Hi all,
I am attempting to use STAR 2.4j in automatic 2Pass mode (starting with unannotated genome and use the switches --twopass1readsN and --sjdbOverhang), but running get the following segmentation fault after I complete the first pass and it finished preparing junctions
and finished SA search (per the attached log files):
"home/ccb15/.lsbatch/1424722972.5239437: line 8: 15490 Segmentation fault"
I noticed in my log files (Attached) that there is an extra '/' in the SJ path:
Feb 23 15:38:57 Loaded database junctions from the 1st pass file: ./TAC_L1/TAC_L1._STARpass1//SJ.out.tab: 112762 junctions
Could that be throwing the error?
Attached are my log files. here is my command line (submitted to our cluster, with 12 cores and 72000 MB memory:
STAR --genomeDir STAR_1Pass_Genome_NoAnno --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --runThreadN 12 --seedSearchStartLmax 25 --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.08 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outStd BAM_SortedByCoordinate --readFilesCommand zcat --readFilesIn R1.fq.gz R2.fq.gz --twopass1readsN 40000000 --sjdbOverhang 49 --outFileNamePrefix ./TAC_L1/TAC_L1. > ./TAC_L1/TAC_L1.Accepted.out.bam
Any ideas? I also tried with the --limitBAMsortRAM switch, but same error.
Thanks,
Craig