| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:40 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 976/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jens Reeder
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the HTSeqGenie package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: HTSeqGenie |
| Version: 4.37.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.37.1.tar.gz |
| StartedAt: 2025-01-10 22:59:45 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 23:39:46 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 2400.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: HTSeqGenie.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.37.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
‘data’
.plot.in.out.min.max.readlength: no visible global function definition
for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
‘ranges’
buildTP53FastaGenome: no visible global function definition for
‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
‘sjobs’
processChunks : tracefun: no visible binding for global variable
‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
Views chunkid coverage data gaps getSeq logging.file logging.handlers
logging.loglevel median quantile ranges resize seqinfo sjobs subseq
viewMeans
Consider adding
importFrom("stats", "median", "quantile")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
| ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
18 | Setup logging file in {save_dir}/progress.log
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
‘dir_path’
Documented arguments not in \usage in Rd file 'logdebug.Rd':
‘...’
Documented arguments not in \usage in Rd file 'logerror.Rd':
‘...’
Documented arguments not in \usage in Rd file 'loginfo.Rd':
‘...’
Documented arguments not in \usage in Rd file 'logwarn.Rd':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
HTSeqGenie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HTSeqGenie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘HTSeqGenie’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'HTSeqGenie' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'HTSeqGenie' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (HTSeqGenie)
HTSeqGenie.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Warning message:
In fun(libname, pkgname) :
Package 'HTSeqGenie' is deprecated and will be removed from
Bioconductor version 3.22
>
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R
Executing test function test.alignReads ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:05:38.436816 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:05:38.445522 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:05:38.449482 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-10 23:05:38.451727 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:05:41.876893 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:05:41.878283 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000001/logs/progress.log
2025-01-10 23:05:44.626976 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-10 23:05:44.628573 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000002/logs/progress.log
2025-01-10 23:05:47.380398 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-10 23:05:47.381951 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000003/logs/progress.log
2025-01-10 23:05:50.137029 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-10 23:05:50.189329 DEBUG::tools.R/processChunks: done
2025-01-10 23:05:50.195292 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:05:50.198762 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.adapter_contaminated_1.RData
2025-01-10 23:05:50.202984 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:05:50.205848 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.adapter_contaminated_2.RData
2025-01-10 23:05:50.219646 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:05:50.223319 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.summary_preprocess.tab
2025-01-10 23:05:50.228921 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:05:50.236878 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:05:50.242685 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/reports/shortReadReport_1 ...
2025-01-10 23:05:51.666314 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/reports/shortReadReport_2 ...
2025-01-10 23:05:54.161015 INFO::preprocessReads.R/preprocessReads: done
2025-01-10 23:05:54.251261 INFO::alignReads.R/alignReads: starting alignment...
2025-01-10 23:05:54.257626 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:05:57.496227 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:05:57.497881 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000001/logs/progress.log
2025-01-10 23:06:00.328539 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-10 23:06:00.33004 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:06:03.001279 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-10 23:06:03.003227 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:06:05.668075 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-10 23:06:05.670491 DEBUG::tools.R/processChunks: done
2025-01-10 23:06:05.671898 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:06:05.87566 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-10 23:06:05.883373 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.summary_alignment.tab
2025-01-10 23:06:05.890095 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.summary_analyzed_bamstats.tab
2025-01-10 23:06:05.891726 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-10 23:06:06.123855 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.22398a43539c61/results/test_pe.summary_target_lengths.tab
2025-01-10 23:06:06.171031 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-10 23:06:06.172074 INFO::alignReads.R/alignReads: done
done successfully.
Executing test function test.alignReads.sparsechunks ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:06:06.466305 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:06:06.470162 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:06:06.550944 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-10 23:06:06.556677 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:06:06.560008 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-10 23:06:06.56244 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:06:09.758705 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:06:09.760161 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/chunks/chunk_000001/logs/progress.log
2025-01-10 23:06:12.639713 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-10 23:06:12.641156 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/chunks/chunk_000002/logs/progress.log
2025-01-10 23:06:15.369297 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-10 23:06:15.370763 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/chunks/chunk_000003/logs/progress.log
2025-01-10 23:06:18.172699 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-01-10 23:06:18.174419 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/chunks/chunk_000004/logs/progress.log
2025-01-10 23:06:20.866225 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-01-10 23:06:20.910109 DEBUG::tools.R/processChunks: done
2025-01-10 23:06:20.915093 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:06:20.918447 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/results/test_pe.adapter_contaminated_1.RData
2025-01-10 23:06:20.92281 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:06:20.925542 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/results/test_pe.adapter_contaminated_2.RData
2025-01-10 23:06:20.940525 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:06:20.943902 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/results/test_pe.summary_preprocess.tab
2025-01-10 23:06:20.949169 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:06:20.957562 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:06:20.967505 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/reports/shortReadReport_1 ...
2025-01-10 23:06:22.293532 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.alignReads.sparsechunks.22398a3e47c3e/reports/shortReadReport_2 ...
2025-01-10 23:06:24.733665 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.alignReadsOneSingleEnd ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:06:24.933282 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-10 23:06:24.937977 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/RtmpPBMldF/test.alignReadsOneSingleEnd.22398a14b485bf/bams/test.alignReads /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-01-10 23:06:25.177069 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-10 23:06:25.274038 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReadsOneSingleEnd.22398a14b485bf/results/test.alignReads.summary_alignment.tab
2025-01-10 23:06:25.342373 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.alignReadsOneSingleEnd.22398a14b485bf/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-10 23:06:25.344159 INFO::alignReads.R/alignReadsChunk: done
done successfully.
Executing test function test.annotateVariants ... Timing stopped at: 0 0.003 0.003
Error in DEACTIVATED("Skipped annotateVariants() test") :
Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
done successfully.
Executing test function test.callVariantsVariantTools.genotype ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:06:25.691026 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.genotype.22398a4c02167a/results/test_pe.coverage.RData
2025-01-10 23:06:25.692915 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpPBMldF/test.genotype.22398a4c02167a/results/test_pe.coverage.bw
2025-01-10 23:06:25.826371 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.genotype.22398a4c02167a/results/test_pe.summary_coverage.tab
2025-01-10 23:06:25.828184 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:06:36.675711 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:06:36.765337 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:06:36.783224 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:06:36.785075 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.genotype.22398a4c02167a/results/test_pe.raw_variants.RData
2025-01-10 23:06:36.787897 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.genotype.22398a4c02167a/results/test_pe.filtered_variants.RData
2025-01-10 23:06:36.789485 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-10 23:06:36.790862 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:06:37.229612 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-10 23:06:37.23118 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-10 23:07:40.336935 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:07:40.730438 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-10 23:07:40.731338 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/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:07:41.138939 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:07:51.375396 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:07:51.455023 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:07:51.473531 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:07:51.47507 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.22398a43ef7308/results/test_pe.raw_variants.RData
2025-01-10 23:07:51.477517 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.22398a43ef7308/results/test_pe.filtered_variants.RData
2025-01-10 23:07:51.47892 INFO::analyzeVariants.R/wrap.callVariants: ...done
done successfully.
Executing test function test.wrap.callVariants.filters ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:07:51.620961 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:08:03.123926 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:08:03.200701 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:08:03.222474 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:08:03.224282 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.filters.22398a4034817d/results/test_pe.raw_variants.RData
2025-01-10 23:08:03.227311 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.filters.22398a4034817d/results/test_pe.filtered_variants.RData
2025-01-10 23:08:03.229287 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-10 23:08:03.231122 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:08:13.35462 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:08:13.393488 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:08:13.410183 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:08:13.41153 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.filters.22398a4034817d/results/test_pe.raw_variants.RData
2025-01-10 23:08:13.413962 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.filters.22398a4034817d/results/test_pe.filtered_variants.RData
2025-01-10 23:08:13.415894 INFO::analyzeVariants.R/wrap.callVariants: ...done
done successfully.
Executing test function test.wrap.callVariants.which ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:08:13.666573 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:08:13.668059 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-10 23:08:16.454614 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:08:16.536168 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:08:16.55409 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:08:16.555705 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.which.22398a2bcde9c1/results/test_pe.raw_variants.RData
2025-01-10 23:08:16.557477 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.wrap.callVariants.which.22398a2bcde9c1/results/test_pe.filtered_variants.RData
2025-01-10 23:08:16.558835 INFO::analyzeVariants.R/wrap.callVariants: ...done
done successfully.
Executing test function test.writeVCF.NULL ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:08:16.733405 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:08:16.734802 INFO::analyzeVariants.R/writeVCF: ...done
done successfully.
Executing test function test.writeVCF.vcfStat ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:08:16.918583 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:08:17.146908 INFO::analyzeVariants.R/writeVCF: ...done
done successfully.
Executing test function test.isFirstFragment ... done successfully.
Executing test function test.buildCountsGRangesList ... 403 genes were dropped because they have exons located on both strands of the
same reference sequence or on more than one reference sequence, so cannot be
represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
object, or use suppressMessages() to suppress this message.
done successfully.
Executing test function test.generateSingleGeneDERs ... done successfully.
Executing test function test.computeCoverage ... done successfully.
Executing test function test.isSparse ... done successfully.
Executing test function test.mergeCoverage ... 2025-01-10 23:09:09.561887 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/uwrgaelx/merged/results/bla.coverage.RData
2025-01-10 23:09:09.565174 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpPBMldF/uwrgaelx/merged/results/bla.coverage.bw
2025-01-10 23:09:09.651899 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/uwrgaelx/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.mergeCoverage.sparse ... 2025-01-10 23:09:10.844561 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/olqzfanh/merged/results/bla.coverage.RData
2025-01-10 23:09:10.846345 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpPBMldF/olqzfanh/merged/results/bla.coverage.bw
2025-01-10 23:09:10.85845 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/olqzfanh/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.checkConfig.analyzeVariants ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
done successfully.
Executing test function test.findTemplate ... done successfully.
Executing test function test.checkConfig ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
done successfully.
Executing test function test.checkConfig.alignReads ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
done successfully.
Executing test function test.getConfig ... done successfully.
Executing test function test.loadConfig ... done successfully.
Executing test function test.parseDCF ... done successfully.
Executing test function test.updateConfig ... done successfully.
Executing test function test.getAdapterSeqs ... done successfully.
Executing test function test.isAdapter ... done successfully.
Executing test function test.isAdapter3.primeEnd ... done successfully.
Executing test function test.detectRRNA ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:12.13346 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-10 23:09:12.134585 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpPBMldF/test.detectRRNA.22398a63bc8883/bams/rRNA_contam/input1.fastq
2025-01-10 23:09:12.137668 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/RtmpPBMldF/test.detectRRNA.22398a63bc8883/bams/rRNA_contam/test_se /tmp/RtmpPBMldF/test.detectRRNA.22398a63bc8883/bams/rRNA_contam/input1.fastq 2>&1
2025-01-10 23:09:12.309799 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-10 23:09:12.310841 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.detectRRNA.paired_end ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:12.460529 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-10 23:09:12.461535 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpPBMldF/test.detectRRNA.paired_end.22398a6e6ea76/bams/rRNA_contam/input1.fastq
2025-01-10 23:09:12.462997 INFO::io.R/writeFastQFiles: writing filename= /tmp/RtmpPBMldF/test.detectRRNA.paired_end.22398a6e6ea76/bams/rRNA_contam/input2.fastq
2025-01-10 23:09:12.46515 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/RtmpPBMldF/test.detectRRNA.paired_end.22398a6e6ea76/bams/rRNA_contam/test_pe /tmp/RtmpPBMldF/test.detectRRNA.paired_end.22398a6e6ea76/bams/rRNA_contam/input1.fastq -a paired /tmp/RtmpPBMldF/test.detectRRNA.paired_end.22398a6e6ea76/bams/rRNA_contam/input2.fastq 2>&1
2025-01-10 23:09:12.710284 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-10 23:09:12.711325 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.getRRNAIds ... 2025-01-10 23:09:12.730721 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/RtmpPBMldF/test_get_rRNA_idsrkfpwnxb/test_pe /tmp/RtmpPBMldF/test_get_rRNA_idsrkfpwnxb/1.fastq -a paired /tmp/RtmpPBMldF/test_get_rRNA_idsrkfpwnxb/2.fastq 2>&1
done successfully.
Executing test function test.getRRNAIds_random ... 2025-01-10 23:09:12.978597 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/RtmpPBMldF/test_get_rRNAIds_randomyjmalqur/test_pe /tmp/RtmpPBMldF/test_get_rRNAIds_randomyjmalqur/1.fastq 2>&1
done successfully.
Executing test function test.filterByLength ... 2025-01-10 23:09:13.228193 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-10 23:09:13.229666 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-10 23:09:13.230577 INFO::filterQuality.R/filterByLength: done
2025-01-10 23:09:13.277001 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-10 23:09:13.277992 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-10 23:09:13.27895 INFO::filterQuality.R/filterByLength: done
done successfully.
Executing test function test.isAboveQualityThresh ... done successfully.
Executing test function test.trimTailsByQuality ... 2025-01-10 23:09:13.356671 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-10 23:09:13.365642 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-10 23:09:13.366808 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-10 23:09:13.371176 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-10 23:09:13.372208 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-10 23:09:13.376544 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-10 23:09:13.377478 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-10 23:09:13.381718 INFO::preprocessReads.R/preprocessReadsChunk: done
done successfully.
Executing test function test.callVariantsGATK ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") :
callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
done successfully.
Executing test function test.callVariantsGATK.withFiltering ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") :
callVariantsGATK() tests need gatk.path option set
done successfully.
Executing test function test.checkGATKJar ... Timing stopped at: 0 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") :
checkGATKJar() test needs gatk.path option set
done successfully.
Executing test function test.excludeVariantsByRegion ... done successfully.
Executing test function test.gatk ... Timing stopped at: 0 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") :
gatk() tests need gatk.path option set
done successfully.
Executing test function test.realignIndels ... Timing stopped at: 0 0 0
Error in DEACTIVATED("test.realignIndels() tests need gatk.path option set") :
test.realignIndels() tests need gatk.path option set
done successfully.
Executing test function test.realignIndelsGATK ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") :
realignIndelsGATK() tests need gatk.path option set
done successfully.
Executing test function test.realignIndelsGATK.parallel ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") :
realignIndelsGATK() tests need gatk.path option set
done successfully.
Executing test function test_zipUp ... done successfully.
Executing test function test.FastQStreamer.getReads.pefq ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:13.698865 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:13.701369 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
done successfully.
Executing test function test.FastQStreamer.getReads.pefq.subsample ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:13.874223 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:13.970639 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-10 23:09:13.973487 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:13.975739 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
done successfully.
Executing test function test.FastQStreamer.getReads.segz ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:15.327241 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/reads.fastq.gz
done successfully.
Executing test function test.FastQStreamer.getReads.truncated ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:15.514238 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/truncated.fastq.gz
done successfully.
Executing test function test.FastQStreamer.subsampler.isdeterministic ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:15.69403 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:15.778016 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-10 23:09:15.782272 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:15.786087 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:16.000899 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:16.044674 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-10 23:09:16.047086 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:16.049264 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
done successfully.
Executing test function test.createTmpDir ... done successfully.
Executing test function test.detectQualityInFASTQFile ... done successfully.
Executing test function test.getObjectFilename ... done successfully.
Executing test function test.safeUnlink ... done successfully.
Executing test function test.writeAudit ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
done successfully.
Executing test function test.mergeLanes ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:09:16.78725 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:09:16.793297 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:09:16.796798 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-10 23:09:16.799186 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:09:19.728962 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:09:19.730621 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000001/logs/progress.log
2025-01-10 23:09:22.338845 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-10 23:09:22.3413 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000002/logs/progress.log
2025-01-10 23:09:24.937847 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-01-10 23:09:24.939522 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000003/logs/progress.log
2025-01-10 23:09:27.522369 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-10 23:09:27.573051 DEBUG::tools.R/processChunks: done
2025-01-10 23:09:27.576142 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:09:27.578104 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.adapter_contaminated_1.RData
2025-01-10 23:09:27.580528 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:09:27.582177 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.adapter_contaminated_2.RData
2025-01-10 23:09:27.590865 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:09:27.592776 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_preprocess.tab
2025-01-10 23:09:27.595333 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:09:27.599267 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:09:27.602424 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/reports/shortReadReport_1 ...
2025-01-10 23:09:28.991715 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/reports/shortReadReport_2 ...
2025-01-10 23:09:30.133892 INFO::preprocessReads.R/preprocessReads: done
2025-01-10 23:09:30.25089 INFO::alignReads.R/alignReads: starting alignment...
2025-01-10 23:09:30.255838 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:09:33.401604 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:09:33.403854 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000001/logs/progress.log
2025-01-10 23:09:35.989111 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-10 23:09:35.991237 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:09:38.629099 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-10 23:09:38.630891 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:09:41.261642 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-10 23:09:41.265269 DEBUG::tools.R/processChunks: done
2025-01-10 23:09:41.267317 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:09:41.500479 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-10 23:09:41.508428 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_alignment.tab
2025-01-10 23:09:41.515249 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_analyzed_bamstats.tab
2025-01-10 23:09:41.517119 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-10 23:09:41.734616 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_target_lengths.tab
2025-01-10 23:09:41.780845 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-10 23:09:41.782129 INFO::alignReads.R/alignReads: done
2025-01-10 23:09:41.893529 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-10 23:09:41.915013 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:09:45.154517 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:09:45.156514 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000001/logs/progress.log
2025-01-10 23:09:47.590652 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-01-10 23:09:47.592223 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000002/logs/progress.log
2025-01-10 23:09:49.998735 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.04 minutes
2025-01-10 23:09:50.000289 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000003/logs/progress.log
2025-01-10 23:09:52.802741 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-01-10 23:09:52.808874 DEBUG::tools.R/processChunks: done
2025-01-10 23:09:52.812285 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-10 23:09:52.838059 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_exon.tab
2025-01-10 23:09:52.860658 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_exon_disjoint.tab
2025-01-10 23:09:52.87536 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_gene.tab
2025-01-10 23:09:52.88616 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_gene_coding.tab
2025-01-10 23:09:52.897197 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_gene_exonic.tab
2025-01-10 23:09:52.908956 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_intergenic.tab
2025-01-10 23:09:52.929543 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.counts_intron.tab
2025-01-10 23:09:52.935567 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-10 23:09:52.948012 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_counts.tab
2025-01-10 23:09:52.951877 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-10 23:09:53.49398 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-10 23:09:53.495689 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-10 23:09:53.731909 INFO::coverage.R/calculateCoverage: starting...
2025-01-10 23:09:53.738765 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:09:59.915368 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:09:59.9188 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000001/logs/progress.log
2025-01-10 23:10:02.393078 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-01-10 23:10:02.399427 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000002/logs/progress.log
2025-01-10 23:10:05.183744 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-10 23:10:05.18972 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/chunks/chunk_000003/logs/progress.log
2025-01-10 23:10:07.919839 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-10 23:10:07.928981 DEBUG::tools.R/processChunks: done
2025-01-10 23:10:13.067421 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.coverage.RData
2025-01-10 23:10:13.075602 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.coverage.bw
2025-01-10 23:10:13.151541 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_coverage.tab
2025-01-10 23:10:13.155138 INFO::coverage.R/calculateCoverage: done
2025-01-10 23:10:13.159289 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-10 23:10:13.723917 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:10:18.182115 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:10:18.260999 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:10:18.278599 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:10:18.280062 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.raw_variants.RData
2025-01-10 23:10:18.281828 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.filtered_variants.RData
2025-01-10 23:10:18.283123 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-10 23:10:18.284106 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:10:18.523088 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-10 23:10:18.632717 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/results/test_pe.summary_variants.tab
2025-01-10 23:10:18.634968 INFO::analyzeVariants/analyzeVariants: done
2025-01-10 23:10:18.63973 INFO::Pipeline run successful.
2025-01-10 23:10:18.870748 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-10 23:10:18.875966 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:10:18.878347 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.adapter_contaminated_1.RData
2025-01-10 23:10:18.881556 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:10:18.883661 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.adapter_contaminated_2.RData
2025-01-10 23:10:18.896616 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:10:18.899028 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_preprocess.tab
2025-01-10 23:10:18.90123 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-10 23:10:19.167838 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-10 23:10:19.175035 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_alignment.tab
2025-01-10 23:10:19.183151 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-10 23:10:19.185445 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-10 23:10:19.453992 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_target_lengths.tab
2025-01-10 23:10:19.516113 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-10 23:10:19.68696 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-10 23:10:19.727337 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_exon.tab
2025-01-10 23:10:19.750994 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_exon_disjoint.tab
2025-01-10 23:10:19.763947 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_gene.tab
2025-01-10 23:10:19.774552 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_gene_coding.tab
2025-01-10 23:10:19.78542 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_gene_exonic.tab
2025-01-10 23:10:19.796486 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_intergenic.tab
2025-01-10 23:10:19.819323 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.counts_intron.tab
2025-01-10 23:10:19.824844 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-10 23:10:19.836407 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_counts.tab
2025-01-10 23:10:19.83973 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-10 23:10:20.224058 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-10 23:10:24.582057 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.coverage.RData
2025-01-10 23:10:24.587936 INFO::coverage.R/saveCoverage: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.coverage.bw
2025-01-10 23:10:24.616935 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_coverage.tab
2025-01-10 23:10:24.78783 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-10 23:10:25.065397 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-10 23:10:31.975045 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-10 23:10:32.188618 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-10 23:10:32.237229 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-10 23:10:32.240719 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.raw_variants.RData
2025-01-10 23:10:32.244751 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.filtered_variants.RData
2025-01-10 23:10:32.248094 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-10 23:10:32.250504 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-10 23:10:32.878938 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-10 23:10:33.178293 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.mergeLanes.22398a14569f63/merged/results/merged.summary_variants.tab
2025-01-10 23:10:33.199281 INFO::analyzeVariants/analyzeVariants: done
2025-01-10 23:10:33.205605 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
done successfully.
Executing test function test.markDuplicates ... Timing stopped at: 0 0.001 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
done successfully.
Executing test function test.markDuplicates_w_outfile ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
done successfully.
Executing test function test.preprocessReads ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:10:33.949598 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:10:33.958111 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:10:33.963871 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-10 23:10:33.967523 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:10:39.46103 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:10:39.463519 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/chunks/chunk_000001/logs/progress.log
2025-01-10 23:10:42.209108 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-10 23:10:42.26324 DEBUG::tools.R/processChunks: done
2025-01-10 23:10:42.265774 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:10:42.267564 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/results/test_pe.adapter_contaminated_1.RData
2025-01-10 23:10:42.269666 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:10:42.271275 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/results/test_pe.adapter_contaminated_2.RData
2025-01-10 23:10:42.27867 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:10:42.28087 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/results/test_pe.summary_preprocess.tab
2025-01-10 23:10:42.283174 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:10:42.287495 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:10:42.291174 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/reports/shortReadReport_1 ...
2025-01-10 23:10:43.770846 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.preprocessReads.22398a72fea6ca/reports/shortReadReport_2 ...
2025-01-10 23:10:44.925478 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads.minichunks ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:10:45.237086 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:10:45.244492 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:10:45.248949 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-10 23:10:45.251695 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:10:49.918327 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:10:49.920502 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/chunks/chunk_000001/logs/progress.log
2025-01-10 23:10:52.508638 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-10 23:10:52.510615 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/chunks/chunk_000002/logs/progress.log
2025-01-10 23:10:55.099725 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-01-10 23:10:55.101553 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/chunks/chunk_000003/logs/progress.log
2025-01-10 23:10:57.713052 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-10 23:10:57.764014 DEBUG::tools.R/processChunks: done
2025-01-10 23:10:57.767067 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:10:57.769242 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/results/test_pe.adapter_contaminated_1.RData
2025-01-10 23:10:57.771832 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:10:57.773685 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/results/test_pe.adapter_contaminated_2.RData
2025-01-10 23:10:57.783194 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:10:57.785247 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/results/test_pe.summary_preprocess.tab
2025-01-10 23:10:57.787874 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:10:57.792853 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:10:57.796234 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/reports/shortReadReport_1 ...
2025-01-10 23:10:59.245543 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.preprocessReads.minichunks.22398a6c858625/reports/shortReadReport_2 ...
2025-01-10 23:11:00.36299 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads_single_end ... checkConfig.R/checkConfig.template: loading template config= //tmp/RtmpPBMldF/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:11:00.673183 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:11:00.695469 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-10 23:11:00.69838 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:11:03.837304 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:11:03.839073 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/RtmpPBMldF/test.preprocessReads_single_end.22398a145ae8a9/chunks/chunk_000001/logs/progress.log
2025-01-10 23:11:06.192223 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2025-01-10 23:11:06.201735 DEBUG::tools.R/processChunks: done
2025-01-10 23:11:06.203931 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:11:06.205469 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads_single_end.22398a145ae8a9/results/test_se.adapter_contaminated_1.RData
2025-01-10 23:11:06.211796 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-10 23:11:06.213499 INFO::io.R/saveWithID: saving file= /tmp/RtmpPBMldF/test.preprocessReads_single_end.22398a145ae8a9/results/test_se.summary_preprocess.tab
2025-01-10 23:11:06.215472 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/RtmpPBMldF/test.preprocessReads_single_end.22398a145ae8a9/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:11:06.21984 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/RtmpPBMldF/test.preprocessReads_single_end.22398a145ae8a9/reports/shortReadReport_1 ...
2025-01-10 23:11:07.513773 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-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt
2025-01-10 23:11:08.151995 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-10 23:11:08.173033 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-01-10 23:11:08.192245 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-01-10 23:11:08.194901 DEBUG::tools.R/processChunks: starting...
2025-01-10 23:11:11.299449 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-10 23:11:11.300994 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-10 23:11:14.039214 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-10 23:11:14.083868 DEBUG::tools.R/processChunks: done
2025-01-10 23:11:14.086329 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-10 23:11:14.088009 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-01-10 23:11:14.089901 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-10 23:11:14.091424 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-01-10 23:11:14.097823 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
2025-01-10 23:11:14.099731 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-01-10 23:11:14.101741 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-01-10 23:11:14.106528 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-01-10 23:11:14.110972 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-01-10 23:12:08.171413 DEBUG::tools.R/traceMem: wired.mem=17.631715 GiB
2025-01-10 23:13:08.237696 DEBUG::tools.R/traceMem: wired.mem=18.159346 GiB
2025-01-10 23:14:08.303073 DEBUG::tools.R/traceMem: wired.mem=18.950971 GiB
2025-01-10 23:15:08.368184 DEBUG::tools.R/traceMem: wired.mem=21.084111 GiB
2025-01-10 23:16:08.43393 DEBUG::tools.R/traceMem: wired.mem=17.922277 GiB
2025-01-10 23:17:08.498869 DEBUG::tools.R/traceMem: wired.mem=24.422703 GiB
2025-01-10 23:18:08.56479 DEBUG::tools.R/traceMem: wired.mem=28.039234 GiB
2025-01-10 23:19:08.631329 DEBUG::tools.R/traceMem: wired.mem=30.026826 GiB
2025-01-10 23:20:08.697407 DEBUG::tools.R/traceMem: wired.mem=22.437773 GiB
2025-01-10 23:21:08.762719 DEBUG::tools.R/traceMem: wired.mem=25.901801 GiB
2025-01-10 23:22:08.829626 DEBUG::tools.R/traceMem: wired.mem=26.537689 GiB
2025-01-10 23:23:08.895832 DEBUG::tools.R/traceMem: wired.mem=21.577564 GiB
2025-01-10 23:24:08.961995 DEBUG::tools.R/traceMem: wired.mem=27.792671 GiB
2025-01-10 23:25:09.02709 DEBUG::tools.R/traceMem: wired.mem=29.637960 GiB
2025-01-10 23:26:09.093633 DEBUG::tools.R/traceMem: wired.mem=22.957294 GiB
2025-01-10 23:27:09.159578 DEBUG::tools.R/traceMem: wired.mem=23.700832 GiB
2025-01-10 23:28:09.224341 DEBUG::tools.R/traceMem: wired.mem=23.927005 GiB
2025-01-10 23:29:09.288323 DEBUG::tools.R/traceMem: wired.mem=13.026738 GiB
2025-01-10 23:30:09.354274 DEBUG::tools.R/traceMem: wired.mem=17.576288 GiB
2025-01-10 23:31:09.419667 DEBUG::tools.R/traceMem: wired.mem=20.088136 GiB
2025-01-10 23:32:09.462669 DEBUG::tools.R/traceMem: wired.mem=32.784794 GiB
2025-01-10 23:33:09.528328 DEBUG::tools.R/traceMem: wired.mem=24.143913 GiB
2025-01-10 23:34:09.593903 DEBUG::tools.R/traceMem: wired.mem=14.734647 GiB
2025-01-10 23:35:09.658374 DEBUG::tools.R/traceMem: wired.mem=29.342384 GiB
2025-01-10 23:36:09.724102 DEBUG::tools.R/traceMem: wired.mem=24.621335 GiB
2025-01-10 23:37:09.789826 DEBUG::tools.R/traceMem: wired.mem=35.662438 GiB
2025-01-10 23:38:09.856988 DEBUG::tools.R/traceMem: wired.mem=28.748038 GiB
2025-01-10 23:39:09.923184 DEBUG::tools.R/traceMem: wired.mem=26.596532 GiB
HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings
| name | user | system | elapsed | |
| HTSeqGenie | 0.001 | 0.000 | 0.000 | |
| buildGenomicFeaturesFromTxDb | 0 | 0 | 0 | |
| runPipeline | 0.000 | 0.000 | 0.001 | |