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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Qualimap fails #16

Closed vezzi closed 10 years ago

vezzi commented 10 years ago

Testing Piper, alignments run ok but qualimap fails with the error shown below

/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap  --java-mem-size=64G  bamqc  -bam /apus/v1/a2010002_nobackup/NGI/analysis_ready/G.Grigelioniene_14_01_UUSNP/pipeline_output/01_raw_alignments/P1142_101.BC423WACXX.P1142_101.4.bam --paint-chromosome-limits  -outdir /apus/v1/a2010002_nobackup/NGI/analysis_ready/G.Grigelioniene_14_01_UUSNP/pipeline_output/02_preliminary_alignment_qc/P1142_101.BC423WACXX.P1142_101.4.qc/ -nt 8 
Java memory size is set to 64G
Launching application...

/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap: line 41: JAVA_OPTS: unbound variable

if i run

export JAVA_MEM_SIZE=64G

and rerun I get this:

/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap: line 41: JAVA_OPTS: unbound variable
johandahlberg commented 10 years ago

Ok. I know the reason for this. I'll fix it when I get in to the office today.

johandahlberg commented 10 years ago

I was a bit to hasty to add set -o nounset which I consider good practice for bash scripts. However, I didn't check check that it actually worked with it set (which I guess is bad practice). However, this should now be fixed on Uppmax.

No commit for this one, since this is something that I changed in the qualimap start script on Uppmax.

johandahlberg commented 10 years ago

@vezzi Reopen this if my fix didn't work.