Multiple platform build/check report for BioC 3.20 - CHECK results for HTSeqGenie on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4420
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*

CHECK results for HTSeqGenie on nebbiolo2

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.

raw results

Summary

Package: HTSeqGenie

Version: 4.36.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HTSeqGenie_4.36.0.tar.gz

StartedAt: 2025-03-24 23:11:10 -0400 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 23:51:11 -0400 (Mon, 24 Mar 2025)

EllapsedTime: 2400.9 seconds

RetCode: None

Status: TIMEOUT

CheckDir: HTSeqGenie.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HTSeqGenie_4.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.36.0’
* 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’

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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

> 
> 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:16:30.085343 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:16:30.093141 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:16:30.096394 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-24 23:16:30.098379 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:16:32.748796 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:16:32.750317 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/chunks/chunk_000001/logs/progress.log
2025-03-24 23:16:35.506347 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-24 23:16:35.507919 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/chunks/chunk_000002/logs/progress.log
2025-03-24 23:16:38.30346 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-03-24 23:16:38.304833 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/chunks/chunk_000003/logs/progress.log
2025-03-24 23:16:41.07656 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-24 23:16:41.105904 DEBUG::tools.R/processChunks: done
2025-03-24 23:16:41.109837 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:16:41.11215 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.adapter_contaminated_1.RData
2025-03-24 23:16:41.114959 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:16:41.116585 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.adapter_contaminated_2.RData
2025-03-24 23:16:41.125674 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
2025-03-24 23:16:41.127794 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.summary_preprocess.tab
2025-03-24 23:16:41.130958 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:16:41.136249 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:16:41.139895 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/reports/shortReadReport_1 ...
2025-03-24 23:16:42.551828 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/reports/shortReadReport_2 ...
2025-03-24 23:16:43.733858 INFO::preprocessReads.R/preprocessReads: done
2025-03-24 23:16:43.83263 INFO::alignReads.R/alignReads: starting alignment...
2025-03-24 23:16:43.83866 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:16:47.065147 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:16:47.066625 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/chunks/chunk_000001/logs/progress.log
2025-03-24 23:16:49.956796 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-24 23:16:49.958617 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/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.
2025-03-24 23:16:52.612692 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-24 23:16:52.614473 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/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.
2025-03-24 23:16:55.224344 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-24 23:16:55.227674 DEBUG::tools.R/processChunks: done
2025-03-24 23:16:55.229521 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.
2025-03-24 23:16:55.497331 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-24 23:16:55.505291 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.summary_alignment.tab
2025-03-24 23:16:55.512108 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.summary_analyzed_bamstats.tab
2025-03-24 23:16:55.513676 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-24 23:16:55.752947 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.36d4cb5341aafc/results/test_pe.summary_target_lengths.tab
2025-03-24 23:16:55.799098 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-24 23:16:55.800096 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:16:56.089419 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:16:56.092488 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:16:56.152904 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-24 23:16:56.157955 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:16:56.160935 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-24 23:16:56.162761 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:16:59.062555 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:16:59.063959 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/chunks/chunk_000001/logs/progress.log
2025-03-24 23:17:01.798602 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-24 23:17:01.799995 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/chunks/chunk_000002/logs/progress.log
2025-03-24 23:17:04.494455 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-24 23:17:04.496467 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/chunks/chunk_000003/logs/progress.log
2025-03-24 23:17:07.258257 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-24 23:17:07.259587 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/chunks/chunk_000004/logs/progress.log
2025-03-24 23:17:09.962419 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-03-24 23:17:09.992053 DEBUG::tools.R/processChunks: done
2025-03-24 23:17:09.995355 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:17:09.997605 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/results/test_pe.adapter_contaminated_1.RData
2025-03-24 23:17:10.000417 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:17:10.002017 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/results/test_pe.adapter_contaminated_2.RData
2025-03-24 23:17:10.012992 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
2025-03-24 23:17:10.015195 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/results/test_pe.summary_preprocess.tab
2025-03-24 23:17:10.018663 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:17:10.023604 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:17:10.026943 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/reports/shortReadReport_1 ...
2025-03-24 23:17:11.318875 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReads.sparsechunks.36d4cb74de9312/reports/shortReadReport_2 ...
2025-03-24 23:17:12.367297 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:17:12.505596 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-24 23:17:12.509561 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReadsOneSingleEnd.36d4cb7305ae31/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-24 23:17:12.704878 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-24 23:17:12.78783 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReadsOneSingleEnd.36d4cb7305ae31/results/test.alignReads.summary_alignment.tab
2025-03-24 23:17:12.833401 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.alignReadsOneSingleEnd.36d4cb7305ae31/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-24 23:17:12.834776 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.001 0.001 0.002
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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:17:13.105077 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.genotype.36d4cb4af50de5/results/test_pe.coverage.RData
2025-03-24 23:17:13.10676 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.genotype.36d4cb4af50de5/results/test_pe.coverage.bw
2025-03-24 23:17:13.217231 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.genotype.36d4cb4af50de5/results/test_pe.summary_coverage.tab
2025-03-24 23:17:13.218776 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:17:23.337263 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:17:23.477249 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:17:23.501593 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:17:23.503531 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.genotype.36d4cb4af50de5/results/test_pe.raw_variants.RData
2025-03-24 23:17:23.506553 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.genotype.36d4cb4af50de5/results/test_pe.filtered_variants.RData
2025-03-24 23:17:23.508342 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-24 23:17:23.509868 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:17:23.946637 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-24 23:17:23.948227 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-24 23:18:24.732915 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:18:25.210861 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-24 23:18:25.211988 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:18:25.701062 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:18:36.503669 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:18:36.627347 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:18:36.648526 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:18:36.650211 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.36d4cb522822dd/results/test_pe.raw_variants.RData
2025-03-24 23:18:36.652915 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.36d4cb522822dd/results/test_pe.filtered_variants.RData
2025-03-24 23:18:36.654543 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:18:36.810666 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:18:47.360728 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:18:47.420021 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:18:47.437315 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:18:47.438643 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.filters.36d4cb7f041976/results/test_pe.raw_variants.RData
2025-03-24 23:18:47.441015 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.filters.36d4cb7f041976/results/test_pe.filtered_variants.RData
2025-03-24 23:18:47.442223 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-24 23:18:47.443855 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:18:57.765008 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:18:57.809285 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:18:57.82571 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:18:57.827065 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.filters.36d4cb7f041976/results/test_pe.raw_variants.RData
2025-03-24 23:18:57.829617 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.filters.36d4cb7f041976/results/test_pe.filtered_variants.RData
2025-03-24 23:18:57.831585 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:18:59.731928 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:18:59.733259 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-24 23:19:02.341921 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:19:02.411908 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:19:02.427545 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:19:02.428793 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.which.36d4cb13cb6b9/results/test_pe.raw_variants.RData
2025-03-24 23:19:02.4303 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.wrap.callVariants.which.36d4cb13cb6b9/results/test_pe.filtered_variants.RData
2025-03-24 23:19:02.431453 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:19:02.553705 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:19:02.55502 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:19:02.731475 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:19:02.930988 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  ... 2025-03-24 23:19:57.129455 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/jmftverd/merged/results/bla.coverage.RData
2025-03-24 23:19:57.133206 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/jmftverd/merged/results/bla.coverage.bw
2025-03-24 23:19:57.211882 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/jmftverd/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-24 23:19:58.479923 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/uiotgndk/merged/results/bla.coverage.RData
2025-03-24 23:19:58.481896 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/uiotgndk/merged/results/bla.coverage.bw
2025-03-24 23:19:58.495021 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/uiotgndk/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:19:59.710133 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-24 23:19:59.711267 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.36d4cb4c48f693/bams/rRNA_contam/input1.fastq
2025-03-24 23:19:59.714532 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.36d4cb4c48f693/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.36d4cb4c48f693/bams/rRNA_contam/input1.fastq 2>&1
2025-03-24 23:19:59.858936 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-24 23:19:59.860001 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:00.005719 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-24 23:20:00.006728 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.paired_end.36d4cb28601ebe/bams/rRNA_contam/input1.fastq
2025-03-24 23:20:00.008243 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.paired_end.36d4cb28601ebe/bams/rRNA_contam/input2.fastq
2025-03-24 23:20:00.010407 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.paired_end.36d4cb28601ebe/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.paired_end.36d4cb28601ebe/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.detectRRNA.paired_end.36d4cb28601ebe/bams/rRNA_contam/input2.fastq 2>&1
2025-03-24 23:20:00.246085 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-24 23:20:00.247078 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-24 23:20:00.266145 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/test_get_rRNA_idsjbmsnfeu/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test_get_rRNA_idsjbmsnfeu/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test_get_rRNA_idsjbmsnfeu/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-24 23:20:00.563019 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/test_get_rRNAIds_randomfkotanrj/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test_get_rRNAIds_randomfkotanrj/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-24 23:20:00.774273 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-24 23:20:00.775765 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-24 23:20:00.776628 INFO::filterQuality.R/filterByLength: done
2025-03-24 23:20:00.82385 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-24 23:20:00.824844 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-24 23:20:00.825666 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-24 23:20:00.873333 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-24 23:20:00.882464 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-24 23:20:00.883641 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-24 23:20:00.888201 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-24 23:20:00.889193 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-24 23:20:00.893718 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-24 23:20:00.894673 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-24 23:20:00.899078 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 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: 0.001 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



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



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



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



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:01.191903 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:01.19425 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:01.370795 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:01.469591 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-24 23:20:01.472493 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:01.474745 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:01.719481 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:01.862775 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:02.018444 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:02.112031 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-24 23:20:02.115113 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:02.118085 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:02.339034 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:02.379957 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-24 23:20:02.382427 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:02.384655 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:20:03.092951 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:20:03.100396 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:20:03.104237 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-24 23:20:03.106755 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:20:06.096334 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:20:06.097807 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000001/logs/progress.log
2025-03-24 23:20:08.699164 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-24 23:20:08.700443 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000002/logs/progress.log
2025-03-24 23:20:11.330848 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-24 23:20:11.333138 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000003/logs/progress.log
2025-03-24 23:20:13.975285 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-24 23:20:14.011784 DEBUG::tools.R/processChunks: done
2025-03-24 23:20:14.016417 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:20:14.018368 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.adapter_contaminated_1.RData
2025-03-24 23:20:14.020779 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:20:14.02244 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.adapter_contaminated_2.RData
2025-03-24 23:20:14.031112 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
2025-03-24 23:20:14.03291 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_preprocess.tab
2025-03-24 23:20:14.035306 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:20:14.039775 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:20:14.043527 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/reports/shortReadReport_1 ...
2025-03-24 23:20:15.327456 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/reports/shortReadReport_2 ...
2025-03-24 23:20:16.345851 INFO::preprocessReads.R/preprocessReads: done
2025-03-24 23:20:16.468341 INFO::alignReads.R/alignReads: starting alignment...
2025-03-24 23:20:16.473088 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:20:19.361614 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:20:19.363137 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000001/logs/progress.log
2025-03-24 23:20:21.94631 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-24 23:20:21.947962 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/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.
2025-03-24 23:20:24.52768 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-24 23:20:24.529216 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/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.
2025-03-24 23:20:27.11063 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-24 23:20:27.113877 DEBUG::tools.R/processChunks: done
2025-03-24 23:20:27.115775 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.
2025-03-24 23:20:27.346251 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-24 23:20:27.353187 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_alignment.tab
2025-03-24 23:20:27.359352 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_analyzed_bamstats.tab
2025-03-24 23:20:27.361011 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-24 23:20:27.573217 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_target_lengths.tab
2025-03-24 23:20:27.617445 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-24 23:20:27.618383 INFO::alignReads.R/alignReads: done
2025-03-24 23:20:27.732411 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-24 23:20:27.75194 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:20:31.294678 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:20:31.29642 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000001/logs/progress.log
2025-03-24 23:20:33.738955 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-03-24 23:20:33.740329 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000002/logs/progress.log
2025-03-24 23:20:36.20906 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.041 minutes
2025-03-24 23:20:36.212266 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000003/logs/progress.log
2025-03-24 23:20:38.671575 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-03-24 23:20:38.674372 DEBUG::tools.R/processChunks: done
2025-03-24 23:20:38.676288 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-24 23:20:38.691841 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_exon.tab
2025-03-24 23:20:38.704416 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_exon_disjoint.tab
2025-03-24 23:20:38.712116 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_gene.tab
2025-03-24 23:20:38.717723 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_gene_coding.tab
2025-03-24 23:20:38.723186 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_gene_exonic.tab
2025-03-24 23:20:38.72873 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_intergenic.tab
2025-03-24 23:20:38.738205 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.counts_intron.tab
2025-03-24 23:20:38.740777 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-24 23:20:38.746034 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_counts.tab
2025-03-24 23:20:38.747622 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-24 23:20:39.059979 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-24 23:20:39.060959 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-24 23:20:39.165394 INFO::coverage.R/calculateCoverage: starting...
2025-03-24 23:20:39.169754 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:20:42.292569 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:20:42.294196 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000001/logs/progress.log
2025-03-24 23:20:44.479203 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2025-03-24 23:20:44.481137 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000002/logs/progress.log
2025-03-24 23:20:46.688909 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-03-24 23:20:46.69055 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/chunks/chunk_000003/logs/progress.log
2025-03-24 23:20:48.88184 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-03-24 23:20:48.884426 DEBUG::tools.R/processChunks: done
2025-03-24 23:20:52.513436 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.coverage.RData
2025-03-24 23:20:52.516967 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.coverage.bw
2025-03-24 23:20:52.547035 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_coverage.tab
2025-03-24 23:20:52.550031 INFO::coverage.R/calculateCoverage: done
2025-03-24 23:20:52.55391 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-24 23:20:52.988186 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:21:02.2047 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:21:02.544774 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:21:02.599518 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:21:02.602222 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.raw_variants.RData
2025-03-24 23:21:02.605536 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.filtered_variants.RData
2025-03-24 23:21:02.608111 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-24 23:21:02.610038 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:21:03.131975 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-24 23:21:03.343166 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/results/test_pe.summary_variants.tab
2025-03-24 23:21:03.347086 INFO::analyzeVariants/analyzeVariants: done
2025-03-24 23:21:03.360143 INFO::Pipeline run successful.
2025-03-24 23:21:04.063411 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-24 23:21:04.084548 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:21:04.097599 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.adapter_contaminated_1.RData
2025-03-24 23:21:04.106116 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:21:04.116933 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.adapter_contaminated_2.RData
2025-03-24 23:21:04.172804 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
2025-03-24 23:21:04.185018 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_preprocess.tab
2025-03-24 23:21:04.19405 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.
2025-03-24 23:21:04.866448 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-24 23:21:04.902689 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_alignment.tab
2025-03-24 23:21:04.921432 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-24 23:21:04.926157 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-24 23:21:05.552629 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_target_lengths.tab
2025-03-24 23:21:05.653769 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-24 23:21:05.822978 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-24 23:21:05.92623 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_exon.tab
2025-03-24 23:21:05.985109 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_exon_disjoint.tab
2025-03-24 23:21:06.019871 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_gene.tab
2025-03-24 23:21:06.044921 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_gene_coding.tab
2025-03-24 23:21:06.0706 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_gene_exonic.tab
2025-03-24 23:21:06.096016 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_intergenic.tab
2025-03-24 23:21:06.160409 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.counts_intron.tab
2025-03-24 23:21:06.171327 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-24 23:21:06.197412 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_counts.tab
2025-03-24 23:21:06.201742 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-24 23:21:06.721308 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-24 23:21:12.671974 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.coverage.RData
2025-03-24 23:21:12.678275 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.coverage.bw
2025-03-24 23:21:12.704954 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_coverage.tab
2025-03-24 23:21:12.817627 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-24 23:21:13.069013 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-24 23:21:18.587637 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-24 23:21:18.875739 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-24 23:21:18.935996 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-24 23:21:18.94048 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.raw_variants.RData
2025-03-24 23:21:18.94524 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.filtered_variants.RData
2025-03-24 23:21:18.949099 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-24 23:21:18.952144 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-24 23:21:19.748737 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-24 23:21:20.063338 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.mergeLanes.36d4cb7219650c/merged/results/merged.summary_variants.tab
2025-03-24 23:21:20.069995 INFO::analyzeVariants/analyzeVariants: done
2025-03-24 23:21:20.077121 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/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:21:20.963034 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:21:20.97671 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:21:20.984498 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-24 23:21:20.989192 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:21:28.046193 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:21:28.049978 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/chunks/chunk_000001/logs/progress.log
2025-03-24 23:21:31.333935 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.055 minutes
2025-03-24 23:21:31.414012 DEBUG::tools.R/processChunks: done
2025-03-24 23:21:31.417464 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:21:31.419792 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/results/test_pe.adapter_contaminated_1.RData
2025-03-24 23:21:31.422463 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:21:31.42438 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/results/test_pe.adapter_contaminated_2.RData
2025-03-24 23:21:31.433701 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
2025-03-24 23:21:31.436244 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/results/test_pe.summary_preprocess.tab
2025-03-24 23:21:31.439268 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:21:31.445546 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:21:31.451143 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/reports/shortReadReport_1 ...
2025-03-24 23:21:33.323157 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.36d4cb7c22bcc9/reports/shortReadReport_2 ...
2025-03-24 23:21:34.993711 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:21:35.525342 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:21:35.537567 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:21:35.545513 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-24 23:21:35.550272 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:21:40.241789 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:21:40.244012 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/chunks/chunk_000001/logs/progress.log
2025-03-24 23:21:42.884598 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-24 23:21:42.885918 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/chunks/chunk_000002/logs/progress.log
2025-03-24 23:21:45.502498 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-24 23:21:45.503972 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/chunks/chunk_000003/logs/progress.log
2025-03-24 23:21:48.095251 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-24 23:21:48.140256 DEBUG::tools.R/processChunks: done
2025-03-24 23:21:48.144404 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:21:48.147062 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/results/test_pe.adapter_contaminated_1.RData
2025-03-24 23:21:48.150279 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:21:48.152739 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/results/test_pe.adapter_contaminated_2.RData
2025-03-24 23:21:48.164706 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
2025-03-24 23:21:48.167336 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/results/test_pe.summary_preprocess.tab
2025-03-24 23:21:48.170985 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:21:48.176939 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:21:48.181672 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/reports/shortReadReport_1 ...
2025-03-24 23:21:49.461035 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads.minichunks.36d4cb6766e483/reports/shortReadReport_2 ...
2025-03-24 23:21:50.541379 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:21:50.814042 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:21:50.8354 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-24 23:21:50.838127 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:21:54.009763 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:21:54.011362 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads_single_end.36d4cb1e673193/chunks/chunk_000001/logs/progress.log
2025-03-24 23:21:56.42762 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-24 23:21:56.437942 DEBUG::tools.R/processChunks: done
2025-03-24 23:21:56.44042 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:21:56.442014 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads_single_end.36d4cb1e673193/results/test_se.adapter_contaminated_1.RData
2025-03-24 23:21:56.449236 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
2025-03-24 23:21:56.451127 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads_single_end.36d4cb1e673193/results/test_se.summary_preprocess.tab
2025-03-24 23:21:56.453204 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads_single_end.36d4cb1e673193/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:21:56.456916 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpccffFO/test.preprocessReads_single_end.36d4cb1e673193/reports/shortReadReport_1 ...
2025-03-24 23:21:57.818084 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/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-24 23:21:58.509516 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-24 23:21:58.515831 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-03-24 23:21:58.520211 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-03-24 23:21:58.522681 DEBUG::tools.R/processChunks: starting...
2025-03-24 23:22:01.953934 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-24 23:22:01.955468 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-03-24 23:22:04.785996 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-24 23:22:04.823959 DEBUG::tools.R/processChunks: done
2025-03-24 23:22:04.826425 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-24 23:22:04.828017 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-03-24 23:22:04.829793 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-24 23:22:04.831221 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-03-24 23:22:04.838841 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
2025-03-24 23:22:04.840932 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-03-24 23:22:04.842963 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-03-24 23:22:04.847241 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-03-24 23:22:04.852068 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-03-24 23:22:58.532483 DEBUG::tools.R/traceMem: wired.mem=-72.406188 GiB
2025-03-24 23:23:58.601478 DEBUG::tools.R/traceMem: wired.mem=-72.977424 GiB
2025-03-24 23:24:58.670336 DEBUG::tools.R/traceMem: wired.mem=-75.291845 GiB
2025-03-24 23:25:58.736579 DEBUG::tools.R/traceMem: wired.mem=-70.343418 GiB
2025-03-24 23:26:58.802877 DEBUG::tools.R/traceMem: wired.mem=-70.651560 GiB
2025-03-24 23:27:58.869208 DEBUG::tools.R/traceMem: wired.mem=-75.866415 GiB
2025-03-24 23:28:58.93591 DEBUG::tools.R/traceMem: wired.mem=-71.021511 GiB
2025-03-24 23:29:59.001343 DEBUG::tools.R/traceMem: wired.mem=-61.107323 GiB
2025-03-24 23:30:59.065822 DEBUG::tools.R/traceMem: wired.mem=-72.213496 GiB
2025-03-24 23:31:59.130376 DEBUG::tools.R/traceMem: wired.mem=-72.921793 GiB
2025-03-24 23:32:59.195677 DEBUG::tools.R/traceMem: wired.mem=-72.310645 GiB
2025-03-24 23:33:59.261675 DEBUG::tools.R/traceMem: wired.mem=-68.539589 GiB
2025-03-24 23:34:59.328432 DEBUG::tools.R/traceMem: wired.mem=-75.347083 GiB
2025-03-24 23:35:59.394734 DEBUG::tools.R/traceMem: wired.mem=-71.525294 GiB
2025-03-24 23:36:59.461263 DEBUG::tools.R/traceMem: wired.mem=-70.570877 GiB
2025-03-24 23:37:59.5255 DEBUG::tools.R/traceMem: wired.mem=-71.177929 GiB
2025-03-24 23:38:59.59001 DEBUG::tools.R/traceMem: wired.mem=-77.558825 GiB
2025-03-24 23:39:59.60037 DEBUG::tools.R/traceMem: wired.mem=-81.021780 GiB
2025-03-24 23:40:59.666831 DEBUG::tools.R/traceMem: wired.mem=-76.382765 GiB
2025-03-24 23:41:59.731992 DEBUG::tools.R/traceMem: wired.mem=-76.992545 GiB
2025-03-24 23:42:59.797113 DEBUG::tools.R/traceMem: wired.mem=-83.011412 GiB
2025-03-24 23:43:59.863578 DEBUG::tools.R/traceMem: wired.mem=-81.064116 GiB
2025-03-24 23:44:59.928745 DEBUG::tools.R/traceMem: wired.mem=-79.034630 GiB
2025-03-24 23:45:59.993252 DEBUG::tools.R/traceMem: wired.mem=-80.092676 GiB
2025-03-24 23:47:00.057644 DEBUG::tools.R/traceMem: wired.mem=-78.200242 GiB
2025-03-24 23:48:00.12338 DEBUG::tools.R/traceMem: wired.mem=-66.714051 GiB
2025-03-24 23:49:00.187813 DEBUG::tools.R/traceMem: wired.mem=-77.201302 GiB
2025-03-24 23:50:00.25262 DEBUG::tools.R/traceMem: wired.mem=-74.644677 GiB
2025-03-24 23:51:00.318905 DEBUG::tools.R/traceMem: wired.mem=-79.398797 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

name	user	system	elapsed
HTSeqGenie	0	0	0
buildGenomicFeaturesFromTxDb	0.000	0.000	0.001
runPipeline	0	0	0