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This page was generated on 2024-05-04 11:36:40 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 989/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.34.0  (landing page)
Jens Reeder
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: RELEASE_3_19
git_last_commit: e25c9ee
git_last_commit_date: 2024-04-30 10:29:18 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for HTSeqGenie on nebbiolo1


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

raw results


Summary

Package: HTSeqGenie
Version: 4.34.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HTSeqGenie_4.34.0.tar.gz
StartedAt: 2024-05-04 00:09:02 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:23:12 -0400 (Sat, 04 May 2024)
EllapsedTime: 849.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HTSeqGenie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HTSeqGenie_4.34.0.tar.gz
###
##############################################################################
##############################################################################


* 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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, 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= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:14:57.288279 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:14:57.297285 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:14:57.301091 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-04 00:14:57.30343 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:15:00.274926 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:15:00.27654 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/chunks/chunk_000001/logs/progress.log
2024-05-04 00:15:03.211948 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-05-04 00:15:03.21402 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/chunks/chunk_000002/logs/progress.log
2024-05-04 00:15:06.032706 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2024-05-04 00:15:06.034841 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/chunks/chunk_000003/logs/progress.log
2024-05-04 00:15:08.75263 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2024-05-04 00:15:08.777642 DEBUG::tools.R/processChunks: done
2024-05-04 00:15:08.781831 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:15:08.784145 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.adapter_contaminated_1.RData
2024-05-04 00:15:08.786977 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:15:08.788538 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.adapter_contaminated_2.RData
2024-05-04 00:15:08.797336 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
2024-05-04 00:15:08.799676 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.summary_preprocess.tab
2024-05-04 00:15:08.802969 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:15:08.806901 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:15:08.809894 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/reports/shortReadReport_1 ...
2024-05-04 00:15:10.113153 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/reports/shortReadReport_2 ...
2024-05-04 00:15:11.156255 INFO::preprocessReads.R/preprocessReads: done
2024-05-04 00:15:11.232605 INFO::alignReads.R/alignReads: starting alignment...
2024-05-04 00:15:11.238771 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:15:14.27828 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:15:14.279917 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/chunks/chunk_000001/logs/progress.log
2024-05-04 00:15:17.199462 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-05-04 00:15:17.201564 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/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.
2024-05-04 00:15:19.865245 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-05-04 00:15:19.867323 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/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.
2024-05-04 00:15:22.531371 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-05-04 00:15:22.533922 DEBUG::tools.R/processChunks: done
2024-05-04 00:15:22.535402 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2024-05-04 00:15:22.772935 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-04 00:15:22.782655 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.summary_alignment.tab
2024-05-04 00:15:22.790684 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.summary_analyzed_bamstats.tab
2024-05-04 00:15:22.792619 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-04 00:15:23.047032 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.8e5cd4a612d0a/results/test_pe.summary_target_lengths.tab
2024-05-04 00:15:23.095556 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-04 00:15:23.096778 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:15:23.351137 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:15:23.355052 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:15:23.432468 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2024-05-04 00:15:23.438236 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:15:23.4415 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-04 00:15:23.443682 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:15:26.295993 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:15:26.297434 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/chunks/chunk_000001/logs/progress.log
2024-05-04 00:15:28.978923 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2024-05-04 00:15:28.980202 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/chunks/chunk_000002/logs/progress.log
2024-05-04 00:15:31.71809 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-05-04 00:15:31.72017 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/chunks/chunk_000003/logs/progress.log
2024-05-04 00:15:34.497587 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-05-04 00:15:34.499121 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/chunks/chunk_000004/logs/progress.log
2024-05-04 00:15:37.195279 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2024-05-04 00:15:37.229733 DEBUG::tools.R/processChunks: done
2024-05-04 00:15:37.233618 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:15:37.236286 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/results/test_pe.adapter_contaminated_1.RData
2024-05-04 00:15:37.239519 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:15:37.241332 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/results/test_pe.adapter_contaminated_2.RData
2024-05-04 00:15:37.25347 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
2024-05-04 00:15:37.255919 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/results/test_pe.summary_preprocess.tab
2024-05-04 00:15:37.259653 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:15:37.264059 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:15:37.267239 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/reports/shortReadReport_1 ...
2024-05-04 00:15:38.563593 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.alignReads.sparsechunks.8e5cd39f0d2d/reports/shortReadReport_2 ...
2024-05-04 00:15:39.533343 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:15:39.7115 INFO::alignReads.R/alignReadsChunk: running gsnap...
2024-05-04 00:15:39.716273 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 /tmp/RtmpiPLrBl/test.alignReadsOneSingleEnd.8e5cd46971aa5/bams/test.alignReads /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2024-05-04 00:15:39.937717 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2024-05-04 00:15:40.029772 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReadsOneSingleEnd.8e5cd46971aa5/results/test.alignReads.summary_alignment.tab
2024-05-04 00:15:40.071811 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.alignReadsOneSingleEnd.8e5cd46971aa5/results/test.alignReads.summary_analyzed_bamstats.tab
2024-05-04 00:15:40.073451 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0 0.002
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= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:15:40.362828 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.genotype.8e5cd7a146142/results/test_pe.coverage.RData
2024-05-04 00:15:40.364606 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiPLrBl/test.genotype.8e5cd7a146142/results/test_pe.coverage.bw
2024-05-04 00:15:40.478503 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.genotype.8e5cd7a146142/results/test_pe.summary_coverage.tab
2024-05-04 00:15:40.480289 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:15:50.766113 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:15:50.851002 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:15:50.867348 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:15:50.868841 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.genotype.8e5cd7a146142/results/test_pe.raw_variants.RData
2024-05-04 00:15:50.871228 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.genotype.8e5cd7a146142/results/test_pe.filtered_variants.RData
2024-05-04 00:15:50.872506 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-04 00:15:50.873665 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:15:51.267804 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-04 00:15:51.269314 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2024-05-04 00:16:46.790871 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:16:47.250937 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-04 00:16:47.251969 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= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:16:47.703733 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:16:57.856356 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:16:57.937571 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:16:57.955552 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:16:57.957183 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.8e5cd74e27a0f/results/test_pe.raw_variants.RData
2024-05-04 00:16:57.959756 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.8e5cd74e27a0f/results/test_pe.filtered_variants.RData
2024-05-04 00:16:57.961249 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:16:58.115008 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:17:08.464527 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:17:08.522703 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:17:08.539545 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:17:08.540972 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.filters.8e5cd7dddfb66/results/test_pe.raw_variants.RData
2024-05-04 00:17:08.543397 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.filters.8e5cd7dddfb66/results/test_pe.filtered_variants.RData
2024-05-04 00:17:08.544653 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-04 00:17:08.546165 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:17:18.630251 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:17:18.668053 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:17:18.684443 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:17:18.685909 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.filters.8e5cd7dddfb66/results/test_pe.raw_variants.RData
2024-05-04 00:17:18.688552 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.filters.8e5cd7dddfb66/results/test_pe.filtered_variants.RData
2024-05-04 00:17:18.690616 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:17:18.947925 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:17:18.949456 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2024-05-04 00:17:22.228167 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:17:22.303983 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:17:22.32231 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:17:22.323751 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.which.8e5cd8b08479/results/test_pe.raw_variants.RData
2024-05-04 00:17:22.325438 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.wrap.callVariants.which.8e5cd8b08479/results/test_pe.filtered_variants.RData
2024-05-04 00:17:22.326718 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:17:22.468819 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:17:22.47019 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:17:24.310781 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:17:24.52137 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  ... 2024-05-04 00:18:16.852803 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/uqxalpos/merged/results/bla.coverage.RData
2024-05-04 00:18:16.855507 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiPLrBl/uqxalpos/merged/results/bla.coverage.bw
2024-05-04 00:18:16.930755 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/uqxalpos/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2024-05-04 00:18:18.100232 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/jefmgbuc/merged/results/bla.coverage.RData
2024-05-04 00:18:18.101899 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiPLrBl/jefmgbuc/merged/results/bla.coverage.bw
2024-05-04 00:18:18.113111 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/jefmgbuc/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



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



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



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



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



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



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



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



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:19.370552 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-05-04 00:18:19.371674 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiPLrBl/test.detectRRNA.8e5cd21e47230/bams/rRNA_contam/input1.fastq
2024-05-04 00:18:19.374835 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 /tmp/RtmpiPLrBl/test.detectRRNA.8e5cd21e47230/bams/rRNA_contam/test_se /tmp/RtmpiPLrBl/test.detectRRNA.8e5cd21e47230/bams/rRNA_contam/input1.fastq 2>&1
2024-05-04 00:18:19.649477 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-05-04 00:18:19.650568 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:19.802733 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-05-04 00:18:19.803766 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiPLrBl/test.detectRRNA.paired_end.8e5cd721a2dad/bams/rRNA_contam/input1.fastq
2024-05-04 00:18:19.805315 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiPLrBl/test.detectRRNA.paired_end.8e5cd721a2dad/bams/rRNA_contam/input2.fastq
2024-05-04 00:18:19.80748 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 /tmp/RtmpiPLrBl/test.detectRRNA.paired_end.8e5cd721a2dad/bams/rRNA_contam/test_pe /tmp/RtmpiPLrBl/test.detectRRNA.paired_end.8e5cd721a2dad/bams/rRNA_contam/input1.fastq -a paired /tmp/RtmpiPLrBl/test.detectRRNA.paired_end.8e5cd721a2dad/bams/rRNA_contam/input2.fastq 2>&1
2024-05-04 00:18:20.101756 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-05-04 00:18:20.102738 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2024-05-04 00:18:20.120911 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 /tmp/RtmpiPLrBl/test_get_rRNA_idstuawgvpk/test_pe /tmp/RtmpiPLrBl/test_get_rRNA_idstuawgvpk/1.fastq -a paired /tmp/RtmpiPLrBl/test_get_rRNA_idstuawgvpk/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2024-05-04 00:18:20.436081 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 /tmp/RtmpiPLrBl/test_get_rRNAIds_randomxwrgqeau/test_pe /tmp/RtmpiPLrBl/test_get_rRNAIds_randomxwrgqeau/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2024-05-04 00:18:20.680065 INFO::filterQuality.R/filterQuality: filterByLength...
2024-05-04 00:18:20.681617 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2024-05-04 00:18:20.682502 INFO::filterQuality.R/filterByLength: done
2024-05-04 00:18:20.727609 INFO::filterQuality.R/filterQuality: filterByLength...
2024-05-04 00:18:20.728558 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2024-05-04 00:18:20.729425 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2024-05-04 00:18:20.777189 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-04 00:18:20.786066 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-04 00:18:20.787231 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-04 00:18:20.791905 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-04 00:18:20.792905 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-04 00:18:20.797331 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-05-04 00:18:20.798267 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-05-04 00:18:20.80259 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



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



Executing test function test.checkGATKJar  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



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



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



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



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



Executing test function test.realignIndelsGATK.parallel  ... Timing stopped at: 0 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= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:21.090303 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:21.092541 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:21.275113 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:21.385744 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-04 00:18:21.388638 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:21.390879 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:21.650129 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:21.809599 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:21.990687 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:22.082384 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-04 00:18:22.085166 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:22.087605 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:22.333894 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:22.386525 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-05-04 00:18:22.389121 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:22.391407 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



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



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



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



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



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:18:23.252067 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:18:23.259781 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:18:23.264094 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-04 00:18:23.266989 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:18:26.537317 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:18:26.538715 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000001/logs/progress.log
2024-05-04 00:18:29.137575 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-04 00:18:29.139554 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000002/logs/progress.log
2024-05-04 00:18:31.710243 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-05-04 00:18:31.711823 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000003/logs/progress.log
2024-05-04 00:18:34.318053 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-05-04 00:18:34.360951 DEBUG::tools.R/processChunks: done
2024-05-04 00:18:34.364142 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:18:34.365896 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.adapter_contaminated_1.RData
2024-05-04 00:18:34.368082 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:18:34.369701 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.adapter_contaminated_2.RData
2024-05-04 00:18:34.378539 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
2024-05-04 00:18:34.380249 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_preprocess.tab
2024-05-04 00:18:34.382657 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:18:34.386446 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:18:34.389646 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/reports/shortReadReport_1 ...
2024-05-04 00:18:35.682539 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/reports/shortReadReport_2 ...
2024-05-04 00:18:36.668021 INFO::preprocessReads.R/preprocessReads: done
2024-05-04 00:18:36.774297 INFO::alignReads.R/alignReads: starting alignment...
2024-05-04 00:18:36.779553 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:18:39.819785 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:18:39.821604 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000001/logs/progress.log
2024-05-04 00:18:42.417361 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-04 00:18:42.418978 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/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.
2024-05-04 00:18:45.063694 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-05-04 00:18:45.065997 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/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.
2024-05-04 00:18:47.694351 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-05-04 00:18:47.699318 DEBUG::tools.R/processChunks: done
2024-05-04 00:18:47.701599 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2024-05-04 00:18:47.884215 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-04 00:18:47.892359 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_alignment.tab
2024-05-04 00:18:47.898995 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_analyzed_bamstats.tab
2024-05-04 00:18:47.900798 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-04 00:18:48.12509 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_target_lengths.tab
2024-05-04 00:18:48.171273 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-04 00:18:48.172321 INFO::alignReads.R/alignReads: done
2024-05-04 00:18:48.253009 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-05-04 00:18:48.276167 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:18:51.456554 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:18:51.458293 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000001/logs/progress.log
2024-05-04 00:18:53.914047 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2024-05-04 00:18:53.916105 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000002/logs/progress.log
2024-05-04 00:18:56.358563 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.041 minutes
2024-05-04 00:18:56.361645 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000003/logs/progress.log
2024-05-04 00:18:58.811049 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2024-05-04 00:18:58.813636 DEBUG::tools.R/processChunks: done
2024-05-04 00:18:58.815329 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-04 00:18:58.829083 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_exon.tab
2024-05-04 00:18:58.841349 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_exon_disjoint.tab
2024-05-04 00:18:58.849262 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_gene.tab
2024-05-04 00:18:58.854625 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_gene_coding.tab
2024-05-04 00:18:58.859631 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_gene_exonic.tab
2024-05-04 00:18:58.864903 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_intergenic.tab
2024-05-04 00:18:58.873814 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.counts_intron.tab
2024-05-04 00:18:58.877049 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-04 00:18:58.882122 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_counts.tab
2024-05-04 00:18:58.883674 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-04 00:18:59.165602 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-04 00:18:59.166471 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-05-04 00:18:59.25983 INFO::coverage.R/calculateCoverage: starting...
2024-05-04 00:18:59.264702 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:19:02.822871 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:19:02.824598 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000001/logs/progress.log
2024-05-04 00:19:04.971953 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2024-05-04 00:19:04.973532 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000002/logs/progress.log
2024-05-04 00:19:07.144102 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2024-05-04 00:19:07.145922 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/chunks/chunk_000003/logs/progress.log
2024-05-04 00:19:09.319959 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2024-05-04 00:19:09.323981 DEBUG::tools.R/processChunks: done
2024-05-04 00:19:10.732483 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.coverage.RData
2024-05-04 00:19:10.733895 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.coverage.bw
2024-05-04 00:19:10.744747 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_coverage.tab
2024-05-04 00:19:10.745987 INFO::coverage.R/calculateCoverage: done
2024-05-04 00:19:10.747729 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-04 00:19:10.821254 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:19:14.673326 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:19:14.742315 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:19:14.75802 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:19:14.759392 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.raw_variants.RData
2024-05-04 00:19:14.761014 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.filtered_variants.RData
2024-05-04 00:19:14.762234 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-04 00:19:14.763161 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:19:14.96877 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-04 00:19:15.061391 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/results/test_pe.summary_variants.tab
2024-05-04 00:19:15.063681 INFO::analyzeVariants/analyzeVariants: done
2024-05-04 00:19:15.067322 INFO::Pipeline run successful.
2024-05-04 00:19:15.242584 INFO::mergeLanes.R/doMergeLanes: starting...
2024-05-04 00:19:15.247734 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:19:15.250113 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.adapter_contaminated_1.RData
2024-05-04 00:19:15.253073 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:19:15.255167 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.adapter_contaminated_2.RData
2024-05-04 00:19:15.267699 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
2024-05-04 00:19:15.270337 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_preprocess.tab
2024-05-04 00:19:15.272864 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2024-05-04 00:19:15.528522 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-04 00:19:15.535728 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_alignment.tab
2024-05-04 00:19:15.543461 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_analyzed_bamstats.tab
2024-05-04 00:19:15.545616 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-04 00:19:15.794952 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_target_lengths.tab
2024-05-04 00:19:15.847988 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-04 00:19:15.891466 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-04 00:19:15.912581 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_exon.tab
2024-05-04 00:19:15.92568 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_exon_disjoint.tab
2024-05-04 00:19:15.933342 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_gene.tab
2024-05-04 00:19:15.939251 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_gene_coding.tab
2024-05-04 00:19:15.94492 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_gene_exonic.tab
2024-05-04 00:19:15.950852 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_intergenic.tab
2024-05-04 00:19:15.963083 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.counts_intron.tab
2024-05-04 00:19:15.96672 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-04 00:19:15.973296 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_counts.tab
2024-05-04 00:19:15.975211 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-04 00:19:16.195728 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-04 00:19:18.740963 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.coverage.RData
2024-05-04 00:19:18.744064 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.coverage.bw
2024-05-04 00:19:18.76228 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_coverage.tab
2024-05-04 00:19:18.801191 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-04 00:19:18.884937 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:19:22.153747 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:19:22.220786 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:19:22.235816 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:19:22.237127 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.raw_variants.RData
2024-05-04 00:19:22.238636 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.filtered_variants.RData
2024-05-04 00:19:22.239801 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-04 00:19:22.240723 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:19:22.438448 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-04 00:19:22.529604 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.mergeLanes.8e5cdc573e82/merged/results/merged.summary_variants.tab
2024-05-04 00:19:22.531804 INFO::analyzeVariants/analyzeVariants: done
2024-05-04 00:19:22.535059 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 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= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:19:22.840369 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:19:22.860637 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:19:22.877366 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-04 00:19:22.880078 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:19:25.912374 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:19:25.913837 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/chunks/chunk_000001/logs/progress.log
2024-05-04 00:19:28.497183 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-05-04 00:19:28.536325 DEBUG::tools.R/processChunks: done
2024-05-04 00:19:28.538939 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:19:28.540562 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/results/test_pe.adapter_contaminated_1.RData
2024-05-04 00:19:28.542378 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:19:28.54382 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/results/test_pe.adapter_contaminated_2.RData
2024-05-04 00:19:28.550608 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
2024-05-04 00:19:28.552346 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/results/test_pe.summary_preprocess.tab
2024-05-04 00:19:28.554326 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:19:28.557713 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:19:28.560718 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/reports/shortReadReport_1 ...
2024-05-04 00:19:29.853262 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.preprocessReads.8e5cd3b20ca7f/reports/shortReadReport_2 ...
2024-05-04 00:19:30.861557 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:19:31.122404 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:19:31.129191 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:19:31.133041 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-05-04 00:19:31.135542 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:19:34.434772 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:19:34.436189 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/chunks/chunk_000001/logs/progress.log
2024-05-04 00:19:37.082052 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2024-05-04 00:19:37.083558 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/chunks/chunk_000002/logs/progress.log
2024-05-04 00:19:39.698079 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-05-04 00:19:39.699615 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/chunks/chunk_000003/logs/progress.log
2024-05-04 00:19:42.366353 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-05-04 00:19:42.424961 DEBUG::tools.R/processChunks: done
2024-05-04 00:19:42.428377 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:19:42.430336 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/results/test_pe.adapter_contaminated_1.RData
2024-05-04 00:19:42.432839 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:19:42.434702 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/results/test_pe.adapter_contaminated_2.RData
2024-05-04 00:19:42.445118 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
2024-05-04 00:19:42.447307 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/results/test_pe.summary_preprocess.tab
2024-05-04 00:19:42.450293 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:19:42.454395 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:19:42.45834 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/reports/shortReadReport_1 ...
2024-05-04 00:19:43.772185 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.preprocessReads.minichunks.8e5cd7773221c/reports/shortReadReport_2 ...
2024-05-04 00:19:44.810709 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:19:45.341839 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:19:45.376541 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-05-04 00:19:45.381311 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:19:54.212658 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:19:54.216085 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiPLrBl/test.preprocessReads_single_end.8e5cdf93edd1/chunks/chunk_000001/logs/progress.log
2024-05-04 00:19:57.178119 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-05-04 00:19:57.214272 DEBUG::tools.R/processChunks: done
2024-05-04 00:19:57.219434 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:19:57.239832 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads_single_end.8e5cdf93edd1/results/test_se.adapter_contaminated_1.RData
2024-05-04 00:19:57.253161 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
2024-05-04 00:19:57.273185 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.preprocessReads_single_end.8e5cdf93edd1/results/test_se.summary_preprocess.tab
2024-05-04 00:19:57.277745 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiPLrBl/test.preprocessReads_single_end.8e5cdf93edd1/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:19:57.319529 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiPLrBl/test.preprocessReads_single_end.8e5cdf93edd1/reports/shortReadReport_1 ...
2024-05-04 00:20:02.887492 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



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



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



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



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



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



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:20:05.144671 INFO::preprocessReads.R/preprocessReads: starting...
2024-05-04 00:20:05.181495 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2024-05-04 00:20:05.244472 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2024-05-04 00:20:05.251266 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:20:10.849649 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:20:10.851965 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-04 00:20:14.198313 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.056 minutes
2024-05-04 00:20:14.302505 DEBUG::tools.R/processChunks: done
2024-05-04 00:20:14.30885 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-05-04 00:20:14.31269 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2024-05-04 00:20:14.316975 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-05-04 00:20:14.320091 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2024-05-04 00:20:14.334337 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
2024-05-04 00:20:14.337944 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2024-05-04 00:20:14.342141 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2024-05-04 00:20:14.350467 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2024-05-04 00:20:14.358454 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2024-05-04 00:20:17.207472 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2024-05-04 00:20:19.131247 INFO::preprocessReads.R/preprocessReads: done
2024-05-04 00:20:19.396368 INFO::alignReads.R/alignReads: starting alignment...
2024-05-04 00:20:19.405655 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:20:25.698772 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:20:25.702001 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.
2024-05-04 00:20:31.252431 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.092 minutes
2024-05-04 00:20:31.256689 DEBUG::tools.R/processChunks: done
2024-05-04 00:20:31.259335 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2024-05-04 00:20:31.315154 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-05-04 00:20:31.326094 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2024-05-04 00:20:31.335355 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2024-05-04 00:20:31.339732 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-05-04 00:20:31.618649 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2024-05-04 00:20:31.707135 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-05-04 00:20:31.709286 INFO::alignReads.R/alignReads: done
2024-05-04 00:20:31.904277 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-05-04 00:20:31.941552 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:20:36.219194 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:20:36.22227 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-04 00:20:38.916548 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2024-05-04 00:20:38.921146 DEBUG::tools.R/processChunks: done
2024-05-04 00:20:38.924381 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-05-04 00:20:38.936596 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2024-05-04 00:20:38.946555 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2024-05-04 00:20:38.953849 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2024-05-04 00:20:38.958559 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2024-05-04 00:20:38.963062 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2024-05-04 00:20:38.967445 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2024-05-04 00:20:38.97447 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2024-05-04 00:20:38.978482 INFO::countGenomicFeatures.R/mergeCounts: done
2024-05-04 00:20:38.982524 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2024-05-04 00:20:38.984465 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-05-04 00:20:39.217681 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-05-04 00:20:39.218723 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-05-04 00:20:39.353949 INFO::coverage.R/calculateCoverage: starting...
2024-05-04 00:20:39.359494 DEBUG::tools.R/processChunks: starting...
2024-05-04 00:20:43.840253 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-05-04 00:20:43.842329 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-05-04 00:20:46.387069 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2024-05-04 00:20:46.39005 DEBUG::tools.R/processChunks: done
2024-05-04 00:20:48.038632 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2024-05-04 00:20:48.040452 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2024-05-04 00:20:48.123569 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2024-05-04 00:20:48.125093 INFO::coverage.R/calculateCoverage: done
2024-05-04 00:20:48.126432 INFO::analyzeVariants/analyzeVariants: starting ...
2024-05-04 00:20:48.203835 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-05-04 00:20:59.025367 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-05-04 00:20:59.093708 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-05-04 00:20:59.10859 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-05-04 00:20:59.109943 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2024-05-04 00:20:59.112585 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2024-05-04 00:20:59.11391 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-05-04 00:20:59.114859 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-05-04 00:20:59.316048 INFO::analyzeVariants.R/writeVCF: ...done
2024-05-04 00:20:59.407946 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2024-05-04 00:20:59.410089 INFO::analyzeVariants/analyzeVariants: done
2024-05-04 00:20:59.418819 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiPLrBl/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-05-04 00:20:59.673975 INFO::io.R/saveWithID: saving file= /tmp/RtmpiPLrBl/test.calcTargetLengths.8e5cd49630652/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 -- Sat May  4 00:21:14 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/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (27.34 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (16.42 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.54 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (67.49 seconds)
test.wrap.callVariants: (4 checks) ... OK (10.39 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (20.73 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (3.64 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.14 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (2.15 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (26.51 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (23.66 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (0.62 seconds)
test.isSparse: (5 checks) ... OK (0.09 seconds)
test.mergeCoverage: (1 checks) ... OK (1.42 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.2 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.14 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.33 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.37 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/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.04 seconds)
test.isAdapter: (5 checks) ... OK (0.12 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.08 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.43 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.45 seconds)
test.getRRNAIds: (1 checks) ... OK (0.31 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.26 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.05 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.04 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.03 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/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 (0.14 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/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.18 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.36 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.16 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.19 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.63 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.16 seconds)
test.getObjectFilename: (4 checks) ... OK (0 seconds)
test.safeUnlink: (2 checks) ... OK (0 seconds)
test.writeAudit: (0 checks) ... OK (0.23 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (59.68 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (8.29 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (13.95 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (18.09 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.59 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.29 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.32 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.17 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (55.12 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.25 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (14.85 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.19-bioc/R/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.05 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.16 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
252.385  87.694 396.095 

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie0.0000.0000.001
buildGenomicFeaturesFromTxDb000
runPipeline0.0010.0000.000