Mstep - Error fetching reference sequence

[pawanchk]

Hi Caveman Team,

I am running Caveman version 1.15.1, I have successfully executed the first two steps of - setup and split, however when I run mstep I am getting an error - "Error fetching reference sequence for region xxxxx". I am working with GRCh38 and I noticed this error for certain regions in a few chromosomes.

The detailed error is as below, can I please know how to overcome this error so that I can run the merge step ?

[W::fai_get_val] Reference chr1:125184588-125184586 not found in FASTA file, returning empty sequence
[ERROR] (src/fai_access.c: fai_access_get_ref_seqeuence_for_pos:116 errno: No such file or directory) Error fetching reference sequence for region chr1:125184588-125184586.
/var/spool/pbs/mom_priv/jobs/xxxxxx.xxxx.SC: line 94: 27824 Segmentation fault   ~/bin/caveman mstep -f ./caveman.cfg.ini -i 163

Please let me know if you require any other details to find the exact issue. I look forward to hearing from you.

[zyllifeworld]

I encountered the same problem, I downgraded the Caveman to 1.13.15, and this error not happened, maybe it helped you.