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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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final report fails #12

Closed vezzi closed 10 years ago

vezzi commented 10 years ago

Friday first run (WholeGenome.sh full pipeline on G.Grigelione manually started) ended with an error during the reporting. This is likely linked to issue #9 

INFO  13:10:06,547 QGraph - 0 Pend, 1 Run, 0 Fail, 176 Done
INFO  13:10:36,332 FunctionEdge - Done: SetupDeliveryStructure: List(/apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/pipeline_output/processed_alignments/P1142_101.clean.dedup.recal.bam, /apus/v1/a2010002_nobackup/vezzi/ANALYSIS
/G.Grigelioniene_14_01/pipeline_output/final_alignment_qc/P1142_101.clean.dedup.recal.qc.log, /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/pipeline_output/variant_calls/G.Grigelioniene_14_01_SNPseq.raw.vcf, /apus/v1/a2010002_
nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/pipeline_output/variant_calls/G.Grigelioniene_14_01_SNPseq.snp.eval, /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/pipeline_output/variant_calls/G.Grigelioniene_14_01_SNPseq.indel.
eval) > List(/apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/pipeline_output/delivery)
INFO  13:10:36,332 QGraph - Writing incremental jobs reports...
INFO  13:10:36,333 QJobsReporter - Writing JobLogging GATKReport to file /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/DNABestPracticeVariantCalling.jobreport.txt
INFO  13:10:36,339 QGraph - 0 Pend, 0 Run, 0 Fail, 177 Done
INFO  13:10:36,341 QCommandLine - Writing final jobs report...
INFO  13:10:36,341 QJobsReporter - Writing JobLogging GATKReport to file /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/DNABestPracticeVariantCalling.jobreport.txt
INFO  13:10:36,346 QJobsReporter - Plotting JobLogging GATKReport to file /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/DNABestPracticeVariantCalling.jobreport.pdf
DEBUG 13:10:36,411 RScriptExecutor - Executing:
DEBUG 13:10:36,411 RScriptExecutor -   Rscript
DEBUG 13:10:36,411 RScriptExecutor -   -e
DEBUG 13:10:36,411 RScriptExecutor -   tempLibDir = '/tmp/Rlib.2669751579767907782';install.packages(pkgs=c('/tmp/RlibSources.7076489217819491840/gsalib'), lib=tempLibDir, repos=NULL, type='source', INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec'));library('gsalib', lib.loc=tempLibDir);source('/tmp/queueJobReport.7118150041361181671.R');
DEBUG 13:10:36,411 RScriptExecutor -   /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/DNABestPracticeVariantCalling.jobreport.txt
DEBUG 13:10:36,411 RScriptExecutor -   /apus/v1/a2010002_nobackup/vezzi/ANALYSIS/G.Grigelioniene_14_01/DNABestPracticeVariantCalling.jobreport.pdf
ERROR: dependencies ‘gplots’, ‘ggplot2’, ‘png’ are not available for package ‘gsalib’
* removing ‘/tmp/Rlib.2669751579767907782/gsalib’
Warning message:
In install.packages(pkgs = c("/tmp/RlibSources.7076489217819491840/gsalib"),  :
  installation of package ‘/tmp/RlibSources.7076489217819491840/gsalib’ had non-zero exit status
Error in library("gsalib", lib.loc = tempLibDir) :
  there is no package called ‘gsalib’
Execution halted
DEBUG 13:10:37,038 RScriptExecutor - Result: 1
WARN  13:10:37,038 RScriptExecutor - RScript exited with 1
INFO  13:10:37,041 QCommandLine - Script completed successfully with 177 total jobs
DEBUG 13:10:37,043 IOUtils - Deleted /tmp/Q-Classes-3649970956736343354
johandahlberg commented 10 years ago

This is a problem with Queue and R. However the report does not contain any useful info anyway, since the slurm-drmaa library does not report back the correct info. This can be fixed by adding --disableJobReport if you don't want to see it. I can throw that onto the workflow command line to avoid confusing people.