Segmentation fault 11 encountered for STAR v2.7.10a #1469
Description
Hello,
I encountered a segmentation fault 11 error at the "sorting BAM" step when running 10x 5' data with STAR v2.7.10a within a Debian 10 docker container. The detailed Log.out.txt file is attached.
The detailed STAR command is below:
STAR --genomeDir genome_ref --runThreadN 28 --outFileNamePrefix result/ --soloType CB_UMI_Simple --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR --outFilterScoreMin 30 --outSAMtype BAM SortedByCoordinate --outSAMattributes CR UR CY UY CB UB \
--soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloBarcodeMate 1 --clip5pNbases 39 0 \
--readFilesCommand zcat --readFilesIn \
data/LIB5452773_SAM24411654_S1_L001_R1_001.fastq.gz,data/LIB5452773_SAM24411654_S1_L002_R1_001.fastq.gz \
data/LIB5452773_SAM24411654_S1_L001_R2_001.fastq.gz,data/LIB5452773_SAM24411654_S1_L002_R2_001.fastq.gz \
--soloCBwhitelist 737K-august-2016.txt --soloFeatures Gene GeneFull SJ Velocyto --soloCellFilter EmptyDrops_CR
However, when I ran exactly the same command with STAR v2.7.9a within a Debian 10 docker container, everything worked properly.
Could you please help me diagnose this issue?
In case you want to inspect the docker image we built, it's quay.io/cumulus/starsolo:2.7.10a, with Dockerfile specified here.
Thanks!
Sincerely,
Yiming