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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4489
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4387
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 taishan

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: HTSeqGenie

Version: 4.36.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.36.0.tar.gz

StartedAt: 2025-01-14 00:34:06 -0000 (Tue, 14 Jan 2025)

EndedAt: 2025-01-14 01:14:06 -0000 (Tue, 14 Jan 2025)

EllapsedTime: 2400.0 seconds

RetCode: None

Status: TIMEOUT

CheckDir: HTSeqGenie.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.36.0’
* 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/R/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

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/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:40:32.870966 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 00:40:32.880337 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:40:32.885984 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 00:40:32.888699 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:40:35.327729 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:40:35.329688 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/chunks/chunk_000001/logs/progress.log
2025-01-14 00:40:38.130795 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-14 00:40:38.132673 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/chunks/chunk_000002/logs/progress.log
2025-01-14 00:40:40.946615 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-14 00:40:40.948681 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/chunks/chunk_000003/logs/progress.log
2025-01-14 00:40:43.76019 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-01-14 00:40:43.795453 DEBUG::tools.R/processChunks: done
2025-01-14 00:40:43.80028 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 00:40:43.803409 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.adapter_contaminated_1.RData
2025-01-14 00:40:43.807223 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 00:40:43.809688 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.adapter_contaminated_2.RData
2025-01-14 00:40:43.821668 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 00:40:43.824795 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.summary_preprocess.tab
2025-01-14 00:40:43.829245 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/bams/processed.aligner_input_1.fastq ...
2025-01-14 00:40:43.835301 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/bams/processed.aligner_input_2.fastq ...
2025-01-14 00:40:43.840637 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/reports/shortReadReport_1 ...
2025-01-14 00:40:45.627218 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/reports/shortReadReport_2 ...
2025-01-14 00:40:47.100516 INFO::preprocessReads.R/preprocessReads: done
2025-01-14 00:40:47.155544 INFO::alignReads.R/alignReads: starting alignment...
2025-01-14 00:40:47.163632 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:40:49.763056 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:40:49.765097 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/chunks/chunk_000001/logs/progress.log
2025-01-14 00:40:52.448798 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-01-14 00:40:52.451103 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/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.
2025-01-14 00:40:55.098582 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-14 00:40:55.100711 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 00:40:57.746013 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-14 00:40:57.749235 DEBUG::tools.R/processChunks: done
2025-01-14 00:40:57.751004 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 00:40:58.058464 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 00:40:58.069404 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.summary_alignment.tab
2025-01-14 00:40:58.079642 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.summary_analyzed_bamstats.tab
2025-01-14 00:40:58.08206 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 00:40:58.354497 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.2801e8725043a0/results/test_pe.summary_target_lengths.tab
2025-01-14 00:40:58.412013 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 00:40:58.413272 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:40:58.709168 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 00:40:58.712482 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:40:58.810724 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-14 00:40:58.817287 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:40:58.821922 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 00:40:58.824562 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:41:01.501599 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:41:01.503582 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/chunks/chunk_000001/logs/progress.log
2025-01-14 00:41:04.275235 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-14 00:41:04.277174 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/chunks/chunk_000002/logs/progress.log
2025-01-14 00:41:07.024888 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-14 00:41:07.026629 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/chunks/chunk_000003/logs/progress.log
2025-01-14 00:41:09.893162 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-01-14 00:41:09.895223 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/chunks/chunk_000004/logs/progress.log
2025-01-14 00:41:12.625568 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-01-14 00:41:12.663689 DEBUG::tools.R/processChunks: done
2025-01-14 00:41:12.668177 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 00:41:12.671412 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/results/test_pe.adapter_contaminated_1.RData
2025-01-14 00:41:12.675648 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 00:41:12.678207 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/results/test_pe.adapter_contaminated_2.RData
2025-01-14 00:41:12.69173 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 00:41:12.694699 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/results/test_pe.summary_preprocess.tab
2025-01-14 00:41:12.699349 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/bams/processed.aligner_input_1.fastq ...
2025-01-14 00:41:12.706007 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/bams/processed.aligner_input_2.fastq ...
2025-01-14 00:41:12.711204 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/reports/shortReadReport_1 ...
2025-01-14 00:41:14.429665 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReads.sparsechunks.2801e812f49eb4/reports/shortReadReport_2 ...
2025-01-14 00:41:15.798031 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:41:15.991482 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-14 00:41:15.997403 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -D /home/biocbuild/.local/share/gmap -t 1 -d TP53_demo_3.2.2 --quality-protocol=illumina  -A sam --read-group-id=test_se -m 0 --split-output /home/biocbuild/tmp/RtmpM1KoKl/test.alignReadsOneSingleEnd.2801e82acac3c4/bams/test.alignReads /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-01-14 00:41:16.120077 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-14 00:41:16.255945 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReadsOneSingleEnd.2801e82acac3c4/results/test.alignReads.summary_alignment.tab
2025-01-14 00:41:16.305105 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.alignReadsOneSingleEnd.2801e82acac3c4/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-14 00:41:16.307133 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.003 0 0.004
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:41:16.707433 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.genotype.2801e845ce0d53/results/test_pe.coverage.RData
2025-01-14 00:41:16.71007 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.genotype.2801e845ce0d53/results/test_pe.coverage.bw
2025-01-14 00:41:16.860245 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.genotype.2801e845ce0d53/results/test_pe.summary_coverage.tab
2025-01-14 00:41:16.862626 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:41:28.715921 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:41:28.83769 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:41:28.861125 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:41:28.863153 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.genotype.2801e845ce0d53/results/test_pe.raw_variants.RData
2025-01-14 00:41:28.866192 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.genotype.2801e845ce0d53/results/test_pe.filtered_variants.RData
2025-01-14 00:41:28.86807 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 00:41:28.869725 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:41:29.426249 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 00:41:29.427872 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-14 00:42:51.730511 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:42:52.319913 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 00:42:52.321106 INFO::analyzeVariants.R/.callGenotypes: done
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
 done successfully.



Executing test function test.wrap.callVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:42:52.879593 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:43:03.880719 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:43:03.987432 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:43:04.010639 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:43:04.012544 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.2801e84916e0d8/results/test_pe.raw_variants.RData
2025-01-14 00:43:04.015536 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.2801e84916e0d8/results/test_pe.filtered_variants.RData
2025-01-14 00:43:04.01738 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:43:04.190903 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:43:15.305005 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:43:15.3912 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:43:15.416637 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:43:15.418616 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.filters.2801e856ad7d6c/results/test_pe.raw_variants.RData
2025-01-14 00:43:15.42177 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.filters.2801e856ad7d6c/results/test_pe.filtered_variants.RData
2025-01-14 00:43:15.423837 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 00:43:15.426147 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:43:26.855032 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:43:26.911647 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:43:26.936213 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:43:26.938215 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.filters.2801e856ad7d6c/results/test_pe.raw_variants.RData
2025-01-14 00:43:26.941532 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.filters.2801e856ad7d6c/results/test_pe.filtered_variants.RData
2025-01-14 00:43:26.944125 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:43:27.273803 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:43:27.276306 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-14 00:43:30.424669 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:43:30.531714 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:43:30.555164 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:43:30.556966 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.which.2801e8487d3839/results/test_pe.raw_variants.RData
2025-01-14 00:43:30.559252 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.wrap.callVariants.which.2801e8487d3839/results/test_pe.filtered_variants.RData
2025-01-14 00:43:30.561016 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:43:30.76297 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:43:30.764789 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:43:32.415063 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:43:32.700311 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



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



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



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



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



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



Executing test function test.mergeCoverage  ... 2025-01-14 00:44:39.309727 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/hgoxaqvc/merged/results/bla.coverage.RData
2025-01-14 00:44:39.313702 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpM1KoKl/hgoxaqvc/merged/results/bla.coverage.bw
2025-01-14 00:44:39.396388 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/hgoxaqvc/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-01-14 00:44:40.451871 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/ehwgrkda/merged/results/bla.coverage.RData
2025-01-14 00:44:40.45378 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpM1KoKl/ehwgrkda/merged/results/bla.coverage.bw
2025-01-14 00:44:40.468097 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/ehwgrkda/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



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



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



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



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



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



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



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:42.025624 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-14 00:44:42.027133 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.2801e83b6a979e/bams/rRNA_contam/input1.fastq
2025-01-14 00:44:42.031818 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.2801e83b6a979e/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.2801e83b6a979e/bams/rRNA_contam/input1.fastq 2>&1
2025-01-14 00:44:42.167164 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-14 00:44:42.168606 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:42.327197 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-14 00:44:42.328659 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.paired_end.2801e848c4267/bams/rRNA_contam/input1.fastq
2025-01-14 00:44:42.330884 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.paired_end.2801e848c4267/bams/rRNA_contam/input2.fastq
2025-01-14 00:44:42.334234 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.paired_end.2801e848c4267/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.paired_end.2801e848c4267/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpM1KoKl/test.detectRRNA.paired_end.2801e848c4267/bams/rRNA_contam/input2.fastq 2>&1
2025-01-14 00:44:42.618418 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-14 00:44:42.61996 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-01-14 00:44:42.650285 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpM1KoKl/test_get_rRNA_idslxgiesqh/test_pe /home/biocbuild/tmp/RtmpM1KoKl/test_get_rRNA_idslxgiesqh/1.fastq -a paired /home/biocbuild/tmp/RtmpM1KoKl/test_get_rRNA_idslxgiesqh/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-01-14 00:44:42.994454 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpM1KoKl/test_get_rRNAIds_randompbozcdyn/test_pe /home/biocbuild/tmp/RtmpM1KoKl/test_get_rRNAIds_randompbozcdyn/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-01-14 00:44:43.159233 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-14 00:44:43.161332 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-14 00:44:43.162651 INFO::filterQuality.R/filterByLength: done
2025-01-14 00:44:43.230794 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-14 00:44:43.232059 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-14 00:44:43.233291 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-01-14 00:44:43.308839 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 00:44:43.321527 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 00:44:43.32302 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 00:44:43.329586 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 00:44:43.331079 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 00:44:43.337665 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 00:44:43.339125 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 00:44:43.345672 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



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



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



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



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



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



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



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



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:43.699894 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:43.70316 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:43.924614 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.014995 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 00:44:44.018812 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.022019 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:44.273009 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:44.454525 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:44.628024 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.688667 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 00:44:44.692222 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.695529 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:44.924867 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.979879 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 00:44:44.98326 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:44.986501 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



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



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



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



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



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:44:45.816822 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 00:44:45.823858 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:44:45.828505 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 00:44:45.831829 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:44:48.546053 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:44:48.548103 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000001/logs/progress.log
2025-01-14 00:44:51.202367 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-14 00:44:51.204329 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000002/logs/progress.log
2025-01-14 00:44:53.895838 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-14 00:44:53.897855 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000003/logs/progress.log
2025-01-14 00:44:56.614781 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-14 00:44:56.668102 DEBUG::tools.R/processChunks: done
2025-01-14 00:44:56.671721 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 00:44:56.673963 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.adapter_contaminated_1.RData
2025-01-14 00:44:56.676786 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 00:44:56.6789 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.adapter_contaminated_2.RData
2025-01-14 00:44:56.68966 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 00:44:56.692355 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_preprocess.tab
2025-01-14 00:44:56.695853 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/bams/processed.aligner_input_1.fastq ...
2025-01-14 00:44:56.702523 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/bams/processed.aligner_input_2.fastq ...
2025-01-14 00:44:56.708138 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/reports/shortReadReport_1 ...
2025-01-14 00:44:58.515157 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/reports/shortReadReport_2 ...
2025-01-14 00:45:00.050147 INFO::preprocessReads.R/preprocessReads: done
2025-01-14 00:45:00.13054 INFO::alignReads.R/alignReads: starting alignment...
2025-01-14 00:45:00.135319 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:45:02.868274 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:45:02.870442 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000001/logs/progress.log
2025-01-14 00:45:05.472347 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-14 00:45:05.474499 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/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.
2025-01-14 00:45:08.110362 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-14 00:45:08.112536 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 00:45:10.788589 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-14 00:45:10.792287 DEBUG::tools.R/processChunks: done
2025-01-14 00:45:10.794299 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 00:45:11.087589 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 00:45:11.097946 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_alignment.tab
2025-01-14 00:45:11.107568 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_analyzed_bamstats.tab
2025-01-14 00:45:11.110188 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 00:45:11.368218 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_target_lengths.tab
2025-01-14 00:45:11.428957 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 00:45:11.430332 INFO::alignReads.R/alignReads: done
2025-01-14 00:45:11.509521 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-14 00:45:11.527915 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:45:14.289109 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:45:14.291283 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000001/logs/progress.log
2025-01-14 00:45:16.848441 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-14 00:45:16.850561 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000002/logs/progress.log
2025-01-14 00:45:19.389009 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2025-01-14 00:45:19.391084 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000003/logs/progress.log
2025-01-14 00:45:21.93738 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.042 minutes
2025-01-14 00:45:21.940615 DEBUG::tools.R/processChunks: done
2025-01-14 00:45:21.94266 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-14 00:45:21.958429 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_exon.tab
2025-01-14 00:45:21.971226 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_exon_disjoint.tab
2025-01-14 00:45:21.979801 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_gene.tab
2025-01-14 00:45:21.986451 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_gene_coding.tab
2025-01-14 00:45:21.992966 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_gene_exonic.tab
2025-01-14 00:45:21.999719 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_intergenic.tab
2025-01-14 00:45:22.010538 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.counts_intron.tab
2025-01-14 00:45:22.014014 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-14 00:45:22.021086 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_counts.tab
2025-01-14 00:45:22.023205 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-14 00:45:22.369736 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-14 00:45:22.37091 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-14 00:45:22.457113 INFO::coverage.R/calculateCoverage: starting...
2025-01-14 00:45:22.463007 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:45:25.172491 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:45:25.174586 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000001/logs/progress.log
2025-01-14 00:45:27.371356 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-01-14 00:45:27.373687 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000002/logs/progress.log
2025-01-14 00:45:29.583857 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-01-14 00:45:29.586147 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/chunks/chunk_000003/logs/progress.log
2025-01-14 00:45:31.794602 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-01-14 00:45:31.798213 DEBUG::tools.R/processChunks: done
2025-01-14 00:45:33.342803 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.coverage.RData
2025-01-14 00:45:33.344698 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.coverage.bw
2025-01-14 00:45:33.359909 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_coverage.tab
2025-01-14 00:45:33.361745 INFO::coverage.R/calculateCoverage: done
2025-01-14 00:45:33.364032 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-14 00:45:33.456816 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:45:36.728068 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:45:36.841682 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:45:36.866479 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:45:36.868526 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.raw_variants.RData
2025-01-14 00:45:36.871131 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.filtered_variants.RData
2025-01-14 00:45:36.873129 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 00:45:36.874646 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:45:37.21307 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 00:45:37.359536 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/results/test_pe.summary_variants.tab
2025-01-14 00:45:37.362763 INFO::analyzeVariants/analyzeVariants: done
2025-01-14 00:45:37.371099 INFO::Pipeline run successful.
2025-01-14 00:45:37.600431 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-14 00:45:37.606066 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 00:45:37.609304 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.adapter_contaminated_1.RData
2025-01-14 00:45:37.613279 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 00:45:37.616332 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.adapter_contaminated_2.RData
2025-01-14 00:45:37.631125 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 00:45:37.634667 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_preprocess.tab
2025-01-14 00:45:37.637902 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 00:45:37.973937 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 00:45:37.984012 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_alignment.tab
2025-01-14 00:45:37.995837 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-14 00:45:37.999052 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 00:45:38.269587 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_target_lengths.tab
2025-01-14 00:45:38.332699 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 00:45:38.374837 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-14 00:45:38.397873 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_exon.tab
2025-01-14 00:45:38.413211 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_exon_disjoint.tab
2025-01-14 00:45:38.42297 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_gene.tab
2025-01-14 00:45:38.43101 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_gene_coding.tab
2025-01-14 00:45:38.439138 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_gene_exonic.tab
2025-01-14 00:45:38.447329 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_intergenic.tab
2025-01-14 00:45:38.462798 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.counts_intron.tab
2025-01-14 00:45:38.466952 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-14 00:45:38.476059 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_counts.tab
2025-01-14 00:45:38.478765 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-14 00:45:38.778234 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-14 00:45:40.7586 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.coverage.RData
2025-01-14 00:45:40.761235 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.coverage.bw
2025-01-14 00:45:40.776564 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_coverage.tab
2025-01-14 00:45:40.821162 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-14 00:45:40.902149 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 00:45:44.087938 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 00:45:44.201208 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 00:45:44.226414 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 00:45:44.228394 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.raw_variants.RData
2025-01-14 00:45:44.230784 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.filtered_variants.RData
2025-01-14 00:45:44.232594 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 00:45:44.234072 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 00:45:44.561206 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 00:45:44.706241 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.mergeLanes.2801e8725dc418/merged/results/merged.summary_variants.tab
2025-01-14 00:45:44.709184 INFO::analyzeVariants/analyzeVariants: done
2025-01-14 00:45:44.717337 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



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



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:45:45.005788 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 00:45:45.014651 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:45:45.01916 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 00:45:45.022007 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:45:47.908865 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-14 00:45:47.910821 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/chunks/chunk_000001/logs/progress.log
2025-01-14 00:45:50.657127 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-14 00:45:50.707632 DEBUG::tools.R/processChunks: done
2025-01-14 00:45:50.71042 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 00:45:50.712355 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/results/test_pe.adapter_contaminated_1.RData
2025-01-14 00:45:50.71454 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 00:45:50.716407 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/results/test_pe.adapter_contaminated_2.RData
2025-01-14 00:45:50.724135 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 00:45:50.726504 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/results/test_pe.summary_preprocess.tab
2025-01-14 00:45:50.72923 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/bams/processed.aligner_input_1.fastq ...
2025-01-14 00:45:50.734956 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/bams/processed.aligner_input_2.fastq ...
2025-01-14 00:45:50.740263 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/reports/shortReadReport_1 ...
2025-01-14 00:45:52.553519 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpM1KoKl/test.preprocessReads.2801e862de2662/reports/shortReadReport_2 ...
2025-01-14 00:45:54.117362 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpM1KoKl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/config/default-config.txt 
2025-01-14 00:45:54.431588 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 00:45:54.438526 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 00:45:54.443536 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.2/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 00:45:54.446561 DEBUG::tools.R/processChunks: starting...
2025-01-14 00:46:54.467438 DEBUG::tools.R/traceMem: wired.mem=-26.831069 GiB
2025-01-14 00:47:54.533728 DEBUG::tools.R/traceMem: wired.mem=-25.083642 GiB
2025-01-14 00:48:54.597371 DEBUG::tools.R/traceMem: wired.mem=-25.627206 GiB
2025-01-14 00:49:54.663949 DEBUG::tools.R/traceMem: wired.mem=-28.958663 GiB
2025-01-14 00:50:54.729589 DEBUG::tools.R/traceMem: wired.mem=-19.084165 GiB
2025-01-14 00:51:54.793592 DEBUG::tools.R/traceMem: wired.mem=-22.916940 GiB
2025-01-14 00:52:54.860838 DEBUG::tools.R/traceMem: wired.mem=-19.451855 GiB
2025-01-14 00:53:54.873782 DEBUG::tools.R/traceMem: wired.mem=-19.924664 GiB
2025-01-14 00:54:54.937777 DEBUG::tools.R/traceMem: wired.mem=-29.299261 GiB
2025-01-14 00:55:55.001387 DEBUG::tools.R/traceMem: wired.mem=-34.761261 GiB
2025-01-14 00:56:55.065848 DEBUG::tools.R/traceMem: wired.mem=-26.585055 GiB
2025-01-14 00:57:55.130083 DEBUG::tools.R/traceMem: wired.mem=-33.643749 GiB
2025-01-14 00:58:55.193549 DEBUG::tools.R/traceMem: wired.mem=-27.338326 GiB
2025-01-14 00:59:55.273113 DEBUG::tools.R/traceMem: wired.mem=-22.532202 GiB
2025-01-14 01:00:55.339975 DEBUG::tools.R/traceMem: wired.mem=-30.432903 GiB
2025-01-14 01:01:55.409356 DEBUG::tools.R/traceMem: wired.mem=-31.515279 GiB
2025-01-14 01:02:55.473983 DEBUG::tools.R/traceMem: wired.mem=-27.775615 GiB
2025-01-14 01:03:55.54165 DEBUG::tools.R/traceMem: wired.mem=-29.474914 GiB
2025-01-14 01:04:55.605752 DEBUG::tools.R/traceMem: wired.mem=-24.209908 GiB
2025-01-14 01:05:55.673759 DEBUG::tools.R/traceMem: wired.mem=-23.818928 GiB
2025-01-14 01:06:55.737759 DEBUG::tools.R/traceMem: wired.mem=-23.641465 GiB
2025-01-14 01:07:55.80157 DEBUG::tools.R/traceMem: wired.mem=-20.218601 GiB
2025-01-14 01:08:55.865771 DEBUG::tools.R/traceMem: wired.mem=-21.532754 GiB
2025-01-14 01:09:55.930074 DEBUG::tools.R/traceMem: wired.mem=-21.804098 GiB
2025-01-14 01:10:55.993222 DEBUG::tools.R/traceMem: wired.mem=-21.738684 GiB
2025-01-14 01:11:56.061976 DEBUG::tools.R/traceMem: wired.mem=-18.486952 GiB
2025-01-14 01:12:56.126077 DEBUG::tools.R/traceMem: wired.mem=-22.632776 GiB
2025-01-14 01:13:56.14194 DEBUG::tools.R/traceMem: wired.mem=-23.473365 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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