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This page was generated on 2025-03-27 11:47 -0400 (Thu, 27 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4783
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4552
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4581
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4533
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4463
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 990/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.37.1  (landing page)
Jens Reeder
Snapshot Date: 2025-03-26 13:40 -0400 (Wed, 26 Mar 2025)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: devel
git_last_commit: 3775db8
git_last_commit_date: 2024-12-17 11:20:20 -0400 (Tue, 17 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kjohnson3macOS 13.7.1 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  

CHECK results for HTSeqGenie on kunpeng2

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

raw results


Summary

Package: HTSeqGenie
Version: 4.37.1
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_4.37.1.tar.gz
StartedAt: 2025-03-27 07:54:57 -0000 (Thu, 27 Mar 2025)
EndedAt: 2025-03-27 08:34:57 -0000 (Thu, 27 Mar 2025)
EllapsedTime: 2400.4 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_4.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.1’
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** this is package ‘HTSeqGenie’ version ‘4.37.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

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

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Warning message:
In fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:02:39.937126 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-27 08:02:39.946482 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:02:39.952011 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-27 08:02:39.955099 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:02:43.215039 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:02:43.217259 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/chunks/chunk_000001/logs/progress.log
2025-03-27 08:02:46.085902 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-27 08:02:46.087747 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/chunks/chunk_000002/logs/progress.log
2025-03-27 08:02:49.003303 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2025-03-27 08:02:49.005287 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/chunks/chunk_000003/logs/progress.log
2025-03-27 08:02:51.877837 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-03-27 08:02:51.932061 DEBUG::tools.R/processChunks: done
2025-03-27 08:02:51.93695 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-27 08:02:51.939975 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.adapter_contaminated_1.RData
2025-03-27 08:02:51.943798 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-27 08:02:51.946291 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.adapter_contaminated_2.RData
2025-03-27 08:02:51.958317 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
2025-03-27 08:02:51.961326 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.summary_preprocess.tab
2025-03-27 08:02:51.965724 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/bams/processed.aligner_input_1.fastq ...
2025-03-27 08:02:51.972015 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/bams/processed.aligner_input_2.fastq ...
2025-03-27 08:02:51.977307 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/reports/shortReadReport_1 ...
2025-03-27 08:02:53.888204 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/reports/shortReadReport_2 ...
2025-03-27 08:02:56.960761 INFO::preprocessReads.R/preprocessReads: done
2025-03-27 08:02:57.026873 INFO::alignReads.R/alignReads: starting alignment...
2025-03-27 08:02:57.041713 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:03:00.410588 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:03:00.412909 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/chunks/chunk_000001/logs/progress.log
2025-03-27 08:03:03.651277 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.054 minutes
2025-03-27 08:03:03.658781 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/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.
2025-03-27 08:03:06.423973 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-27 08:03:06.426468 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/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.
2025-03-27 08:03:09.172254 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-27 08:03:09.175879 DEBUG::tools.R/processChunks: done
2025-03-27 08:03:09.186208 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.
2025-03-27 08:03:09.546104 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-27 08:03:09.55832 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.summary_alignment.tab
2025-03-27 08:03:09.569306 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.summary_analyzed_bamstats.tab
2025-03-27 08:03:09.571838 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-27 08:03:09.863658 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.3dbe53eb4e575/results/test_pe.summary_target_lengths.tab
2025-03-27 08:03:09.929298 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-27 08:03:09.930709 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:03:10.248554 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-27 08:03:10.252206 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:03:10.332574 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-27 08:03:10.339478 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:03:10.343958 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-27 08:03:10.346749 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:03:13.634417 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:03:13.636451 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/chunks/chunk_000001/logs/progress.log
2025-03-27 08:03:16.485729 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-27 08:03:16.48773 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/chunks/chunk_000002/logs/progress.log
2025-03-27 08:03:19.341587 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-03-27 08:03:19.343581 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/chunks/chunk_000003/logs/progress.log
2025-03-27 08:03:22.286932 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-03-27 08:03:22.288807 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/chunks/chunk_000004/logs/progress.log
2025-03-27 08:03:25.24333 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.049 minutes
2025-03-27 08:03:25.32368 DEBUG::tools.R/processChunks: done
2025-03-27 08:03:25.332361 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-27 08:03:25.339867 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/results/test_pe.adapter_contaminated_1.RData
2025-03-27 08:03:25.344114 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-27 08:03:25.355005 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/results/test_pe.adapter_contaminated_2.RData
2025-03-27 08:03:25.372411 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
2025-03-27 08:03:25.375639 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/results/test_pe.summary_preprocess.tab
2025-03-27 08:03:25.381272 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/bams/processed.aligner_input_1.fastq ...
2025-03-27 08:03:25.388141 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/bams/processed.aligner_input_2.fastq ...
2025-03-27 08:03:25.393802 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/reports/shortReadReport_1 ...
2025-03-27 08:03:27.323263 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReads.sparsechunks.3dbe543b45c23/reports/shortReadReport_2 ...
2025-03-27 08:03:30.453873 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:03:30.739159 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-27 08:03:30.755306 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/RtmpeZBEWE/test.alignReadsOneSingleEnd.3dbe525ff1035/bams/test.alignReads /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-27 08:03:30.908317 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-27 08:03:31.049299 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReadsOneSingleEnd.3dbe525ff1035/results/test.alignReads.summary_alignment.tab
2025-03-27 08:03:31.11105 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.alignReadsOneSingleEnd.3dbe525ff1035/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-27 08:03:31.113318 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



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



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:03:31.557508 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.genotype.3dbe5375d11cb/results/test_pe.coverage.RData
2025-03-27 08:03:31.560236 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.genotype.3dbe5375d11cb/results/test_pe.coverage.bw
2025-03-27 08:03:31.752362 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.genotype.3dbe5375d11cb/results/test_pe.summary_coverage.tab
2025-03-27 08:03:31.754915 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:03:43.856124 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:03:43.988865 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:03:44.014828 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:03:44.016991 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.genotype.3dbe5375d11cb/results/test_pe.raw_variants.RData
2025-03-27 08:03:44.020166 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.genotype.3dbe5375d11cb/results/test_pe.filtered_variants.RData
2025-03-27 08:03:44.022279 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-27 08:03:44.024065 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:03:44.633799 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-27 08:03:44.635524 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-27 08:05:12.346533 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:05:12.963957 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-27 08:05:12.965183 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/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:05:13.543114 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:05:25.465686 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:05:25.589495 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:05:25.617162 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:05:25.619256 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.3dbe5742ff665/results/test_pe.raw_variants.RData
2025-03-27 08:05:25.622658 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.3dbe5742ff665/results/test_pe.filtered_variants.RData
2025-03-27 08:05:25.624833 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/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:05:25.813973 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:05:37.616061 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:05:37.704494 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:05:37.729985 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:05:37.731938 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.filters.3dbe51cb24932/results/test_pe.raw_variants.RData
2025-03-27 08:05:37.73509 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.filters.3dbe51cb24932/results/test_pe.filtered_variants.RData
2025-03-27 08:05:37.736864 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-27 08:05:37.738818 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:05:49.605429 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:05:49.668054 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:05:49.694682 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:05:49.696781 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.filters.3dbe51cb24932/results/test_pe.raw_variants.RData
2025-03-27 08:05:49.70027 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.filters.3dbe51cb24932/results/test_pe.filtered_variants.RData
2025-03-27 08:05:49.706454 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/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:05:50.028652 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:05:50.030748 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-27 08:05:53.807334 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:05:53.920835 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:05:53.945644 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:05:53.947525 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.which.3dbe5589b9e55/results/test_pe.raw_variants.RData
2025-03-27 08:05:53.949847 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.wrap.callVariants.which.3dbe5589b9e55/results/test_pe.filtered_variants.RData
2025-03-27 08:05:53.951619 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:05:54.13232 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:05:54.134145 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:05:54.361489 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:05:54.668814 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  ... 2025-03-27 08:07:12.466277 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/blvzxsor/merged/results/bla.coverage.RData
2025-03-27 08:07:12.469431 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpeZBEWE/blvzxsor/merged/results/bla.coverage.bw
2025-03-27 08:07:12.582174 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/blvzxsor/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-27 08:07:13.963583 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/zmharcbf/merged/results/bla.coverage.RData
2025-03-27 08:07:13.965745 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpeZBEWE/zmharcbf/merged/results/bla.coverage.bw
2025-03-27 08:07:13.980475 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/zmharcbf/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



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



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



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



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



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



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



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:15.767758 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-27 08:07:15.769355 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.3dbe56dc9369d/bams/rRNA_contam/input1.fastq
2025-03-27 08:07:15.774177 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/RtmpeZBEWE/test.detectRRNA.3dbe56dc9369d/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.3dbe56dc9369d/bams/rRNA_contam/input1.fastq 2>&1
2025-03-27 08:07:15.892496 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-27 08:07:15.893928 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:16.101217 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-27 08:07:16.102677 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.paired_end.3dbe541de65ff/bams/rRNA_contam/input1.fastq
2025-03-27 08:07:16.104998 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.paired_end.3dbe541de65ff/bams/rRNA_contam/input2.fastq
2025-03-27 08:07:16.108444 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/RtmpeZBEWE/test.detectRRNA.paired_end.3dbe541de65ff/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.paired_end.3dbe541de65ff/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpeZBEWE/test.detectRRNA.paired_end.3dbe541de65ff/bams/rRNA_contam/input2.fastq 2>&1
2025-03-27 08:07:16.378225 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-27 08:07:16.379755 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-27 08:07:16.413065 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/RtmpeZBEWE/test_get_rRNA_idssvmwobgq/test_pe /home/biocbuild/tmp/RtmpeZBEWE/test_get_rRNA_idssvmwobgq/1.fastq -a paired /home/biocbuild/tmp/RtmpeZBEWE/test_get_rRNA_idssvmwobgq/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-27 08:07:16.726881 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/RtmpeZBEWE/test_get_rRNAIds_randommjqbdoih/test_pe /home/biocbuild/tmp/RtmpeZBEWE/test_get_rRNAIds_randommjqbdoih/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-27 08:07:16.898869 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-27 08:07:16.90098 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-27 08:07:16.902378 INFO::filterQuality.R/filterByLength: done
2025-03-27 08:07:16.975262 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-27 08:07:16.976664 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-27 08:07:16.978036 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-27 08:07:17.060255 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-27 08:07:17.074255 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-27 08:07:17.075939 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-27 08:07:17.083392 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-27 08:07:17.085073 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-27 08:07:17.092398 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-27 08:07:17.094103 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-27 08:07:17.101495 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: 0.001 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



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



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



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



Executing test function test.realignIndelsGATK  ... Timing stopped at: 0 0 0.001
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: 0.001 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/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:17.543961 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:17.547693 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:17.837286 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:18.002331 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-27 08:07:18.006659 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:18.010397 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:18.387201 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:18.642972 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:18.936524 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:19.09252 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-27 08:07:19.096231 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:19.099831 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:19.447344 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:19.527385 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-27 08:07:19.531136 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:19.534799 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



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



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



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



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



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:07:20.652636 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-27 08:07:20.660054 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-27 08:07:20.664945 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-27 08:07:20.668172 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:07:24.223118 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:07:24.22518 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000001/logs/progress.log
2025-03-27 08:07:27.298982 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2025-03-27 08:07:27.300882 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000002/logs/progress.log
2025-03-27 08:07:30.566577 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.054 minutes
2025-03-27 08:07:30.568434 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000003/logs/progress.log
2025-03-27 08:07:33.349533 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-27 08:07:33.426093 DEBUG::tools.R/processChunks: done
2025-03-27 08:07:33.429709 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-27 08:07:33.432137 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.adapter_contaminated_1.RData
2025-03-27 08:07:33.43519 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-27 08:07:33.437569 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.adapter_contaminated_2.RData
2025-03-27 08:07:33.448859 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
2025-03-27 08:07:33.451518 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_preprocess.tab
2025-03-27 08:07:33.454956 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/bams/processed.aligner_input_1.fastq ...
2025-03-27 08:07:33.464806 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/bams/processed.aligner_input_2.fastq ...
2025-03-27 08:07:33.4699 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/reports/shortReadReport_1 ...
2025-03-27 08:07:35.418882 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/reports/shortReadReport_2 ...
2025-03-27 08:07:36.977165 INFO::preprocessReads.R/preprocessReads: done
2025-03-27 08:07:37.142989 INFO::alignReads.R/alignReads: starting alignment...
2025-03-27 08:07:37.152182 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:07:40.673161 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:07:40.675383 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000001/logs/progress.log
2025-03-27 08:07:43.529046 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-27 08:07:43.531096 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/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.
2025-03-27 08:07:46.533157 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.05 minutes
2025-03-27 08:07:46.535318 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/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.
2025-03-27 08:07:49.760254 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.054 minutes
2025-03-27 08:07:49.763799 DEBUG::tools.R/processChunks: done
2025-03-27 08:07:49.769854 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.
2025-03-27 08:07:50.127044 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-27 08:07:50.137242 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_alignment.tab
2025-03-27 08:07:50.147007 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_analyzed_bamstats.tab
2025-03-27 08:07:50.149497 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-27 08:07:50.408165 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_target_lengths.tab
2025-03-27 08:07:50.47295 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-27 08:07:50.474407 INFO::alignReads.R/alignReads: done
2025-03-27 08:07:50.674846 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-27 08:07:50.721281 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:07:54.158732 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:07:54.16097 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000001/logs/progress.log
2025-03-27 08:07:56.747909 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-27 08:07:56.750077 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000002/logs/progress.log
2025-03-27 08:07:59.913545 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.053 minutes
2025-03-27 08:07:59.915685 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000003/logs/progress.log
2025-03-27 08:08:02.770765 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-03-27 08:08:02.774466 DEBUG::tools.R/processChunks: done
2025-03-27 08:08:02.785024 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-27 08:08:02.825196 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_exon.tab
2025-03-27 08:08:02.840812 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_exon_disjoint.tab
2025-03-27 08:08:02.850362 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_gene.tab
2025-03-27 08:08:02.857964 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_gene_coding.tab
2025-03-27 08:08:02.86564 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_gene_exonic.tab
2025-03-27 08:08:02.873491 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_intergenic.tab
2025-03-27 08:08:02.885817 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.counts_intron.tab
2025-03-27 08:08:02.889625 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-27 08:08:02.897795 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_counts.tab
2025-03-27 08:08:02.900246 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-27 08:08:03.292232 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-27 08:08:03.29357 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-27 08:08:03.368111 INFO::coverage.R/calculateCoverage: starting...
2025-03-27 08:08:03.373113 DEBUG::tools.R/processChunks: starting...
2025-03-27 08:08:06.859434 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-27 08:08:06.861611 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000001/logs/progress.log
2025-03-27 08:08:09.09808 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-03-27 08:08:09.100287 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000002/logs/progress.log
2025-03-27 08:08:11.308556 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-03-27 08:08:11.310867 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/chunks/chunk_000003/logs/progress.log
2025-03-27 08:08:13.52661 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-03-27 08:08:13.530035 DEBUG::tools.R/processChunks: done
2025-03-27 08:08:15.300122 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.coverage.RData
2025-03-27 08:08:15.302077 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.coverage.bw
2025-03-27 08:08:15.317087 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_coverage.tab
2025-03-27 08:08:15.31889 INFO::coverage.R/calculateCoverage: done
2025-03-27 08:08:15.329916 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-27 08:08:15.484272 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:08:19.313542 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:08:19.425279 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:08:19.450003 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:08:19.451874 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.raw_variants.RData
2025-03-27 08:08:19.454142 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.filtered_variants.RData
2025-03-27 08:08:19.455845 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-27 08:08:19.457263 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:08:19.781282 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-27 08:08:19.920406 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/results/test_pe.summary_variants.tab
2025-03-27 08:08:19.925012 INFO::analyzeVariants/analyzeVariants: done
2025-03-27 08:08:19.940703 INFO::Pipeline run successful.
2025-03-27 08:08:20.292037 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-27 08:08:20.297925 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-27 08:08:20.301167 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.adapter_contaminated_1.RData
2025-03-27 08:08:20.305394 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-27 08:08:20.308257 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.adapter_contaminated_2.RData
2025-03-27 08:08:20.32357 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
2025-03-27 08:08:20.327047 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_preprocess.tab
2025-03-27 08:08:20.33027 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.
2025-03-27 08:08:20.72658 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-27 08:08:20.737434 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_alignment.tab
2025-03-27 08:08:20.750522 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-27 08:08:20.753989 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-27 08:08:21.04202 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_target_lengths.tab
2025-03-27 08:08:21.113573 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-27 08:08:21.156835 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-27 08:08:21.182132 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_exon.tab
2025-03-27 08:08:21.198102 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_exon_disjoint.tab
2025-03-27 08:08:21.208206 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_gene.tab
2025-03-27 08:08:21.217029 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_gene_coding.tab
2025-03-27 08:08:21.225986 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_gene_exonic.tab
2025-03-27 08:08:21.234983 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_intergenic.tab
2025-03-27 08:08:21.251142 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.counts_intron.tab
2025-03-27 08:08:21.255353 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-27 08:08:21.26551 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_counts.tab
2025-03-27 08:08:21.268426 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-27 08:08:21.578811 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-27 08:08:23.959141 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.coverage.RData
2025-03-27 08:08:23.962368 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.coverage.bw
2025-03-27 08:08:23.979834 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_coverage.tab
2025-03-27 08:08:24.045557 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-27 08:08:24.17279 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-27 08:08:28.27434 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-27 08:08:28.395774 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-27 08:08:28.423464 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-27 08:08:28.425608 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.raw_variants.RData
2025-03-27 08:08:28.428141 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.filtered_variants.RData
2025-03-27 08:08:28.430221 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-27 08:08:28.432014 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-27 08:08:28.812032 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-27 08:08:28.970547 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpeZBEWE/test.mergeLanes.3dbe51e7832a5/merged/results/merged.summary_variants.tab
2025-03-27 08:08:28.973374 INFO::analyzeVariants/analyzeVariants: done
2025-03-27 08:08:28.981385 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



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



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpeZBEWE/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-03-27 08:08:29.461631 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-27 08:09:29.498224 DEBUG::tools.R/traceMem: wired.mem=-13.265048 GiB
2025-03-27 08:10:29.569583 DEBUG::tools.R/traceMem: wired.mem=-12.750729 GiB
2025-03-27 08:11:29.648896 DEBUG::tools.R/traceMem: wired.mem=-15.570309 GiB
2025-03-27 08:12:29.713303 DEBUG::tools.R/traceMem: wired.mem=-13.936816 GiB
2025-03-27 08:13:29.780131 DEBUG::tools.R/traceMem: wired.mem=-2.232521 GiB
2025-03-27 08:14:29.86285 DEBUG::tools.R/traceMem: wired.mem=-6.282301 GiB
2025-03-27 08:15:29.940857 DEBUG::tools.R/traceMem: wired.mem=-10.229297 GiB
2025-03-27 08:16:30.016863 DEBUG::tools.R/traceMem: wired.mem=-7.132156 GiB
2025-03-27 08:17:30.092881 DEBUG::tools.R/traceMem: wired.mem=-4.009865 GiB
2025-03-27 08:18:30.164936 DEBUG::tools.R/traceMem: wired.mem=-9.663082 GiB
2025-03-27 08:19:30.233365 DEBUG::tools.R/traceMem: wired.mem=-8.509043 GiB
2025-03-27 08:20:30.301647 DEBUG::tools.R/traceMem: wired.mem=-13.341127 GiB
2025-03-27 08:21:30.380952 DEBUG::tools.R/traceMem: wired.mem=-12.406796 GiB
2025-03-27 08:22:30.456927 DEBUG::tools.R/traceMem: wired.mem=-13.977342 GiB
2025-03-27 08:23:30.524874 DEBUG::tools.R/traceMem: wired.mem=-11.218842 GiB
2025-03-27 08:24:30.596844 DEBUG::tools.R/traceMem: wired.mem=-10.471461 GiB
2025-03-27 08:25:30.665501 DEBUG::tools.R/traceMem: wired.mem=-18.728833 GiB
2025-03-27 08:26:30.7409 DEBUG::tools.R/traceMem: wired.mem=-15.371358 GiB
2025-03-27 08:27:30.813184 DEBUG::tools.R/traceMem: wired.mem=-13.293752 GiB
2025-03-27 08:28:30.888848 DEBUG::tools.R/traceMem: wired.mem=-15.390740 GiB
2025-03-27 08:29:30.964842 DEBUG::tools.R/traceMem: wired.mem=-17.544991 GiB
2025-03-27 08:30:31.03276 DEBUG::tools.R/traceMem: wired.mem=-14.438715 GiB
2025-03-27 08:31:31.108864 DEBUG::tools.R/traceMem: wired.mem=-10.584986 GiB
2025-03-27 08:32:31.184843 DEBUG::tools.R/traceMem: wired.mem=-5.984489 GiB
2025-03-27 08:33:31.260925 DEBUG::tools.R/traceMem: wired.mem=-6.574109 GiB
2025-03-27 08:34:31.336885 DEBUG::tools.R/traceMem: wired.mem=-4.078989 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie000
buildGenomicFeaturesFromTxDb0.0000.0000.001
runPipeline000