I'm running STAR 2.7.10b with a scRNA-Seq from SMARTseq with the following command
STAR --runThreadN 20 --genomeDir $starIndex --sjdbGTFfile $gtf --sjdbOverhang 100 \
--readFilesCommand zcat --readFilesIn $rawdata/$base.trimmed.R1.fastq.gz $rawdata/$base.trimmed.R1.fastq.gz \
--soloType SmartSeq\
--soloUMIdedup Exact --soloStrand Forward \
--soloFeatures Gene GeneFull SJ \
--outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \
--outFileNamePrefix $bamFiles/$base. --soloOutFileNames $base \
--limitBAMsortRAM 168632718037 --readMapNumber 1000 \
--outSAMtype BAM SortedByCoordinate
I have also increased the ulimit parameter to 5000, but I still get the error message when it starts mapping:
Mar 03 12:21:12 ..... started STAR run
Mar 03 12:21:13 ..... loading genome
Mar 03 12:25:04 ..... processing annotations GTF
Mar 03 12:25:26 ..... inserting junctions into the genome indices
Mar 03 12:27:25 ..... started mapping
Segmentation fault (core dumped)
I'm also attaching here the Log.out file in case you need it. But I can't find any errors in the log file
any ideas why it's crashing?
thanks
Assa