It seems that Picard suffers from small memory size:
bash-$ cat MAPPING_SRR5339941_whfBLh.o8138465
Error occurred during initialization of VM
Unable to allocate 1048576KB bitmaps for parallel garbage collection for the requested 33554432KB heap.
I increased the requested memory size for MAPPING job to 40G, and that resolved the problem. Specifically in RNAseqAnalyse.pl file, Line 589:
print QSUB "##MAPPING\nqsub -P $opt{sgeProjectName} -l h_rt=08:00:00,h_vmem=40G -pe threaded $opt{nthreads} -o $rundir/$sample/logs -e $rundir/$sample/logs -R yes -N $job_id $rundir/$sample/jobs/$job_id.sh\n\n";
It seems that Picard suffers from small memory size:
I increased the requested memory size for MAPPING job to 40G, and that resolved the problem. Specifically in RNAseqAnalyse.pl file, Line 589:
print QSUB "##MAPPING\nqsub -P $opt{sgeProjectName} -l h_rt=08:00:00,h_vmem=40G -pe threaded $opt{nthreads} -o $rundir/$sample/logs -e $rundir/$sample/logs -R yes -N $job_id $rundir/$sample/jobs/$job_id.sh\n\n";