Qualimap fails
Closed this issue · 3 comments
vezzi commented
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
Ok. I know the reason for this. I'll fix it when I get in to the office today.
johandahlberg commented
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
@vezzi Reopen this if my fix didn't work.