Multiple platform build/check report for BioC 3.19 - CHECK results for HTSeqGenie on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4748
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4484
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4514
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"	4480
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: HTSeqGenie

Version: 4.34.0

Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HTSeqGenie_4.34.0.tar.gz

StartedAt: 2024-05-09 08:25:26 -0000 (Thu, 09 May 2024)

EndedAt: 2024-05-09 08:40:30 -0000 (Thu, 09 May 2024)

EllapsedTime: 903.6 seconds

RetCode: 0

Status: OK

CheckDir: HTSeqGenie.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HTSeqGenie_4.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (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 ‘4.34.0’
* 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL HTSeqGenie
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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, 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:32:52.940457 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:32:52.949845 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:32:52.95545 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-09 08:32:52.958294 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:32:56.251745 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:32:56.253807 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/chunks/chunk_000001/logs/progress.log
2024-05-09 08:32:59.144454 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2024-05-09 08:32:59.146377 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/chunks/chunk_000002/logs/progress.log
2024-05-09 08:33:02.041733 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2024-05-09 08:33:02.043697 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/chunks/chunk_000003/logs/progress.log
2024-05-09 08:33:04.915894 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2024-05-09 08:33:04.955083 DEBUG::tools.R/processChunks: done
2024-05-09 08:33:04.959891 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:33:04.96286 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.adapter_contaminated_1.RData
2024-05-09 08:33:04.966496 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:33:04.968842 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.adapter_contaminated_2.RData
2024-05-09 08:33:04.980869 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
2024-05-09 08:33:04.98394 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.summary_preprocess.tab
2024-05-09 08:33:04.988364 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:33:04.995121 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:33:05.000819 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/reports/shortReadReport_1 ...
2024-05-09 08:33:06.869645 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/reports/shortReadReport_2 ...
2024-05-09 08:33:08.390033 INFO::preprocessReads.R/preprocessReads: done
2024-05-09 08:33:08.446757 INFO::alignReads.R/alignReads: starting alignment...
2024-05-09 08:33:08.453223 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:33:12.385998 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:33:12.388374 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/chunks/chunk_000001/logs/progress.log
2024-05-09 08:33:15.461185 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2024-05-09 08:33:15.463417 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/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.
2024-05-09 08:33:18.181866 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2024-05-09 08:33:18.184032 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/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.
2024-05-09 08:33:20.9356 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-05-09 08:33:20.938824 DEBUG::tools.R/processChunks: done
2024-05-09 08:33:20.940713 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.
2024-05-09 08:33:21.272243 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-09 08:33:21.283905 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.summary_alignment.tab
2024-05-09 08:33:21.294858 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.summary_analyzed_bamstats.tab
2024-05-09 08:33:21.297385 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-09 08:33:21.575713 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.34aafe6b343d73/results/test_pe.summary_target_lengths.tab
2024-05-09 08:33:21.635963 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-09 08:33:21.637414 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:33:21.934546 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:33:21.938436 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:33:22.025336 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2024-05-09 08:33:22.032114 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:33:22.036591 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-09 08:33:22.039376 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:33:26.541789 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:33:26.544145 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/chunks/chunk_000001/logs/progress.log
2024-05-09 08:33:29.386714 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2024-05-09 08:33:29.388689 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/chunks/chunk_000002/logs/progress.log
2024-05-09 08:33:32.18351 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2024-05-09 08:33:32.185562 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/chunks/chunk_000003/logs/progress.log
2024-05-09 08:33:35.121518 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2024-05-09 08:33:35.123355 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/chunks/chunk_000004/logs/progress.log
2024-05-09 08:33:37.937009 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2024-05-09 08:33:37.975563 DEBUG::tools.R/processChunks: done
2024-05-09 08:33:37.97993 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:33:37.983028 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/results/test_pe.adapter_contaminated_1.RData
2024-05-09 08:33:37.987005 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:33:37.989574 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/results/test_pe.adapter_contaminated_2.RData
2024-05-09 08:33:38.003828 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
2024-05-09 08:33:38.006918 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/results/test_pe.summary_preprocess.tab
2024-05-09 08:33:38.012043 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:33:38.019449 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:33:38.025425 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/reports/shortReadReport_1 ...
2024-05-09 08:33:39.858152 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReads.sparsechunks.34aafe4bcce6fa/reports/shortReadReport_2 ...
2024-05-09 08:33:41.327297 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:33:41.533386 INFO::alignReads.R/alignReadsChunk: running gsnap...
2024-05-09 08:33:41.540112 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/Rtmp8pzJWm/test.alignReadsOneSingleEnd.34aafe4834995d/bams/test.alignReads /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2024-05-09 08:33:41.698015 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2024-05-09 08:33:41.841176 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReadsOneSingleEnd.34aafe4834995d/results/test.alignReads.summary_alignment.tab
2024-05-09 08:33:41.894558 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.alignReadsOneSingleEnd.34aafe4834995d/results/test.alignReads.summary_analyzed_bamstats.tab
2024-05-09 08:33:41.896951 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.003 0.001 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:33:42.331119 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.genotype.34aafe140694ab/results/test_pe.coverage.RData
2024-05-09 08:33:42.333474 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.genotype.34aafe140694ab/results/test_pe.coverage.bw
2024-05-09 08:33:42.519973 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.genotype.34aafe140694ab/results/test_pe.summary_coverage.tab
2024-05-09 08:33:42.522316 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:33:55.755579 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:33:55.880987 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:33:55.906263 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:33:55.90851 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.genotype.34aafe140694ab/results/test_pe.raw_variants.RData
2024-05-09 08:33:55.911677 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.genotype.34aafe140694ab/results/test_pe.filtered_variants.RData
2024-05-09 08:33:55.913661 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-09 08:33:55.915407 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:33:56.47497 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-09 08:33:56.476637 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2024-05-09 08:35:20.404771 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:35:21.043279 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-09 08:35:21.044624 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:35:21.665689 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:35:34.780285 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:35:34.90722 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:35:34.932826 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:35:34.934807 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.34aafe57998bac/results/test_pe.raw_variants.RData
2024-05-09 08:35:34.937927 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.34aafe57998bac/results/test_pe.filtered_variants.RData
2024-05-09 08:35:34.939911 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:35:35.132906 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:35:48.446968 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:35:48.541895 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:35:48.570408 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:35:48.572705 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.filters.34aafe1a4bb805/results/test_pe.raw_variants.RData
2024-05-09 08:35:48.576315 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.filters.34aafe1a4bb805/results/test_pe.filtered_variants.RData
2024-05-09 08:35:48.578493 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-09 08:35:48.580842 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:36:01.812502 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:36:01.873176 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:36:01.899991 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:36:01.901977 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.filters.34aafe1a4bb805/results/test_pe.raw_variants.RData
2024-05-09 08:36:01.905417 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.filters.34aafe1a4bb805/results/test_pe.filtered_variants.RData
2024-05-09 08:36:01.908244 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:36:02.26121 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:36:02.263402 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2024-05-09 08:36:06.151443 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:36:06.267583 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:36:06.293638 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:36:06.295611 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.which.34aafe6d7a8de0/results/test_pe.raw_variants.RData
2024-05-09 08:36:06.297926 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.wrap.callVariants.which.34aafe6d7a8de0/results/test_pe.filtered_variants.RData
2024-05-09 08:36:06.299767 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:36:06.521223 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:36:06.523155 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:36:08.597587 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:36:08.880645 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  ... 2024-05-09 08:37:22.766356 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/mgkyonhc/merged/results/bla.coverage.RData
2024-05-09 08:37:22.770018 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/mgkyonhc/merged/results/bla.coverage.bw
2024-05-09 08:37:22.885813 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/mgkyonhc/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2024-05-09 08:37:24.270086 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/vmqfkbjt/merged/results/bla.coverage.RData
2024-05-09 08:37:24.272088 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/vmqfkbjt/merged/results/bla.coverage.bw
2024-05-09 08:37:24.288209 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/vmqfkbjt/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:25.902457 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-05-09 08:37:25.904107 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.34aafe4ccc45f4/bams/rRNA_contam/input1.fastq
2024-05-09 08:37:25.909079 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/Rtmp8pzJWm/test.detectRRNA.34aafe4ccc45f4/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.34aafe4ccc45f4/bams/rRNA_contam/input1.fastq 2>&1
2024-05-09 08:37:26.024147 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-05-09 08:37:26.025618 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:26.193627 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-05-09 08:37:26.195179 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.paired_end.34aafe2d082592/bams/rRNA_contam/input1.fastq
2024-05-09 08:37:26.197598 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.paired_end.34aafe2d082592/bams/rRNA_contam/input2.fastq
2024-05-09 08:37:26.201304 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/Rtmp8pzJWm/test.detectRRNA.paired_end.34aafe2d082592/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.paired_end.34aafe2d082592/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp8pzJWm/test.detectRRNA.paired_end.34aafe2d082592/bams/rRNA_contam/input2.fastq 2>&1
2024-05-09 08:37:26.51294 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-05-09 08:37:26.514394 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2024-05-09 08:37:26.544172 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/Rtmp8pzJWm/test_get_rRNA_idsspnekabh/test_pe /home/biocbuild/tmp/Rtmp8pzJWm/test_get_rRNA_idsspnekabh/1.fastq -a paired /home/biocbuild/tmp/Rtmp8pzJWm/test_get_rRNA_idsspnekabh/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2024-05-09 08:37:26.831975 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/Rtmp8pzJWm/test_get_rRNAIds_randomfmwketxb/test_pe /home/biocbuild/tmp/Rtmp8pzJWm/test_get_rRNAIds_randomfmwketxb/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2024-05-09 08:37:27.002122 INFO::filterQuality.R/filterQuality: filterByLength...
2024-05-09 08:37:27.00421 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2024-05-09 08:37:27.005556 INFO::filterQuality.R/filterByLength: done
2024-05-09 08:37:27.076298 INFO::filterQuality.R/filterQuality: filterByLength...
2024-05-09 08:37:27.077622 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2024-05-09 08:37:27.078941 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2024-05-09 08:37:27.158442 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-09 08:37:27.172297 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-09 08:37:27.173941 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-09 08:37:27.181104 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-09 08:37:27.182785 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-09 08:37:27.189977 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-09 08:37:27.191651 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-09 08:37:27.200646 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



Executing test function test.callVariantsGATK.withFiltering  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
 done successfully.



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



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



Executing test function test.gatk  ... Timing stopped at: 0 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:27.582947 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:27.586598 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:27.821115 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:27.918437 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-09 08:37:27.92234 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:27.92574 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:28.182146 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:28.369911 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:28.543186 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:28.603192 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-09 08:37:28.606798 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:28.610219 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:28.848625 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:28.906857 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-09 08:37:28.910498 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:28.914039 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:37:29.795336 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:37:29.802153 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:37:29.806786 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-09 08:37:29.809679 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:37:33.243856 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:37:33.245877 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000001/logs/progress.log
2024-05-09 08:37:36.049984 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2024-05-09 08:37:36.052048 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000002/logs/progress.log
2024-05-09 08:37:38.815455 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-05-09 08:37:38.817377 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000003/logs/progress.log
2024-05-09 08:37:41.623964 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2024-05-09 08:37:41.684039 DEBUG::tools.R/processChunks: done
2024-05-09 08:37:41.687829 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:37:41.690237 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.adapter_contaminated_1.RData
2024-05-09 08:37:41.693324 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:37:41.695687 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.adapter_contaminated_2.RData
2024-05-09 08:37:41.707486 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
2024-05-09 08:37:41.710364 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_preprocess.tab
2024-05-09 08:37:41.714168 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:37:41.72137 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:37:41.727584 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/reports/shortReadReport_1 ...
2024-05-09 08:37:43.772659 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/reports/shortReadReport_2 ...
2024-05-09 08:37:45.406059 INFO::preprocessReads.R/preprocessReads: done
2024-05-09 08:37:45.487574 INFO::alignReads.R/alignReads: starting alignment...
2024-05-09 08:37:45.492557 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:37:49.550368 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:37:49.552765 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000001/logs/progress.log
2024-05-09 08:37:52.181744 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2024-05-09 08:37:52.183948 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/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.
2024-05-09 08:37:54.835917 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-05-09 08:37:54.838024 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/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.
2024-05-09 08:37:57.49097 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-05-09 08:37:57.494861 DEBUG::tools.R/processChunks: done
2024-05-09 08:37:57.497372 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.
2024-05-09 08:37:57.804432 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-09 08:37:57.815596 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_alignment.tab
2024-05-09 08:37:57.826269 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_analyzed_bamstats.tab
2024-05-09 08:37:57.829045 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-09 08:37:58.075845 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_target_lengths.tab
2024-05-09 08:37:58.134438 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-09 08:37:58.135848 INFO::alignReads.R/alignReads: done
2024-05-09 08:37:58.215988 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-05-09 08:37:58.235862 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:38:01.732128 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:38:01.734378 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000001/logs/progress.log
2024-05-09 08:38:04.310167 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-09 08:38:04.312535 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000002/logs/progress.log
2024-05-09 08:38:06.88568 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-05-09 08:38:06.887975 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000003/logs/progress.log
2024-05-09 08:38:09.451136 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-05-09 08:38:09.45454 DEBUG::tools.R/processChunks: done
2024-05-09 08:38:09.456898 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-09 08:38:09.475077 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_exon.tab
2024-05-09 08:38:09.490052 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_exon_disjoint.tab
2024-05-09 08:38:09.499998 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_gene.tab
2024-05-09 08:38:09.508071 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_gene_coding.tab
2024-05-09 08:38:09.516016 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_gene_exonic.tab
2024-05-09 08:38:09.523648 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_intergenic.tab
2024-05-09 08:38:09.536064 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.counts_intron.tab
2024-05-09 08:38:09.539931 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-09 08:38:09.547895 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_counts.tab
2024-05-09 08:38:09.550272 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-09 08:38:09.896034 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-09 08:38:09.897316 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-05-09 08:38:09.976683 INFO::coverage.R/calculateCoverage: starting...
2024-05-09 08:38:09.981363 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:38:13.429477 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:38:13.431663 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000001/logs/progress.log
2024-05-09 08:38:15.637289 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2024-05-09 08:38:15.639636 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000002/logs/progress.log
2024-05-09 08:38:17.843482 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2024-05-09 08:38:17.845702 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/chunks/chunk_000003/logs/progress.log
2024-05-09 08:38:20.051412 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2024-05-09 08:38:20.054849 DEBUG::tools.R/processChunks: done
2024-05-09 08:38:23.075751 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.coverage.RData
2024-05-09 08:38:23.078771 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.coverage.bw
2024-05-09 08:38:23.110954 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_coverage.tab
2024-05-09 08:38:23.113134 INFO::coverage.R/calculateCoverage: done
2024-05-09 08:38:23.115355 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-09 08:38:23.196507 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:38:26.947312 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:38:27.054917 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:38:27.079075 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:38:27.080949 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.raw_variants.RData
2024-05-09 08:38:27.083169 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.filtered_variants.RData
2024-05-09 08:38:27.084956 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-09 08:38:27.086356 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:38:27.402442 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-09 08:38:27.546065 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/results/test_pe.summary_variants.tab
2024-05-09 08:38:27.5488 INFO::analyzeVariants/analyzeVariants: done
2024-05-09 08:38:27.552623 INFO::Pipeline run successful.
2024-05-09 08:38:27.738842 INFO::mergeLanes.R/doMergeLanes: starting...
2024-05-09 08:38:27.744522 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:38:27.747663 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.adapter_contaminated_1.RData
2024-05-09 08:38:27.751861 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:38:27.754812 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.adapter_contaminated_2.RData
2024-05-09 08:38:27.769792 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
2024-05-09 08:38:27.77317 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_preprocess.tab
2024-05-09 08:38:27.776235 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.
2024-05-09 08:38:28.126607 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-09 08:38:28.136993 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_alignment.tab
2024-05-09 08:38:28.149451 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_analyzed_bamstats.tab
2024-05-09 08:38:28.152459 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-09 08:38:28.417538 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_target_lengths.tab
2024-05-09 08:38:28.482957 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-09 08:38:28.524698 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-09 08:38:28.548703 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_exon.tab
2024-05-09 08:38:28.564001 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_exon_disjoint.tab
2024-05-09 08:38:28.573354 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_gene.tab
2024-05-09 08:38:28.581201 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_gene_coding.tab
2024-05-09 08:38:28.589185 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_gene_exonic.tab
2024-05-09 08:38:28.597211 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_intergenic.tab
2024-05-09 08:38:28.611163 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.counts_intron.tab
2024-05-09 08:38:28.614998 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-09 08:38:28.623387 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_counts.tab
2024-05-09 08:38:28.625832 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-09 08:38:28.899442 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-09 08:38:31.153301 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.coverage.RData
2024-05-09 08:38:31.156289 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.coverage.bw
2024-05-09 08:38:31.171355 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_coverage.tab
2024-05-09 08:38:31.216367 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-09 08:38:31.304608 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:38:35.122102 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:38:35.232095 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:38:35.25661 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:38:35.25851 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.raw_variants.RData
2024-05-09 08:38:35.261123 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.filtered_variants.RData
2024-05-09 08:38:35.26314 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-09 08:38:35.264716 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:38:35.608091 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-09 08:38:35.765753 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.mergeLanes.34aafe245e23a8/merged/results/merged.summary_variants.tab
2024-05-09 08:38:35.768489 INFO::analyzeVariants/analyzeVariants: done
2024-05-09 08:38:35.771539 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/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:38:36.124926 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:38:36.146023 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:38:36.165232 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-09 08:38:36.168393 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:38:41.383592 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:38:41.385735 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/chunks/chunk_000001/logs/progress.log
2024-05-09 08:38:44.170021 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-05-09 08:38:44.231234 DEBUG::tools.R/processChunks: done
2024-05-09 08:38:44.234504 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:38:44.23688 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/results/test_pe.adapter_contaminated_1.RData
2024-05-09 08:38:44.239526 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:38:44.241744 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/results/test_pe.adapter_contaminated_2.RData
2024-05-09 08:38:44.250868 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
2024-05-09 08:38:44.253626 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/results/test_pe.summary_preprocess.tab
2024-05-09 08:38:44.256864 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:38:44.263648 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:38:44.269859 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/reports/shortReadReport_1 ...
2024-05-09 08:38:46.165525 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.34aafe9d7f8fd/reports/shortReadReport_2 ...
2024-05-09 08:38:47.626406 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:38:47.894566 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:38:47.901508 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:38:47.906201 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-09 08:38:47.909045 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:38:53.058768 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:38:53.060944 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/chunks/chunk_000001/logs/progress.log
2024-05-09 08:38:55.839679 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-05-09 08:38:55.841781 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/chunks/chunk_000002/logs/progress.log
2024-05-09 08:38:58.577369 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-05-09 08:38:58.579274 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/chunks/chunk_000003/logs/progress.log
2024-05-09 08:39:01.338957 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-05-09 08:39:01.395417 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:01.399108 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:39:01.401462 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/results/test_pe.adapter_contaminated_1.RData
2024-05-09 08:39:01.404475 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:39:01.406683 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/results/test_pe.adapter_contaminated_2.RData
2024-05-09 08:39:01.417757 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
2024-05-09 08:39:01.420411 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/results/test_pe.summary_preprocess.tab
2024-05-09 08:39:01.424052 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:39:01.430752 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:39:01.436793 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/reports/shortReadReport_1 ...
2024-05-09 08:39:03.306916 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads.minichunks.34aafe265f45f4/reports/shortReadReport_2 ...
2024-05-09 08:39:04.818905 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:39:05.142323 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:39:05.165264 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-09 08:39:05.168598 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:39:08.698365 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:39:08.700433 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads_single_end.34aafe6240eec/chunks/chunk_000001/logs/progress.log
2024-05-09 08:39:11.260568 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-09 08:39:11.307955 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:11.311341 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:39:11.313906 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads_single_end.34aafe6240eec/results/test_se.adapter_contaminated_1.RData
2024-05-09 08:39:11.323127 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
2024-05-09 08:39:11.325606 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads_single_end.34aafe6240eec/results/test_se.summary_preprocess.tab
2024-05-09 08:39:11.328242 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads_single_end.34aafe6240eec/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:39:11.333663 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp8pzJWm/test.preprocessReads_single_end.34aafe6240eec/reports/shortReadReport_1 ...
2024-05-09 08:39:13.208542 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.readRNASeqEnds  ...  done successfully.



Executing test function test.readRNASeqEnds.dupmark  ...  done successfully.



Executing test function test.how_many  ...  done successfully.



Executing test function test.plotDF  ...  done successfully.



Executing test function test.relativeBarPlot  ...  done successfully.



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:39:13.974142 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-09 08:39:13.999356 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2024-05-09 08:39:14.023388 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2024-05-09 08:39:14.026897 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:39:19.213626 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:39:19.215906 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-09 08:39:22.331351 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2024-05-09 08:39:22.388223 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:22.391202 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-09 08:39:22.39325 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2024-05-09 08:39:22.395659 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-09 08:39:22.397622 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2024-05-09 08:39:22.406069 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2024-05-09 08:39:22.408627 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2024-05-09 08:39:22.411602 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2024-05-09 08:39:22.418617 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2024-05-09 08:39:22.425447 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2024-05-09 08:39:24.560923 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2024-05-09 08:39:26.340084 INFO::preprocessReads.R/preprocessReads: done
2024-05-09 08:39:26.419868 INFO::alignReads.R/alignReads: starting alignment...
2024-05-09 08:39:26.424886 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:39:31.084561 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:39:31.086772 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" 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 "HISEQ1:109:D093LACXX:4:1206:17367:135118" 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 "HISEQ1:109:D093LACXX:4:1304:1838:53573" 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 "HISEQ1:109:D093LACXX:4:2303:2956:116587" 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 "M" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" 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 "HISEQ1:109:D093LACXX:4:1206:20028:108227" 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 "HISEQ1:109:D093LACXX:4:1207:19518:143960" 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 "HISEQ1:109:D093LACXX:4:2207:4065:173048" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2024-05-09 08:39:36.805162 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.095 minutes
2024-05-09 08:39:36.80834 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:36.810158 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2024-05-09 08:39:36.845331 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-09 08:39:36.853635 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2024-05-09 08:39:36.861365 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2024-05-09 08:39:36.864133 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-09 08:39:37.096426 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2024-05-09 08:39:37.160677 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-09 08:39:37.162082 INFO::alignReads.R/alignReads: done
2024-05-09 08:39:37.24996 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-05-09 08:39:37.270232 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:39:41.079474 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:39:41.081703 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-09 08:39:43.690908 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-09 08:39:43.694128 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:43.696231 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-09 08:39:43.708252 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2024-05-09 08:39:43.718449 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2024-05-09 08:39:43.725944 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2024-05-09 08:39:43.731294 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2024-05-09 08:39:43.736686 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2024-05-09 08:39:43.741934 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2024-05-09 08:39:43.749749 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2024-05-09 08:39:43.753765 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-09 08:39:43.758613 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2024-05-09 08:39:43.760953 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-09 08:39:44.026024 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-09 08:39:44.027273 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-05-09 08:39:44.113257 INFO::coverage.R/calculateCoverage: starting...
2024-05-09 08:39:44.117704 DEBUG::tools.R/processChunks: starting...
2024-05-09 08:39:47.577873 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-09 08:39:47.580183 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-09 08:39:49.949212 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2024-05-09 08:39:49.952448 DEBUG::tools.R/processChunks: done
2024-05-09 08:39:51.771864 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2024-05-09 08:39:51.774111 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2024-05-09 08:39:51.884224 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2024-05-09 08:39:51.886022 INFO::coverage.R/calculateCoverage: done
2024-05-09 08:39:51.887692 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-09 08:39:51.975835 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-09 08:40:06.339185 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-09 08:40:06.508942 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-09 08:40:06.544811 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-09 08:40:06.547634 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2024-05-09 08:40:06.551876 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2024-05-09 08:40:06.554528 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-09 08:40:06.556721 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-09 08:40:07.056049 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-09 08:40:07.271657 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2024-05-09 08:40:07.27631 INFO::analyzeVariants/analyzeVariants: done
2024-05-09 08:40:07.282166 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp8pzJWm/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 
2024-05-09 08:40:07.570703 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp8pzJWm/test.calcTargetLengths.34aafe31980237/results/test_pe.summary_target_lengths.tab
 done successfully.



Executing test function test.sclapply  ...  done successfully.



Executing test function test.tryKeepTraceback  ...  done successfully.



Executing test function test.truncateReads  ...  done successfully.



Executing test function test.truncateReads.trim5  ...  done successfully.

RUNIT TEST PROTOCOL -- Thu May  9 08:40:24 2024 
*********************************************** 
Number of test functions: 61 
Number of deactivated test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: HTSeqGenie unit testing 
Test function regexp: ^test.+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (30.4 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (19.68 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.56 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (99.6 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.44 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (26.97 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.39 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.22 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (2.49 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (38.02 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (32.82 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (1.04 seconds)
test.isSparse: (5 checks) ... OK (0.14 seconds)
test.mergeCoverage: (1 checks) ... OK (1.85 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.43 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.2 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.39 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.44 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.05 seconds)
test.isAdapter: (5 checks) ... OK (0.17 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.12 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.32 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.49 seconds)
test.getRRNAIds: (1 checks) ... OK (0.29 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.19 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.06 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.gatk.R 
test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set
test.excludeVariantsByRegion: (3 checks) ... OK (0.23 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.36 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.19 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.21 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.61 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.14 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.22 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (66.39 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.picard.R 
test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test
test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (11.82 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (17.19 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.39 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.12 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.14 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (53.63 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.29 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (16.86 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.08 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.26 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
318.902 111.060 474.316

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

CHECK results for HTSeqGenie on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings