OK (0.29 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.19 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.26 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.4 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.22 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.24 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.76 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.18 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.24 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (65.98 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (10.33 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.62 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.31 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.12 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.15 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (49.69 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.32 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (15.33 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.08 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.26 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
325.515 100.164 474.247

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie000
buildGenomicFeaturesFromTxDb000
runPipeline000