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"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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: 2025-03-17 23:50:59 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-18 00:30:59 -0400 (Tue, 18 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:56:32.227961 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-17 23:56:32.236175 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
2025-03-17 23:56:32.239573 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
2025-03-17 23:56:32.241704 DEBUG::tools.R/processChunks: starting...
2025-03-17 23:56:35.188637 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-17 23:56:35.190009 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/chunks/chunk_000001/logs/progress.log
2025-03-17 23:56:37.987597 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-17 23:56:37.989091 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/chunks/chunk_000002/logs/progress.log
2025-03-17 23:56:40.755061 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-17 23:56:40.757173 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/chunks/chunk_000003/logs/progress.log
2025-03-17 23:56:43.559163 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-03-17 23:56:43.62025 DEBUG::tools.R/processChunks: done
2025-03-17 23:56:43.624466 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-17 23:56:43.626805 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.adapter_contaminated_1.RData
2025-03-17 23:56:43.629644 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-17 23:56:43.631295 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.adapter_contaminated_2.RData
2025-03-17 23:56:43.640389 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
2025-03-17 23:56:43.642573 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.summary_preprocess.tab
2025-03-17 23:56:43.645821 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/bams/processed.aligner_input_1.fastq ...
2025-03-17 23:56:43.650768 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/bams/processed.aligner_input_2.fastq ...
2025-03-17 23:56:43.654004 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/reports/shortReadReport_1 ...
2025-03-17 23:56:45.056953 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/reports/shortReadReport_2 ...
2025-03-17 23:56:46.15364 INFO::preprocessReads.R/preprocessReads: done
2025-03-17 23:56:46.23606 INFO::alignReads.R/alignReads: starting alignment...
2025-03-17 23:56:46.241276 DEBUG::tools.R/processChunks: starting...
2025-03-17 23:56:49.212505 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-17 23:56:49.214093 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/chunks/chunk_000001/logs/progress.log
2025-03-17 23:56:52.145372 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2025-03-17 23:56:52.147236 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/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.
2025-03-17 23:56:54.997334 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-03-17 23:56:54.999271 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/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.
2025-03-17 23:56:57.689052 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-17 23:56:57.691203 DEBUG::tools.R/processChunks: done
2025-03-17 23:56:57.692465 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.
2025-03-17 23:56:57.888466 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-17 23:56:57.89628 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.summary_alignment.tab
2025-03-17 23:56:57.903028 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.summary_analyzed_bamstats.tab
2025-03-17 23:56:57.904577 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-17 23:56:58.138668 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.2656743439627e/results/test_pe.summary_target_lengths.tab
2025-03-17 23:56:58.184124 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-17 23:56:58.185104 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:56:58.462145 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-17 23:56:58.465412 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
2025-03-17 23:56:58.540108 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-17 23:56:58.545505 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
2025-03-17 23:56:58.548767 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
2025-03-17 23:56:58.550767 DEBUG::tools.R/processChunks: starting...
2025-03-17 23:57:01.677675 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-17 23:57:01.679046 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/chunks/chunk_000001/logs/progress.log
2025-03-17 23:57:04.393424 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-03-17 23:57:04.39482 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/chunks/chunk_000002/logs/progress.log
2025-03-17 23:57:07.159147 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-17 23:57:07.160535 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/chunks/chunk_000003/logs/progress.log
2025-03-17 23:57:09.926412 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-17 23:57:09.928031 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/chunks/chunk_000004/logs/progress.log
2025-03-17 23:57:12.637508 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-03-17 23:57:12.668972 DEBUG::tools.R/processChunks: done
2025-03-17 23:57:12.67249 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-17 23:57:12.67497 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/results/test_pe.adapter_contaminated_1.RData
2025-03-17 23:57:12.677995 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-17 23:57:12.679712 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/results/test_pe.adapter_contaminated_2.RData
2025-03-17 23:57:12.690456 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
2025-03-17 23:57:12.692777 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/results/test_pe.summary_preprocess.tab
2025-03-17 23:57:12.696591 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/bams/processed.aligner_input_1.fastq ...
2025-03-17 23:57:12.70115 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/bams/processed.aligner_input_2.fastq ...
2025-03-17 23:57:12.705337 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/reports/shortReadReport_1 ...
2025-03-17 23:57:14.067561 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReads.sparsechunks.265674133eefc8/reports/shortReadReport_2 ...
2025-03-17 23:57:15.146542 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:57:15.295839 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-17 23:57:15.300053 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/RtmptLsreX/test.alignReadsOneSingleEnd.2656746a1fe819/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-17 23:57:15.499207 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-17 23:57:15.59647 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReadsOneSingleEnd.2656746a1fe819/results/test.alignReads.summary_alignment.tab
2025-03-17 23:57:15.646 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.alignReadsOneSingleEnd.2656746a1fe819/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-17 23:57:15.64758 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.001 0.001 0.001
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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:57:15.925552 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.genotype.26567424d21c98/results/test_pe.coverage.RData
2025-03-17 23:57:15.927225 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.genotype.26567424d21c98/results/test_pe.coverage.bw
2025-03-17 23:57:16.042561 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.genotype.26567424d21c98/results/test_pe.summary_coverage.tab
2025-03-17 23:57:16.044273 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-17 23:57:26.551202 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-17 23:57:26.634107 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-17 23:57:26.650943 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-17 23:57:26.652452 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.genotype.26567424d21c98/results/test_pe.raw_variants.RData
2025-03-17 23:57:26.654842 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.genotype.26567424d21c98/results/test_pe.filtered_variants.RData
2025-03-17 23:57:26.65618 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-17 23:57:26.657337 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-17 23:57:27.077775 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-17 23:57:27.079203 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-17 23:58:28.627431 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-17 23:58:29.054573 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-17 23:58:29.05553 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:58:29.539827 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-17 23:58:39.951541 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-17 23:58:40.024948 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-17 23:58:40.040802 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-17 23:58:40.042094 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.265674687785a9/results/test_pe.raw_variants.RData
2025-03-17 23:58:40.044473 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.265674687785a9/results/test_pe.filtered_variants.RData
2025-03-17 23:58:40.045766 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:58:40.183656 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-17 23:58:49.955417 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-17 23:58:50.008389 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-17 23:58:50.023603 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-17 23:58:50.024903 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.filters.2656746f64f0d0/results/test_pe.raw_variants.RData
2025-03-17 23:58:50.027221 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.filters.2656746f64f0d0/results/test_pe.filtered_variants.RData
2025-03-17 23:58:50.028399 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-17 23:58:50.029814 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-17 23:58:59.971304 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-17 23:59:00.01059 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-17 23:59:00.027497 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-17 23:59:00.028832 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.filters.2656746f64f0d0/results/test_pe.raw_variants.RData
2025-03-17 23:59:00.031356 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.filters.2656746f64f0d0/results/test_pe.filtered_variants.RData
2025-03-17 23:59:00.033341 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:59:00.264006 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-17 23:59:00.265426 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-17 23:59:03.104889 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-17 23:59:03.208089 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-17 23:59:03.230092 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-17 23:59:03.231828 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.which.2656741e5cb813/results/test_pe.raw_variants.RData
2025-03-17 23:59:03.233874 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.wrap.callVariants.which.2656741e5cb813/results/test_pe.filtered_variants.RData
2025-03-17 23:59:03.23556 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:59:03.41602 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-17 23:59:03.417357 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:59:04.987547 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-17 23:59:05.174103 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  ... 2025-03-17 23:59:56.421295 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/lnkzydbg/merged/results/bla.coverage.RData
2025-03-17 23:59:56.424263 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/lnkzydbg/merged/results/bla.coverage.bw
2025-03-17 23:59:56.506256 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/lnkzydbg/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-17 23:59:57.594486 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/byqxzolc/merged/results/bla.coverage.RData
2025-03-17 23:59:57.596164 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/byqxzolc/merged/results/bla.coverage.bw
2025-03-17 23:59:57.607087 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/byqxzolc/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:59:58.78962 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-17 23:59:58.790675 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.2656743c552e80/bams/rRNA_contam/input1.fastq
2025-03-17 23:59:58.793673 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/RtmptLsreX/test.detectRRNA.2656743c552e80/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.2656743c552e80/bams/rRNA_contam/input1.fastq 2>&1
2025-03-17 23:59:58.934561 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-17 23:59:58.935506 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-17 23:59:59.075628 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-17 23:59:59.076561 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.paired_end.2656744413e2e9/bams/rRNA_contam/input1.fastq
2025-03-17 23:59:59.078013 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.paired_end.2656744413e2e9/bams/rRNA_contam/input2.fastq
2025-03-17 23:59:59.080081 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/RtmptLsreX/test.detectRRNA.paired_end.2656744413e2e9/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.paired_end.2656744413e2e9/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.detectRRNA.paired_end.2656744413e2e9/bams/rRNA_contam/input2.fastq 2>&1
2025-03-17 23:59:59.300035 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-17 23:59:59.300989 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-17 23:59:59.31914 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/RtmptLsreX/test_get_rRNA_idsisxtdulz/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test_get_rRNA_idsisxtdulz/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test_get_rRNA_idsisxtdulz/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-17 23:59:59.55725 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/RtmptLsreX/test_get_rRNAIds_randomzrnjcyhp/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test_get_rRNAIds_randomzrnjcyhp/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-17 23:59:59.760027 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-17 23:59:59.761449 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-17 23:59:59.762329 INFO::filterQuality.R/filterByLength: done
2025-03-17 23:59:59.807348 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-17 23:59:59.808248 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-17 23:59:59.809038 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-17 23:59:59.857279 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-17 23:59:59.865633 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-17 23:59:59.866631 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-17 23:59:59.870701 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-17 23:59:59.87158 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-17 23:59:59.875602 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-17 23:59:59.876459 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-17 23:59:59.880423 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



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



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



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



Executing test function test.gatk  ... Timing stopped at: 0.001 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 0.001
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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:00.153313 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
2025-03-18 00:00:00.155441 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:00.324725 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
2025-03-18 00:00:00.424164 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-18 00:00:00.42677 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
2025-03-18 00:00:00.428797 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:00.641726 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:00.777047 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:00.937107 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
2025-03-18 00:00:01.030043 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-18 00:00:01.032537 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
2025-03-18 00:00:01.034644 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:01.238718 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
2025-03-18 00:00:01.283285 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-18 00:00:01.285584 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
2025-03-18 00:00:01.287669 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/RtmptLsreX/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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:00:01.991572 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-18 00:00:01.997143 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
2025-03-18 00:00:02.000492 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
2025-03-18 00:00:02.002656 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:00:04.745224 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:00:04.746591 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000001/logs/progress.log
2025-03-18 00:00:07.358204 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-18 00:00:07.359557 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000002/logs/progress.log
2025-03-18 00:00:10.038944 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-18 00:00:10.040342 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000003/logs/progress.log
2025-03-18 00:00:12.664002 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-18 00:00:12.707141 DEBUG::tools.R/processChunks: done
2025-03-18 00:00:12.709952 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:00:12.711731 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.adapter_contaminated_1.RData
2025-03-18 00:00:12.713909 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-18 00:00:12.715504 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.adapter_contaminated_2.RData
2025-03-18 00:00:12.723787 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
2025-03-18 00:00:12.725402 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_preprocess.tab
2025-03-18 00:00:12.727592 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/bams/processed.aligner_input_1.fastq ...
2025-03-18 00:00:12.732144 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/bams/processed.aligner_input_2.fastq ...
2025-03-18 00:00:12.734967 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/reports/shortReadReport_1 ...
2025-03-18 00:00:13.999288 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/reports/shortReadReport_2 ...
2025-03-18 00:00:15.055671 INFO::preprocessReads.R/preprocessReads: done
2025-03-18 00:00:15.146595 INFO::alignReads.R/alignReads: starting alignment...
2025-03-18 00:00:15.150809 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:00:17.892762 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:00:17.894461 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000001/logs/progress.log
2025-03-18 00:00:20.468532 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-18 00:00:20.470349 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/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.
2025-03-18 00:00:23.095091 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-18 00:00:23.096726 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/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.
2025-03-18 00:00:25.704281 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-18 00:00:25.706828 DEBUG::tools.R/processChunks: done
2025-03-18 00:00:25.708931 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.
2025-03-18 00:00:25.900588 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-18 00:00:25.908446 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_alignment.tab
2025-03-18 00:00:25.915251 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_analyzed_bamstats.tab
2025-03-18 00:00:25.917019 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-18 00:00:26.138043 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_target_lengths.tab
2025-03-18 00:00:26.183617 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-18 00:00:26.184636 INFO::alignReads.R/alignReads: done
2025-03-18 00:00:26.296389 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-18 00:00:26.315162 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:00:29.226185 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:00:29.227721 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000001/logs/progress.log
2025-03-18 00:00:31.638102 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-18 00:00:31.639604 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000002/logs/progress.log
2025-03-18 00:00:34.112133 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.041 minutes
2025-03-18 00:00:34.113666 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000003/logs/progress.log
2025-03-18 00:00:36.562318 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-03-18 00:00:36.564693 DEBUG::tools.R/processChunks: done
2025-03-18 00:00:36.566372 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-18 00:00:36.584967 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_exon.tab
2025-03-18 00:00:36.597208 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_exon_disjoint.tab
2025-03-18 00:00:36.604634 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_gene.tab
2025-03-18 00:00:36.610429 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_gene_coding.tab
2025-03-18 00:00:36.616099 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_gene_exonic.tab
2025-03-18 00:00:36.62144 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_intergenic.tab
2025-03-18 00:00:36.630376 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.counts_intron.tab
2025-03-18 00:00:36.632832 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-18 00:00:36.638108 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_counts.tab
2025-03-18 00:00:36.639645 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-18 00:00:36.934824 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-18 00:00:36.935684 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-18 00:00:37.055474 INFO::coverage.R/calculateCoverage: starting...
2025-03-18 00:00:37.05992 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:00:40.282722 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:00:40.284465 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000001/logs/progress.log
2025-03-18 00:00:42.493983 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-03-18 00:00:42.49566 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000002/logs/progress.log
2025-03-18 00:00:44.678582 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2025-03-18 00:00:44.680159 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/chunks/chunk_000003/logs/progress.log
2025-03-18 00:00:46.871287 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2025-03-18 00:00:46.874905 DEBUG::tools.R/processChunks: done
2025-03-18 00:00:48.443629 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.coverage.RData
2025-03-18 00:00:48.445109 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.coverage.bw
2025-03-18 00:00:48.456842 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_coverage.tab
2025-03-18 00:00:48.458082 INFO::coverage.R/calculateCoverage: done
2025-03-18 00:00:48.460346 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-18 00:00:48.557833 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-18 00:00:51.70149 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-18 00:00:51.775492 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-18 00:00:51.791373 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-18 00:00:51.79267 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.raw_variants.RData
2025-03-18 00:00:51.79417 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.filtered_variants.RData
2025-03-18 00:00:51.795349 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-18 00:00:51.796257 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-18 00:00:52.000729 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-18 00:00:52.091707 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/results/test_pe.summary_variants.tab
2025-03-18 00:00:52.093614 INFO::analyzeVariants/analyzeVariants: done
2025-03-18 00:00:52.098438 INFO::Pipeline run successful.
2025-03-18 00:00:52.41927 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-18 00:00:52.429129 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:00:52.433409 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.adapter_contaminated_1.RData
2025-03-18 00:00:52.43903 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-18 00:00:52.442297 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.adapter_contaminated_2.RData
2025-03-18 00:00:52.462087 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
2025-03-18 00:00:52.465773 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_preprocess.tab
2025-03-18 00:00:52.469703 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.
2025-03-18 00:00:52.803831 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-18 00:00:52.811038 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_alignment.tab
2025-03-18 00:00:52.819087 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-18 00:00:52.821105 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-18 00:00:53.058223 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_target_lengths.tab
2025-03-18 00:00:53.108754 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-18 00:00:53.149797 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-18 00:00:53.17149 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_exon.tab
2025-03-18 00:00:53.183545 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_exon_disjoint.tab
2025-03-18 00:00:53.190554 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_gene.tab
2025-03-18 00:00:53.196295 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_gene_coding.tab
2025-03-18 00:00:53.201952 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_gene_exonic.tab
2025-03-18 00:00:53.207927 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_intergenic.tab
2025-03-18 00:00:53.220041 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.counts_intron.tab
2025-03-18 00:00:53.222778 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-18 00:00:53.229339 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_counts.tab
2025-03-18 00:00:53.231139 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-18 00:00:53.474272 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-18 00:00:56.695304 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.coverage.RData
2025-03-18 00:00:56.701278 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.coverage.bw
2025-03-18 00:00:56.736455 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_coverage.tab
2025-03-18 00:00:57.045726 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-18 00:00:57.258363 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-18 00:01:06.773403 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-18 00:01:06.930613 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-18 00:01:06.963413 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-18 00:01:06.966181 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.raw_variants.RData
2025-03-18 00:01:06.969342 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.filtered_variants.RData
2025-03-18 00:01:06.971836 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-18 00:01:06.973576 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-18 00:01:07.433051 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-18 00:01:07.711554 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.mergeLanes.26567459f7af3a/merged/results/merged.summary_variants.tab
2025-03-18 00:01:07.716217 INFO::analyzeVariants/analyzeVariants: done
2025-03-18 00:01:07.721406 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0.001 0 0.004
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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:01:08.906628 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-18 00:01:08.950923 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
2025-03-18 00:01:08.984004 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
2025-03-18 00:01:08.9899 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:01:16.905896 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:01:16.907637 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/chunks/chunk_000001/logs/progress.log
2025-03-18 00:01:19.560288 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-18 00:01:19.609082 DEBUG::tools.R/processChunks: done
2025-03-18 00:01:19.611546 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:01:19.613172 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/results/test_pe.adapter_contaminated_1.RData
2025-03-18 00:01:19.614992 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-18 00:01:19.616397 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/results/test_pe.adapter_contaminated_2.RData
2025-03-18 00:01:19.622838 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
2025-03-18 00:01:19.624552 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/results/test_pe.summary_preprocess.tab
2025-03-18 00:01:19.626486 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/bams/processed.aligner_input_1.fastq ...
2025-03-18 00:01:19.631487 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/bams/processed.aligner_input_2.fastq ...
2025-03-18 00:01:19.634503 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/reports/shortReadReport_1 ...
2025-03-18 00:01:21.157999 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.2656743422639f/reports/shortReadReport_2 ...
2025-03-18 00:01:22.550889 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:01:23.019064 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-18 00:01:23.027544 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
2025-03-18 00:01:23.032803 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
2025-03-18 00:01:23.03612 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:01:28.352024 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:01:28.354499 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/chunks/chunk_000001/logs/progress.log
2025-03-18 00:01:31.647364 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.055 minutes
2025-03-18 00:01:31.65038 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/chunks/chunk_000002/logs/progress.log
2025-03-18 00:01:34.84501 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.053 minutes
2025-03-18 00:01:34.84755 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/chunks/chunk_000003/logs/progress.log
2025-03-18 00:01:37.706717 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-03-18 00:01:37.801993 DEBUG::tools.R/processChunks: done
2025-03-18 00:01:37.805492 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:01:37.807515 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/results/test_pe.adapter_contaminated_1.RData
2025-03-18 00:01:37.810201 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-18 00:01:37.812262 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/results/test_pe.adapter_contaminated_2.RData
2025-03-18 00:01:37.82283 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
2025-03-18 00:01:37.825115 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/results/test_pe.summary_preprocess.tab
2025-03-18 00:01:37.828115 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/bams/processed.aligner_input_1.fastq ...
2025-03-18 00:01:37.83316 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/bams/processed.aligner_input_2.fastq ...
2025-03-18 00:01:37.837284 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/reports/shortReadReport_1 ...
2025-03-18 00:01:39.436821 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads.minichunks.265674494fa22b/reports/shortReadReport_2 ...
2025-03-18 00:01:40.68195 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/RtmptLsreX/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-18 00:01:41.052531 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-18 00:01:41.077086 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
2025-03-18 00:01:41.080248 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:01:44.706961 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:01:44.708553 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads_single_end.2656741163740/chunks/chunk_000001/logs/progress.log
2025-03-18 00:01:47.200365 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2025-03-18 00:01:47.212754 DEBUG::tools.R/processChunks: done
2025-03-18 00:01:47.215746 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:01:47.217564 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads_single_end.2656741163740/results/test_se.adapter_contaminated_1.RData
2025-03-18 00:01:47.226636 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
2025-03-18 00:01:47.228916 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads_single_end.2656741163740/results/test_se.summary_preprocess.tab
2025-03-18 00:01:47.231434 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads_single_end.2656741163740/bams/processed.aligner_input_1.fastq ...
2025-03-18 00:01:47.235401 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmptLsreX/test.preprocessReads_single_end.2656741163740/reports/shortReadReport_1 ...
2025-03-18 00:01:48.600317 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 
2025-03-18 00:01:49.237782 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-18 00:01:49.257557 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
2025-03-18 00:01:49.276572 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
2025-03-18 00:01:49.279302 DEBUG::tools.R/processChunks: starting...
2025-03-18 00:01:53.494123 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-18 00:01:53.495723 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-03-18 00:01:56.30908 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-18 00:01:56.357615 DEBUG::tools.R/processChunks: done
2025-03-18 00:01:56.360196 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-18 00:01:56.361812 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-03-18 00:01:56.36366 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-18 00:01:56.365155 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-03-18 00:01:56.372106 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
2025-03-18 00:01:56.373967 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-03-18 00:01:56.375975 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-03-18 00:01:56.38081 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-03-18 00:01:56.384843 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-03-18 00:02:49.261514 DEBUG::tools.R/traceMem: wired.mem=-80.201286 GiB
2025-03-18 00:03:49.327304 DEBUG::tools.R/traceMem: wired.mem=-75.371037 GiB
2025-03-18 00:04:49.394114 DEBUG::tools.R/traceMem: wired.mem=-74.837541 GiB
2025-03-18 00:05:49.461174 DEBUG::tools.R/traceMem: wired.mem=-75.603288 GiB
2025-03-18 00:06:49.527993 DEBUG::tools.R/traceMem: wired.mem=-72.763490 GiB
2025-03-18 00:07:49.594253 DEBUG::tools.R/traceMem: wired.mem=-72.393155 GiB
2025-03-18 00:08:49.659201 DEBUG::tools.R/traceMem: wired.mem=-70.669550 GiB
2025-03-18 00:09:49.724017 DEBUG::tools.R/traceMem: wired.mem=-68.941341 GiB
2025-03-18 00:10:49.789943 DEBUG::tools.R/traceMem: wired.mem=-63.773663 GiB
2025-03-18 00:11:49.857117 DEBUG::tools.R/traceMem: wired.mem=-69.861786 GiB
2025-03-18 00:12:49.924141 DEBUG::tools.R/traceMem: wired.mem=-71.087079 GiB
2025-03-18 00:13:49.990872 DEBUG::tools.R/traceMem: wired.mem=-75.067736 GiB
2025-03-18 00:14:50.05757 DEBUG::tools.R/traceMem: wired.mem=-73.009988 GiB
2025-03-18 00:15:50.125347 DEBUG::tools.R/traceMem: wired.mem=-68.024558 GiB
2025-03-18 00:16:50.190801 DEBUG::tools.R/traceMem: wired.mem=-67.068944 GiB
2025-03-18 00:17:50.259019 DEBUG::tools.R/traceMem: wired.mem=-76.349932 GiB
2025-03-18 00:18:50.326221 DEBUG::tools.R/traceMem: wired.mem=-74.449584 GiB
2025-03-18 00:19:50.38977 DEBUG::tools.R/traceMem: wired.mem=-72.139276 GiB
2025-03-18 00:20:50.45501 DEBUG::tools.R/traceMem: wired.mem=-81.883685 GiB
2025-03-18 00:21:50.520971 DEBUG::tools.R/traceMem: wired.mem=-80.978477 GiB
2025-03-18 00:22:50.585888 DEBUG::tools.R/traceMem: wired.mem=-71.577223 GiB
2025-03-18 00:23:50.651803 DEBUG::tools.R/traceMem: wired.mem=-76.120203 GiB
2025-03-18 00:24:50.71788 DEBUG::tools.R/traceMem: wired.mem=-66.511585 GiB
2025-03-18 00:25:50.783491 DEBUG::tools.R/traceMem: wired.mem=-70.506766 GiB
2025-03-18 00:26:50.848006 DEBUG::tools.R/traceMem: wired.mem=-77.047423 GiB
2025-03-18 00:27:50.916472 DEBUG::tools.R/traceMem: wired.mem=-62.246453 GiB
2025-03-18 00:28:50.982423 DEBUG::tools.R/traceMem: wired.mem=-71.303430 GiB
2025-03-18 00:29:51.048061 DEBUG::tools.R/traceMem: wired.mem=-79.416205 GiB
2025-03-18 00:30:51.113459 DEBUG::tools.R/traceMem: wired.mem=-74.062545 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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