popscle Segmentation Fault

Hi, I am trying to run popscle demuxlet and keep running into a segmentation fault. It does not seem to be a memory issue as I have already tried up to 512GB of RAM and the logs on the job do not indicate that the job ran out of memory. How can the issue be resolved?

Error message:

NOTICE [2022/09/02 10:50:15] - Finished identifying 6 samples to load from VCF/BCF
/var/spool/slurmd/job61341813/slurm_script: line 10: 67857 Segmentation fault      popscle demuxlet --sam xxx --vcf xxx --field GT --out xxx

Thanks!

Sep 02 '22 22:09 ArpiS

Segmentation fault itself is not informative to explain what went wrong. If you provide a reproducible example, we can look into it.

Sep 07 '22 16:09 hyunminkang

Hi, did you figure out what caused the segmentation fault? I am also stuck with this error.

Dec 28 '22 10:12 wxicu

Hello, I'm having the same problem.

NOTICE [2023/09/01 11:57:23] - Finished loading 12910 droplet/cell barcodes to consider NOTICE [2023/09/01 11:57:23] - Initializing BCF reader.. NOTICE [2023/09/01 11:57:23] - Finished identifying 48 samples to load from VCF/BCF NOTICE [2023/09/01 11:57:23] - Initializing SAM reader.. [W::vcf_parse] Contig '147' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'PR' is not defined in the header, assuming Type=String NOTICE [2023/09/01 11:57:24] - WARNING: Cannot find AF field from INFO field in VCF file, now calculate AF from AC/AN Segmentation fault

Sep 01 '23 19:09 littmanr16