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"	4426
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: 2025-03-31 23:01:38 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 23:41:39 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 2400.8 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:07:04.103571 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:07:04.111554 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
2025-03-31 23:07:04.114994 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
2025-03-31 23:07:04.117152 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:07:06.864841 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:07:06.866211 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/chunks/chunk_000001/logs/progress.log
2025-03-31 23:07:09.650933 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-31 23:07:09.652722 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/chunks/chunk_000002/logs/progress.log
2025-03-31 23:07:12.413583 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-31 23:07:12.41516 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/chunks/chunk_000003/logs/progress.log
2025-03-31 23:07:15.146881 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-31 23:07:15.173593 DEBUG::tools.R/processChunks: done
2025-03-31 23:07:15.177182 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:07:15.179288 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.adapter_contaminated_1.RData
2025-03-31 23:07:15.181862 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:07:15.183351 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.adapter_contaminated_2.RData
2025-03-31 23:07:15.19153 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
2025-03-31 23:07:15.193508 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.summary_preprocess.tab
2025-03-31 23:07:15.196532 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:07:15.200521 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:07:15.204855 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/reports/shortReadReport_1 ...
2025-03-31 23:07:16.529604 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/reports/shortReadReport_2 ...
2025-03-31 23:07:17.599034 INFO::preprocessReads.R/preprocessReads: done
2025-03-31 23:07:17.681975 INFO::alignReads.R/alignReads: starting alignment...
2025-03-31 23:07:17.687954 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:07:20.635501 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:07:20.637088 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/chunks/chunk_000001/logs/progress.log
2025-03-31 23:07:23.515789 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-31 23:07:23.517596 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/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.
2025-03-31 23:07:26.21957 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-31 23:07:26.221533 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/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.
2025-03-31 23:07:28.874699 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-31 23:07:28.877856 DEBUG::tools.R/processChunks: done
2025-03-31 23:07:28.879845 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.
2025-03-31 23:07:29.128716 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-31 23:07:29.138132 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.summary_alignment.tab
2025-03-31 23:07:29.146262 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.summary_analyzed_bamstats.tab
2025-03-31 23:07:29.148321 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-31 23:07:29.423461 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.7c7604036d7fa/results/test_pe.summary_target_lengths.tab
2025-03-31 23:07:29.473042 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-31 23:07:29.474374 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:07:29.750115 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:07:29.75351 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
2025-03-31 23:07:29.829708 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-31 23:07:29.835296 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
2025-03-31 23:07:29.838704 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
2025-03-31 23:07:29.840837 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:07:33.146703 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:07:33.148366 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/chunks/chunk_000001/logs/progress.log
2025-03-31 23:07:35.889618 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-31 23:07:35.891771 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/chunks/chunk_000002/logs/progress.log
2025-03-31 23:07:38.662446 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-31 23:07:38.663949 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/chunks/chunk_000003/logs/progress.log
2025-03-31 23:07:41.475823 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-03-31 23:07:41.47725 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/chunks/chunk_000004/logs/progress.log
2025-03-31 23:07:44.180542 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-03-31 23:07:44.214895 DEBUG::tools.R/processChunks: done
2025-03-31 23:07:44.218349 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:07:44.220665 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/results/test_pe.adapter_contaminated_1.RData
2025-03-31 23:07:44.223615 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:07:44.225332 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/results/test_pe.adapter_contaminated_2.RData
2025-03-31 23:07:44.235554 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
2025-03-31 23:07:44.237664 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/results/test_pe.summary_preprocess.tab
2025-03-31 23:07:44.241328 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:07:44.246736 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:07:44.251372 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/reports/shortReadReport_1 ...
2025-03-31 23:07:45.619751 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReads.sparsechunks.7c7601ea78af5/reports/shortReadReport_2 ...
2025-03-31 23:07:46.812871 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:07:46.979221 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-31 23:07:46.983663 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/RtmpXWab7c/test.alignReadsOneSingleEnd.7c760628d8e40/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-31 23:07:47.204662 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-31 23:07:47.322658 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReadsOneSingleEnd.7c760628d8e40/results/test.alignReads.summary_alignment.tab
2025-03-31 23:07:47.371545 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.alignReadsOneSingleEnd.7c760628d8e40/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-31 23:07:47.373275 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0 0.002 0.003
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:07:47.65009 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.genotype.7c760b0688c9/results/test_pe.coverage.RData
2025-03-31 23:07:47.651859 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.genotype.7c760b0688c9/results/test_pe.coverage.bw
2025-03-31 23:07:47.776539 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.genotype.7c760b0688c9/results/test_pe.summary_coverage.tab
2025-03-31 23:07:47.778457 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:07:58.130748 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:07:58.216342 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:07:58.232997 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:07:58.234509 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.genotype.7c760b0688c9/results/test_pe.raw_variants.RData
2025-03-31 23:07:58.236888 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.genotype.7c760b0688c9/results/test_pe.filtered_variants.RData
2025-03-31 23:07:58.238207 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-31 23:07:58.239345 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:07:58.652674 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-31 23:07:58.653917 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-31 23:08:57.677073 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:08:58.11293 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-31 23:08:58.11404 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:08:58.550467 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:09:08.913892 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:09:08.989212 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:09:09.005458 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:09:09.006893 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.7c76047913bbf/results/test_pe.raw_variants.RData
2025-03-31 23:09:09.009291 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.7c76047913bbf/results/test_pe.filtered_variants.RData
2025-03-31 23:09:09.010625 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:09:09.149773 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:09:18.925405 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:09:18.977861 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:09:18.993054 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:09:18.994299 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.filters.7c7606db9b2a3/results/test_pe.raw_variants.RData
2025-03-31 23:09:18.996662 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.filters.7c7606db9b2a3/results/test_pe.filtered_variants.RData
2025-03-31 23:09:18.997956 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-31 23:09:18.999446 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:09:28.967768 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:09:29.006988 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:09:29.023851 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:09:29.0252 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.filters.7c7606db9b2a3/results/test_pe.raw_variants.RData
2025-03-31 23:09:29.027778 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.filters.7c7606db9b2a3/results/test_pe.filtered_variants.RData
2025-03-31 23:09:29.029779 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:09:29.26894 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:09:29.270396 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-31 23:09:31.875085 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:09:31.948346 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:09:31.964707 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:09:31.96606 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.which.7c76070818ec9/results/test_pe.raw_variants.RData
2025-03-31 23:09:31.967699 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.wrap.callVariants.which.7c76070818ec9/results/test_pe.filtered_variants.RData
2025-03-31 23:09:31.968966 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:09:32.106623 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:09:32.107846 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:09:33.722466 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:09:33.905429 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  ... 2025-03-31 23:10:24.897262 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/malzpwyk/merged/results/bla.coverage.RData
2025-03-31 23:10:24.900143 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/malzpwyk/merged/results/bla.coverage.bw
2025-03-31 23:10:24.990425 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/malzpwyk/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-31 23:10:26.252536 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/klywpvde/merged/results/bla.coverage.RData
2025-03-31 23:10:26.254496 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/klywpvde/merged/results/bla.coverage.bw
2025-03-31 23:10:26.26548 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/klywpvde/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:27.462165 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-31 23:10:27.463304 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.7c7607641f0bb/bams/rRNA_contam/input1.fastq
2025-03-31 23:10:27.466465 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/RtmpXWab7c/test.detectRRNA.7c7607641f0bb/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.7c7607641f0bb/bams/rRNA_contam/input1.fastq 2>&1
2025-03-31 23:10:27.604713 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-31 23:10:27.605724 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:27.751983 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-31 23:10:27.753009 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.paired_end.7c7605485a2ea/bams/rRNA_contam/input1.fastq
2025-03-31 23:10:27.754524 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.paired_end.7c7605485a2ea/bams/rRNA_contam/input2.fastq
2025-03-31 23:10:27.756726 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/RtmpXWab7c/test.detectRRNA.paired_end.7c7605485a2ea/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.paired_end.7c7605485a2ea/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.detectRRNA.paired_end.7c7605485a2ea/bams/rRNA_contam/input2.fastq 2>&1
2025-03-31 23:10:28.026641 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-31 23:10:28.028175 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-31 23:10:28.05655 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/RtmpXWab7c/test_get_rRNA_idskytzbjgs/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test_get_rRNA_idskytzbjgs/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test_get_rRNA_idskytzbjgs/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-31 23:10:28.301432 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/RtmpXWab7c/test_get_rRNAIds_randomhygzlife/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test_get_rRNAIds_randomhygzlife/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-31 23:10:28.506133 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-31 23:10:28.507475 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-31 23:10:28.508299 INFO::filterQuality.R/filterByLength: done
2025-03-31 23:10:28.552049 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-31 23:10:28.552942 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-31 23:10:28.553722 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-31 23:10:28.601023 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-31 23:10:28.609473 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-31 23:10:28.610528 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-31 23:10:28.614802 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-31 23:10:28.615724 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-31 23:10:28.61991 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-31 23:10:28.620802 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-31 23:10:28.624915 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: 0.001 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:28.895162 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
2025-03-31 23:10:28.897369 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:29.059889 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
2025-03-31 23:10:29.152708 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-31 23:10:29.155269 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
2025-03-31 23:10:29.157322 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:29.37209 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:29.511814 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:29.672629 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
2025-03-31 23:10:29.75569 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-31 23:10:29.758243 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
2025-03-31 23:10:29.760385 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:29.960815 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
2025-03-31 23:10:30.010363 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-31 23:10:30.012778 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
2025-03-31 23:10:30.014866 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/RtmpXWab7c/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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:10:30.782821 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:10:30.7887 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
2025-03-31 23:10:30.792358 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
2025-03-31 23:10:30.794676 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:10:33.823646 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:10:33.825158 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000001/logs/progress.log
2025-03-31 23:10:36.421963 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-31 23:10:36.423299 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000002/logs/progress.log
2025-03-31 23:10:39.054946 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-31 23:10:39.056509 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000003/logs/progress.log
2025-03-31 23:10:41.692618 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-31 23:10:41.736998 DEBUG::tools.R/processChunks: done
2025-03-31 23:10:41.740011 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:10:41.741832 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.adapter_contaminated_1.RData
2025-03-31 23:10:41.744122 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:10:41.745782 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.adapter_contaminated_2.RData
2025-03-31 23:10:41.7546 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
2025-03-31 23:10:41.75639 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_preprocess.tab
2025-03-31 23:10:41.758834 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:10:41.764197 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:10:41.767585 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/reports/shortReadReport_1 ...
2025-03-31 23:10:43.145342 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/reports/shortReadReport_2 ...
2025-03-31 23:10:44.240374 INFO::preprocessReads.R/preprocessReads: done
2025-03-31 23:10:44.342421 INFO::alignReads.R/alignReads: starting alignment...
2025-03-31 23:10:44.347114 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:10:48.642732 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:10:48.644641 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000001/logs/progress.log
2025-03-31 23:10:51.227576 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-31 23:10:51.229318 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/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.
2025-03-31 23:10:53.790775 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-31 23:10:53.792393 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/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.
2025-03-31 23:10:56.378835 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-31 23:10:56.381112 DEBUG::tools.R/processChunks: done
2025-03-31 23:10:56.38247 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.
2025-03-31 23:10:56.572922 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-31 23:10:56.580628 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_alignment.tab
2025-03-31 23:10:56.587298 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_analyzed_bamstats.tab
2025-03-31 23:10:56.589102 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-31 23:10:56.812392 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_target_lengths.tab
2025-03-31 23:10:56.859236 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-31 23:10:56.860462 INFO::alignReads.R/alignReads: done
2025-03-31 23:10:56.957196 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-31 23:10:56.976494 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:11:00.075891 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:11:00.077476 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000001/logs/progress.log
2025-03-31 23:11:02.495872 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-31 23:11:02.497381 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000002/logs/progress.log
2025-03-31 23:11:05.049914 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-31 23:11:05.052211 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000003/logs/progress.log
2025-03-31 23:11:08.429728 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.056 minutes
2025-03-31 23:11:08.443929 DEBUG::tools.R/processChunks: done
2025-03-31 23:11:08.457375 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-31 23:11:08.520313 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_exon.tab
2025-03-31 23:11:08.560452 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_exon_disjoint.tab
2025-03-31 23:11:08.588672 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_gene.tab
2025-03-31 23:11:08.609727 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_gene_coding.tab
2025-03-31 23:11:08.629678 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_gene_exonic.tab
2025-03-31 23:11:08.649261 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_intergenic.tab
2025-03-31 23:11:08.688371 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.counts_intron.tab
2025-03-31 23:11:08.697929 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-31 23:11:08.722584 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_counts.tab
2025-03-31 23:11:08.732748 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-31 23:11:09.64202 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-31 23:11:09.643404 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-31 23:11:09.835348 INFO::coverage.R/calculateCoverage: starting...
2025-03-31 23:11:09.848478 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:11:16.305092 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:11:16.3086 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000001/logs/progress.log
2025-03-31 23:11:18.802507 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2025-03-31 23:11:18.813207 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000002/logs/progress.log
2025-03-31 23:11:21.416715 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-31 23:11:21.424322 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/chunks/chunk_000003/logs/progress.log
2025-03-31 23:11:23.971229 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.042 minutes
2025-03-31 23:11:23.979323 DEBUG::tools.R/processChunks: done
2025-03-31 23:11:27.188888 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.coverage.RData
2025-03-31 23:11:27.191581 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.coverage.bw
2025-03-31 23:11:27.214426 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_coverage.tab
2025-03-31 23:11:27.217041 INFO::coverage.R/calculateCoverage: done
2025-03-31 23:11:27.220096 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-31 23:11:27.390364 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:11:31.18743 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:11:31.320718 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:11:31.352134 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:11:31.354867 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.raw_variants.RData
2025-03-31 23:11:31.358126 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.filtered_variants.RData
2025-03-31 23:11:31.360599 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-31 23:11:31.362514 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:11:31.835227 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-31 23:11:32.052035 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/results/test_pe.summary_variants.tab
2025-03-31 23:11:32.05605 INFO::analyzeVariants/analyzeVariants: done
2025-03-31 23:11:32.06206 INFO::Pipeline run successful.
2025-03-31 23:11:32.388384 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-31 23:11:32.396576 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:11:32.400327 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.adapter_contaminated_1.RData
2025-03-31 23:11:32.405136 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:11:32.408334 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.adapter_contaminated_2.RData
2025-03-31 23:11:32.427251 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
2025-03-31 23:11:32.431438 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_preprocess.tab
2025-03-31 23:11:32.435042 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.
2025-03-31 23:11:32.902903 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-31 23:11:32.917124 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_alignment.tab
2025-03-31 23:11:32.931892 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-31 23:11:32.935723 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-31 23:11:33.337853 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_target_lengths.tab
2025-03-31 23:11:33.425454 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-31 23:11:33.537757 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-31 23:11:33.574866 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_exon.tab
2025-03-31 23:11:33.59841 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_exon_disjoint.tab
2025-03-31 23:11:33.611578 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_gene.tab
2025-03-31 23:11:33.622709 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_gene_coding.tab
2025-03-31 23:11:33.634024 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_gene_exonic.tab
2025-03-31 23:11:33.646569 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_intergenic.tab
2025-03-31 23:11:33.670432 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.counts_intron.tab
2025-03-31 23:11:33.676954 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-31 23:11:33.689881 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_counts.tab
2025-03-31 23:11:33.693789 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-31 23:11:34.099931 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-31 23:11:37.657103 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.coverage.RData
2025-03-31 23:11:37.661347 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.coverage.bw
2025-03-31 23:11:37.685336 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_coverage.tab
2025-03-31 23:11:37.776415 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-31 23:11:37.964277 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-31 23:11:43.269257 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-31 23:11:43.441492 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-31 23:11:43.476825 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-31 23:11:43.479043 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.raw_variants.RData
2025-03-31 23:11:43.481729 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.filtered_variants.RData
2025-03-31 23:11:43.483985 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-31 23:11:43.485662 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-31 23:11:43.968626 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-31 23:11:44.242922 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.mergeLanes.7c7604019f787/merged/results/merged.summary_variants.tab
2025-03-31 23:11:44.246896 INFO::analyzeVariants/analyzeVariants: done
2025-03-31 23:11:44.251224 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0.001 0 0
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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:11:44.840736 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:11:44.876991 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
2025-03-31 23:11:44.904033 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
2025-03-31 23:11:44.908561 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:11:50.044025 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:11:50.046076 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/chunks/chunk_000001/logs/progress.log
2025-03-31 23:11:53.029979 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.05 minutes
2025-03-31 23:11:53.09778 DEBUG::tools.R/processChunks: done
2025-03-31 23:11:53.103319 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:11:53.106219 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/results/test_pe.adapter_contaminated_1.RData
2025-03-31 23:11:53.109572 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:11:53.112074 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/results/test_pe.adapter_contaminated_2.RData
2025-03-31 23:11:53.123586 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
2025-03-31 23:11:53.127519 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/results/test_pe.summary_preprocess.tab
2025-03-31 23:11:53.13114 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:11:53.138321 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:11:53.145122 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/reports/shortReadReport_1 ...
2025-03-31 23:11:54.724582 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.7c76041008840/reports/shortReadReport_2 ...
2025-03-31 23:11:56.149998 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:11:56.504127 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:11:56.510983 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
2025-03-31 23:11:56.515342 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
2025-03-31 23:11:56.518026 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:11:59.728914 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:11:59.730416 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/chunks/chunk_000001/logs/progress.log
2025-03-31 23:12:02.366404 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-31 23:12:02.368098 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/chunks/chunk_000002/logs/progress.log
2025-03-31 23:12:05.01985 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-31 23:12:05.021633 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/chunks/chunk_000003/logs/progress.log
2025-03-31 23:12:07.64497 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-31 23:12:07.682287 DEBUG::tools.R/processChunks: done
2025-03-31 23:12:07.684862 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:12:07.686495 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/results/test_pe.adapter_contaminated_1.RData
2025-03-31 23:12:07.688593 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:12:07.690084 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/results/test_pe.adapter_contaminated_2.RData
2025-03-31 23:12:07.698048 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
2025-03-31 23:12:07.699756 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/results/test_pe.summary_preprocess.tab
2025-03-31 23:12:07.702117 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:12:07.706579 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:12:07.709565 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/reports/shortReadReport_1 ...
2025-03-31 23:12:08.986163 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads.minichunks.7c7607215e7a5/reports/shortReadReport_2 ...
2025-03-31 23:12:10.035646 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/RtmpXWab7c/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-31 23:12:10.364488 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:12:10.384731 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
2025-03-31 23:12:10.38747 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:12:13.483791 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:12:13.485257 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads_single_end.7c760d688288/chunks/chunk_000001/logs/progress.log
2025-03-31 23:12:15.867999 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-31 23:12:15.877709 DEBUG::tools.R/processChunks: done
2025-03-31 23:12:15.880023 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:12:15.88158 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads_single_end.7c760d688288/results/test_se.adapter_contaminated_1.RData
2025-03-31 23:12:15.888348 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
2025-03-31 23:12:15.890158 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads_single_end.7c760d688288/results/test_se.summary_preprocess.tab
2025-03-31 23:12:15.892145 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads_single_end.7c760d688288/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:12:15.89654 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpXWab7c/test.preprocessReads_single_end.7c760d688288/reports/shortReadReport_1 ...
2025-03-31 23:12:17.192543 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 
2025-03-31 23:12:17.891869 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-31 23:12:17.915539 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
2025-03-31 23:12:17.937988 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
2025-03-31 23:12:17.940789 DEBUG::tools.R/processChunks: starting...
2025-03-31 23:12:21.114305 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-31 23:12:21.115695 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-03-31 23:12:23.906427 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-31 23:12:23.940607 DEBUG::tools.R/processChunks: done
2025-03-31 23:12:23.942686 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-31 23:12:23.944084 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-03-31 23:12:23.945676 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-31 23:12:23.946979 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-03-31 23:12:23.952693 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
2025-03-31 23:12:23.954396 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-03-31 23:12:23.956216 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-03-31 23:12:23.960875 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-03-31 23:12:23.964368 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-03-31 23:13:17.895461 DEBUG::tools.R/traceMem: wired.mem=-72.883651 GiB
2025-03-31 23:14:17.961958 DEBUG::tools.R/traceMem: wired.mem=-71.517929 GiB
2025-03-31 23:15:18.028071 DEBUG::tools.R/traceMem: wired.mem=-74.308207 GiB
2025-03-31 23:16:18.093915 DEBUG::tools.R/traceMem: wired.mem=-68.770267 GiB
2025-03-31 23:17:18.160018 DEBUG::tools.R/traceMem: wired.mem=-69.992145 GiB
2025-03-31 23:18:18.22582 DEBUG::tools.R/traceMem: wired.mem=-69.968167 GiB
2025-03-31 23:19:18.290342 DEBUG::tools.R/traceMem: wired.mem=-70.295962 GiB
2025-03-31 23:20:18.356581 DEBUG::tools.R/traceMem: wired.mem=-70.503481 GiB
2025-03-31 23:21:18.422169 DEBUG::tools.R/traceMem: wired.mem=-61.036421 GiB
2025-03-31 23:22:18.488464 DEBUG::tools.R/traceMem: wired.mem=-71.887421 GiB
2025-03-31 23:23:18.555049 DEBUG::tools.R/traceMem: wired.mem=-70.587359 GiB
2025-03-31 23:24:18.620347 DEBUG::tools.R/traceMem: wired.mem=-66.498281 GiB
2025-03-31 23:25:18.685187 DEBUG::tools.R/traceMem: wired.mem=-75.178934 GiB
2025-03-31 23:26:18.749907 DEBUG::tools.R/traceMem: wired.mem=-74.777362 GiB
2025-03-31 23:27:18.814914 DEBUG::tools.R/traceMem: wired.mem=-65.306862 GiB
2025-03-31 23:28:18.880045 DEBUG::tools.R/traceMem: wired.mem=-71.248413 GiB
2025-03-31 23:29:18.945675 DEBUG::tools.R/traceMem: wired.mem=-75.850138 GiB
2025-03-31 23:30:19.01122 DEBUG::tools.R/traceMem: wired.mem=-82.460959 GiB
2025-03-31 23:31:19.078449 DEBUG::tools.R/traceMem: wired.mem=-74.518684 GiB
2025-03-31 23:32:19.145552 DEBUG::tools.R/traceMem: wired.mem=-80.048693 GiB
2025-03-31 23:33:19.212318 DEBUG::tools.R/traceMem: wired.mem=-74.453934 GiB
2025-03-31 23:34:19.279308 DEBUG::tools.R/traceMem: wired.mem=-74.585055 GiB
2025-03-31 23:35:19.344428 DEBUG::tools.R/traceMem: wired.mem=-78.125294 GiB
2025-03-31 23:36:19.410113 DEBUG::tools.R/traceMem: wired.mem=-78.683103 GiB
2025-03-31 23:37:19.47662 DEBUG::tools.R/traceMem: wired.mem=-74.166477 GiB
2025-03-31 23:38:19.528116 DEBUG::tools.R/traceMem: wired.mem=-65.306378 GiB
2025-03-31 23:39:19.5928 DEBUG::tools.R/traceMem: wired.mem=-73.515352 GiB
2025-03-31 23:40:19.657575 DEBUG::tools.R/traceMem: wired.mem=-74.718069 GiB
2025-03-31 23:41:19.665961 DEBUG::tools.R/traceMem: wired.mem=-80.354107 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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