##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HTSeqGenie_4.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.18.0’
* 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 R 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 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 ... OK
* 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

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

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

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: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:20:57 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:20:57 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:20:57 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
2020-10-17 02:20:57 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:20:59 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:20:59 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/chunks/chunk_000001/logs/progress.log
2020-10-17 02:21:02 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.054 minutes
2020-10-17 02:21:02 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/chunks/chunk_000002/logs/progress.log
2020-10-17 02:21:05 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2020-10-17 02:21:05 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/chunks/chunk_000003/logs/progress.log
2020-10-17 02:21:08 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.05 minutes
2020-10-17 02:21:08 DEBUG::tools.R/processChunks: done
2020-10-17 02:21:08 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:21:08 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.adapter_contaminated_1.RData
2020-10-17 02:21:08 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:21:08 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.adapter_contaminated_2.RData
2020-10-17 02:21:08 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
2020-10-17 02:21:08 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.summary_preprocess.tab
2020-10-17 02:21:08 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:21:08 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:21:08 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/reports/shortReadReport_1 ...
2020-10-17 02:21:10 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/reports/shortReadReport_2 ...
2020-10-17 02:21:12 INFO::preprocessReads.R/preprocessReads: done
2020-10-17 02:21:12 INFO::alignReads.R/alignReads: starting alignment...
2020-10-17 02:21:12 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:21:15 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:21:15 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/chunks/chunk_000001/logs/progress.log
2020-10-17 02:21:20 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.084 minutes
2020-10-17 02:21:20 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/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.
2020-10-17 02:21:23 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2020-10-17 02:21:23 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/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.
2020-10-17 02:21:26 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2020-10-17 02:21:26 DEBUG::tools.R/processChunks: done
2020-10-17 02:21:26 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.
2020-10-17 02:21:26 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2020-10-17 02:21:26 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.summary_alignment.tab
2020-10-17 02:21:26 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.summary_analyzed_bamstats.tab
2020-10-17 02:21:26 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2020-10-17 02:21:26 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.46fe1e1d6e58/results/test_pe.summary_target_lengths.tab
2020-10-17 02:21:27 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2020-10-17 02:21:27 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:21:27 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:21:27 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:21:27 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2020-10-17 02:21:27 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:21:27 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
2020-10-17 02:21:27 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:21:30 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:21:30 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/chunks/chunk_000001/logs/progress.log
2020-10-17 02:21:33 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2020-10-17 02:21:33 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/chunks/chunk_000002/logs/progress.log
2020-10-17 02:21:36 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.051 minutes
2020-10-17 02:21:36 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/chunks/chunk_000003/logs/progress.log
2020-10-17 02:21:39 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2020-10-17 02:21:39 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/chunks/chunk_000004/logs/progress.log
2020-10-17 02:21:42 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.051 minutes
2020-10-17 02:21:42 DEBUG::tools.R/processChunks: done
2020-10-17 02:21:42 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:21:42 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/results/test_pe.adapter_contaminated_1.RData
2020-10-17 02:21:42 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:21:42 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/results/test_pe.adapter_contaminated_2.RData
2020-10-17 02:21:42 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
2020-10-17 02:21:42 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/results/test_pe.summary_preprocess.tab
2020-10-17 02:21:42 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:21:42 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:21:42 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/reports/shortReadReport_1 ...
2020-10-17 02:21:44 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.alignReads.sparsechunks.46fe1dd0866b/reports/shortReadReport_2 ...
2020-10-17 02:21:45 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:21:46 INFO::alignReads.R/alignReadsChunk: running gsnap...
2020-10-17 02:21:46 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/RtmpiCkDKD/test.alignReadsOneSingleEnd.46fe178201fa/bams/test.alignReads /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2020-10-17 02:21:46 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2020-10-17 02:21:46 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReadsOneSingleEnd.46fe178201fa/results/test.alignReads.summary_alignment.tab
2020-10-17 02:21:46 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.alignReadsOneSingleEnd.46fe178201fa/results/test.alignReads.summary_analyzed_bamstats.tab
2020-10-17 02:21:46 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0.077 0.08
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: Warning messages:
1: In system("gsnap", ignore.stderr = TRUE) : error in running command
2: In system("samtools", ignore.stderr = TRUE) : error in running command
3: In system("gsnap", ignore.stderr = TRUE) : error in running command
4: In system("samtools", ignore.stderr = TRUE) : error in running command
5: In system("gsnap", ignore.stderr = TRUE) : error in running command
6: In system("samtools", ignore.stderr = TRUE) : error in running command
7: In system2("variant_effect_predictor.pl", "--help", stderr = FALSE,  :
  error in running command
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:21:47 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.genotype.46fe6a7dbac/results/test_pe.coverage.RData
2020-10-17 02:21:47 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiCkDKD/test.genotype.46fe6a7dbac/results/test_pe.coverage.bw
2020-10-17 02:21:47 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.genotype.46fe6a7dbac/results/test_pe.summary_coverage.tab
2020-10-17 02:21:47 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:21:58 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:21:58 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:21:58 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:21:58 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.genotype.46fe6a7dbac/results/test_pe.raw_variants.RData
2020-10-17 02:21:58 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.genotype.46fe6a7dbac/results/test_pe.filtered_variants.RData
2020-10-17 02:21:58 INFO::analyzeVariants.R/wrap.callVariants: ...done
2020-10-17 02:21:58 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:21:59 INFO::analyzeVariants.R/writeVCF: ...done
2020-10-17 02:21:59 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2020-10-17 02:23:25 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:23:25 INFO::analyzeVariants.R/writeVCF: ...done
2020-10-17 02:23:25 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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:23:26 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:23:37 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:23:37 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:23:37 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:23:37 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.46fe6c63812f/results/test_pe.raw_variants.RData
2020-10-17 02:23:37 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.46fe6c63812f/results/test_pe.filtered_variants.RData
2020-10-17 02:23:37 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:23:38 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:23:47 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:23:47 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:23:47 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:23:47 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.filters.46fe326d866c/results/test_pe.raw_variants.RData
2020-10-17 02:23:47 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.filters.46fe326d866c/results/test_pe.filtered_variants.RData
2020-10-17 02:23:47 INFO::analyzeVariants.R/wrap.callVariants: ...done
2020-10-17 02:23:47 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:23:58 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:23:58 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:23:58 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:23:58 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.filters.46fe326d866c/results/test_pe.raw_variants.RData
2020-10-17 02:23:58 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.filters.46fe326d866c/results/test_pe.filtered_variants.RData
2020-10-17 02:23:58 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.parallel  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:23:58 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:24:04 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:24:04 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:24:04 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:24:04 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.parallel.46fe2f8f901a/results/test_pe.raw_variants.RData
2020-10-17 02:24:04 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.parallel.46fe2f8f901a/results/test_pe.filtered_variants.RData
2020-10-17 02:24:04 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:24:05 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:24:05 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2020-10-17 02:24:07 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:24:07 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:24:07 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:24:07 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.which.46fe5543512d/results/test_pe.raw_variants.RData
2020-10-17 02:24:07 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.wrap.callVariants.which.46fe5543512d/results/test_pe.filtered_variants.RData
2020-10-17 02:24:07 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:24:07 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:24:07 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:24:08 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:24:08 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  ... 2020-10-17 02:25:12 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/awczkgis/merged/results/bla.coverage.RData
2020-10-17 02:25:12 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiCkDKD/awczkgis/merged/results/bla.coverage.bw
2020-10-17 02:25:12 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/awczkgis/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2020-10-17 02:25:13 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/rtwhvuxk/merged/results/bla.coverage.RData
2020-10-17 02:25:13 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiCkDKD/rtwhvuxk/merged/results/bla.coverage.bw
2020-10-17 02:25:13 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/rtwhvuxk/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:15 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2020-10-17 02:25:15 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiCkDKD/test.detectRRNA.46fe3dd196f4/bams/rRNA_contam/input1.fastq
2020-10-17 02:25:15 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/RtmpiCkDKD/test.detectRRNA.46fe3dd196f4/bams/rRNA_contam/test_se /tmp/RtmpiCkDKD/test.detectRRNA.46fe3dd196f4/bams/rRNA_contam/input1.fastq 2>&1
2020-10-17 02:25:16 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2020-10-17 02:25:16 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:16 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2020-10-17 02:25:16 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiCkDKD/test.detectRRNA.paired_end.46fe7e216988/bams/rRNA_contam/input1.fastq
2020-10-17 02:25:16 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpiCkDKD/test.detectRRNA.paired_end.46fe7e216988/bams/rRNA_contam/input2.fastq
2020-10-17 02:25:16 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/RtmpiCkDKD/test.detectRRNA.paired_end.46fe7e216988/bams/rRNA_contam/test_pe /tmp/RtmpiCkDKD/test.detectRRNA.paired_end.46fe7e216988/bams/rRNA_contam/input1.fastq -a paired /tmp/RtmpiCkDKD/test.detectRRNA.paired_end.46fe7e216988/bams/rRNA_contam/input2.fastq 2>&1
2020-10-17 02:25:17 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2020-10-17 02:25:17 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2020-10-17 02:25:17 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/RtmpiCkDKD/test_get_rRNA_idskrsaoyfx/test_pe /tmp/RtmpiCkDKD/test_get_rRNA_idskrsaoyfx/1.fastq -a paired /tmp/RtmpiCkDKD/test_get_rRNA_idskrsaoyfx/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2020-10-17 02:25:17 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/RtmpiCkDKD/test_get_rRNAIds_randomjvmrbhln/test_pe /tmp/RtmpiCkDKD/test_get_rRNAIds_randomjvmrbhln/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2020-10-17 02:25:18 INFO::filterQuality.R/filterQuality: filterByLength...
2020-10-17 02:25:18 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2020-10-17 02:25:18 INFO::filterQuality.R/filterByLength: done
2020-10-17 02:25:18 INFO::filterQuality.R/filterQuality: filterByLength...
2020-10-17 02:25:18 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2020-10-17 02:25:18 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: done
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: done
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: done
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2020-10-17 02:25:18 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 31 warnings (use warnings() to see them)
 done successfully.



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



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



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



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



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



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



Executing test function test.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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:18 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:18 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:19 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:19 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2020-10-17 02:25:19 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:19 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:19 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:20 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:20 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:22 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:25:24 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:25:24 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:25:24 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
2020-10-17 02:25:24 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:25:27 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:25:27 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000001/logs/progress.log
2020-10-17 02:25:29 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2020-10-17 02:25:29 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000002/logs/progress.log
2020-10-17 02:25:32 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2020-10-17 02:25:32 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000003/logs/progress.log
2020-10-17 02:25:35 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2020-10-17 02:25:35 DEBUG::tools.R/processChunks: done
2020-10-17 02:25:35 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:25:35 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.adapter_contaminated_1.RData
2020-10-17 02:25:35 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:25:35 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.adapter_contaminated_2.RData
2020-10-17 02:25:35 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
2020-10-17 02:25:35 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_preprocess.tab
2020-10-17 02:25:35 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:25:35 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:25:35 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/reports/shortReadReport_1 ...
2020-10-17 02:25:37 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/reports/shortReadReport_2 ...
2020-10-17 02:25:38 INFO::preprocessReads.R/preprocessReads: done
2020-10-17 02:25:38 INFO::alignReads.R/alignReads: starting alignment...
2020-10-17 02:25:38 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:25:41 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:25:41 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000001/logs/progress.log
2020-10-17 02:25:44 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2020-10-17 02:25:44 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/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.
2020-10-17 02:25:47 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2020-10-17 02:25:47 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/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.
2020-10-17 02:25:50 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2020-10-17 02:25:50 DEBUG::tools.R/processChunks: done
2020-10-17 02:25:50 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.
2020-10-17 02:25:50 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2020-10-17 02:25:50 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_alignment.tab
2020-10-17 02:25:50 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_analyzed_bamstats.tab
2020-10-17 02:25:50 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2020-10-17 02:25:51 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_target_lengths.tab
2020-10-17 02:25:51 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2020-10-17 02:25:51 INFO::alignReads.R/alignReads: done
2020-10-17 02:25:51 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2020-10-17 02:25:51 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:25:54 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:25:54 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000001/logs/progress.log
2020-10-17 02:26:00 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.097 minutes
2020-10-17 02:26:00 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000002/logs/progress.log
2020-10-17 02:26:05 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.083 minutes
2020-10-17 02:26:05 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000003/logs/progress.log
2020-10-17 02:26:10 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.086 minutes
2020-10-17 02:26:10 DEBUG::tools.R/processChunks: done
2020-10-17 02:26:10 INFO::countGenomicFeatures.R/mergeCounts: starting...
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_exon.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_exon_disjoint.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_gene.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_gene_coding.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_gene_exonic.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_intergenic.tab
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.counts_intron.tab
2020-10-17 02:26:10 INFO::countGenomicFeatures.R/mergeCounts: done
2020-10-17 02:26:10 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_counts.tab
2020-10-17 02:26:10 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2020-10-17 02:26:10 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2020-10-17 02:26:10 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2020-10-17 02:26:10 INFO::coverage.R/calculateCoverage: starting...
2020-10-17 02:26:10 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:26:13 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:26:13 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000001/logs/progress.log
2020-10-17 02:26:15 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2020-10-17 02:26:15 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000002/logs/progress.log
2020-10-17 02:26:17 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2020-10-17 02:26:17 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/chunks/chunk_000003/logs/progress.log
2020-10-17 02:26:20 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2020-10-17 02:26:20 DEBUG::tools.R/processChunks: done
2020-10-17 02:26:21 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.coverage.RData
2020-10-17 02:26:21 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.coverage.bw
2020-10-17 02:26:21 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_coverage.tab
2020-10-17 02:26:21 INFO::coverage.R/calculateCoverage: done
2020-10-17 02:26:21 INFO::analyzeVariants/analyzeVariants: starting ...
2020-10-17 02:26:21 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:26:23 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:26:23 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:26:23 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:26:23 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.raw_variants.RData
2020-10-17 02:26:23 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.filtered_variants.RData
2020-10-17 02:26:23 INFO::analyzeVariants.R/wrap.callVariants: ...done
2020-10-17 02:26:23 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:26:23 INFO::analyzeVariants.R/writeVCF: ...done
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/results/test_pe.summary_variants.tab
2020-10-17 02:26:24 INFO::analyzeVariants/analyzeVariants: done
2020-10-17 02:26:24 INFO::Pipeline run successful.
2020-10-17 02:26:24 INFO::mergeLanes.R/doMergeLanes: starting...
2020-10-17 02:26:24 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.adapter_contaminated_1.RData
2020-10-17 02:26:24 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.adapter_contaminated_2.RData
2020-10-17 02:26:24 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
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_preprocess.tab
2020-10-17 02:26:24 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.
2020-10-17 02:26:24 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_alignment.tab
2020-10-17 02:26:24 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_analyzed_bamstats.tab
2020-10-17 02:26:25 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_target_lengths.tab
2020-10-17 02:26:25 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2020-10-17 02:26:25 INFO::countGenomicFeatures.R/mergeCounts: starting...
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_exon.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_exon_disjoint.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_gene.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_gene_coding.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_gene_exonic.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_intergenic.tab
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.counts_intron.tab
2020-10-17 02:26:25 INFO::countGenomicFeatures.R/mergeCounts: done
2020-10-17 02:26:25 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_counts.tab
2020-10-17 02:26:25 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2020-10-17 02:26:25 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2020-10-17 02:26:27 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.coverage.RData
2020-10-17 02:26:27 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.coverage.bw
2020-10-17 02:26:27 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_coverage.tab
2020-10-17 02:26:27 INFO::analyzeVariants/analyzeVariants: starting ...
2020-10-17 02:26:27 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:26:29 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:26:29 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:26:29 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:26:29 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.raw_variants.RData
2020-10-17 02:26:29 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.filtered_variants.RData
2020-10-17 02:26:29 INFO::analyzeVariants.R/wrap.callVariants: ...done
2020-10-17 02:26:29 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:26:29 INFO::analyzeVariants.R/writeVCF: ...done
2020-10-17 02:26:30 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.mergeLanes.46fe7f71c9fd/merged/results/merged.summary_variants.tab
2020-10-17 02:26:30 INFO::analyzeVariants/analyzeVariants: done
2020-10-17 02:26:30 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 22 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0.001 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/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:26:32 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:26:32 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:26:32 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
2020-10-17 02:26:32 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:26:34 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:26:34 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/chunks/chunk_000001/logs/progress.log
2020-10-17 02:26:37 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2020-10-17 02:26:37 DEBUG::tools.R/processChunks: done
2020-10-17 02:26:37 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:26:37 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/results/test_pe.adapter_contaminated_1.RData
2020-10-17 02:26:37 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:26:37 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/results/test_pe.adapter_contaminated_2.RData
2020-10-17 02:26:37 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
2020-10-17 02:26:37 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/results/test_pe.summary_preprocess.tab
2020-10-17 02:26:37 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:26:37 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:26:38 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/reports/shortReadReport_1 ...
2020-10-17 02:26:39 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.preprocessReads.46fe606ad3dd/reports/shortReadReport_2 ...
2020-10-17 02:26:40 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:26:41 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:26:41 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:26:41 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
2020-10-17 02:26:41 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:26:43 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:26:43 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/chunks/chunk_000001/logs/progress.log
2020-10-17 02:26:46 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2020-10-17 02:26:46 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/chunks/chunk_000002/logs/progress.log
2020-10-17 02:26:49 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2020-10-17 02:26:49 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/chunks/chunk_000003/logs/progress.log
2020-10-17 02:26:52 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2020-10-17 02:26:52 DEBUG::tools.R/processChunks: done
2020-10-17 02:26:52 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:26:52 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/results/test_pe.adapter_contaminated_1.RData
2020-10-17 02:26:52 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:26:52 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/results/test_pe.adapter_contaminated_2.RData
2020-10-17 02:26:52 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
2020-10-17 02:26:52 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/results/test_pe.summary_preprocess.tab
2020-10-17 02:26:52 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:26:52 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:26:52 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/reports/shortReadReport_1 ...
2020-10-17 02:26:54 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.preprocessReads.minichunks.46fe36a1dbca/reports/shortReadReport_2 ...
2020-10-17 02:26:55 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:26:55 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:26:55 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
2020-10-17 02:26:55 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:26:58 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:26:58 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpiCkDKD/test.preprocessReads_single_end.46fe71f8d005/chunks/chunk_000001/logs/progress.log
2020-10-17 02:27:00 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2020-10-17 02:27:00 DEBUG::tools.R/processChunks: done
2020-10-17 02:27:00 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:27:00 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads_single_end.46fe71f8d005/results/test_se.adapter_contaminated_1.RData
2020-10-17 02:27:00 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
2020-10-17 02:27:00 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.preprocessReads_single_end.46fe71f8d005/results/test_se.summary_preprocess.tab
2020-10-17 02:27:00 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpiCkDKD/test.preprocessReads_single_end.46fe71f8d005/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:27:00 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpiCkDKD/test.preprocessReads_single_end.46fe71f8d005/reports/shortReadReport_1 ...
2020-10-17 02:27:02 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-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:27:03 INFO::preprocessReads.R/preprocessReads: starting...
2020-10-17 02:27:03 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2020-10-17 02:27:03 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2020-10-17 02:27:03 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:27:06 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:27:06 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2020-10-17 02:27:09 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.054 minutes
2020-10-17 02:27:09 DEBUG::tools.R/processChunks: done
2020-10-17 02:27:09 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2020-10-17 02:27:09 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2020-10-17 02:27:09 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2020-10-17 02:27:09 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2020-10-17 02:27:09 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
2020-10-17 02:27:09 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2020-10-17 02:27:09 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2020-10-17 02:27:09 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2020-10-17 02:27:09 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2020-10-17 02:27:12 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2020-10-17 02:27:13 INFO::preprocessReads.R/preprocessReads: done
2020-10-17 02:27:14 INFO::alignReads.R/alignReads: starting alignment...
2020-10-17 02:27:14 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:27:16 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:27:16 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.
2020-10-17 02:27:22 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.088 minutes
2020-10-17 02:27:22 DEBUG::tools.R/processChunks: done
2020-10-17 02:27:22 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2020-10-17 02:27:22 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2020-10-17 02:27:22 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2020-10-17 02:27:22 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2020-10-17 02:27:22 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2020-10-17 02:27:22 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2020-10-17 02:27:22 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2020-10-17 02:27:22 INFO::alignReads.R/alignReads: done
2020-10-17 02:27:22 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2020-10-17 02:27:22 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:27:25 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:27:25 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2020-10-17 02:27:30 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.082 minutes
2020-10-17 02:27:30 DEBUG::tools.R/processChunks: done
2020-10-17 02:27:30 INFO::countGenomicFeatures.R/mergeCounts: starting...
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2020-10-17 02:27:30 INFO::countGenomicFeatures.R/mergeCounts: done
2020-10-17 02:27:30 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2020-10-17 02:27:30 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2020-10-17 02:27:31 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2020-10-17 02:27:31 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2020-10-17 02:27:31 INFO::coverage.R/calculateCoverage: starting...
2020-10-17 02:27:31 DEBUG::tools.R/processChunks: starting...
2020-10-17 02:27:33 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2020-10-17 02:27:33 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2020-10-17 02:27:36 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2020-10-17 02:27:36 DEBUG::tools.R/processChunks: done
2020-10-17 02:27:37 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2020-10-17 02:27:37 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2020-10-17 02:27:37 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2020-10-17 02:27:37 INFO::coverage.R/calculateCoverage: done
2020-10-17 02:27:37 INFO::analyzeVariants/analyzeVariants: starting ...
2020-10-17 02:27:37 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2020-10-17 02:27:47 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2020-10-17 02:27:47 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2020-10-17 02:27:47 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2020-10-17 02:27:47 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2020-10-17 02:27:47 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2020-10-17 02:27:47 INFO::analyzeVariants.R/wrap.callVariants: ...done
2020-10-17 02:27:47 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2020-10-17 02:27:47 INFO::analyzeVariants.R/writeVCF: ...done
2020-10-17 02:27:48 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2020-10-17 02:27:48 INFO::analyzeVariants/analyzeVariants: done
2020-10-17 02:27:48 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpiCkDKD/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/config/default-config.txt 
2020-10-17 02:27:48 INFO::io.R/saveWithID: saving file= /tmp/RtmpiCkDKD/test.calcTargetLengths.46fe2ff50dc1/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 Oct 17 02:28:04 2020 
*********************************************** 
Number of test functions: 62 
Number of deactivated test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HTSeqGenie unit testing - 62 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-3.11-bioc/R/library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (31.44 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (18.63 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.93 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (99.69 seconds)
test.wrap.callVariants: (4 checks) ... OK (10.98 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (21.17 seconds)
test.wrap.callVariants.parallel: (1 checks) ... OK (6.29 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (2.4 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.41 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (1.1 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (31.65 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (29.84 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (0.74 seconds)
test.isSparse: (5 checks) ... OK (0.11 seconds)
test.mergeCoverage: (1 checks) ... OK (1.21 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.11 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.39 seconds)
test.findTemplate: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.55 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.79 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-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.08 seconds)
test.isAdapter: (5 checks) ... OK (0.21 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.1 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.6 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.9 seconds)
test.getRRNAIds: (1 checks) ... OK (0.51 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.36 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.gatk.R 
test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set
test.excludeVariantsByRegion: (3 checks) ... OK (0.23 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.42 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.57 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.39 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.4 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (2.5 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.21 seconds)
test.getObjectFilename: (4 checks) ... OK (0.17 seconds)
test.safeUnlink: (2 checks) ... OK (0.19 seconds)
test.writeAudit: (0 checks) ... OK (0.59 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (67.12 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (9.01 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (14.52 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (7.11 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.12 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.14 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.19 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.07 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (45.29 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.54 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (15.27 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.11-bioc/R/library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.06 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.17 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
322.367  75.363 447.548