I used the command to run demuxlet, and it took 3-4 days running smoothly, and today it gives me a message:
demuxlet --sam SAMPLE.bam --vcf SAMPLE.vcf --field GT --out SAMPLE
Has anyone encountered this before?
complete screenshot here:
NOTICE [2018/07/11 09:28:50] - Total number of gapped/noninformative reads : 283047021
NOTICE [2018/07/11 09:28:50] - Total number of base-QC-failed reads : 1195369
NOTICE [2018/07/11 09:28:50] - Total number of redundant reads : 32619271
NOTICE [2018/07/11 09:28:50] - Total number of pass-filtered reads : 23393737
NOTICE [2018/07/11 09:28:50] - Total number of pass-filtered reads overlapping with multiple SNPs : 10782274
NOTICE [2018/07/11 09:28:50] - Starting to prune out cells with too few reads...
NOTICE [2018/07/11 09:28:50] - Finishing pruning out 0 cells with too few reads...
NOTICE [2018/07/11 09:28:51] - Starting to identify best matching individual IDs
[E::hts_open_format] Failed to open file /PATH/SAMPLE.single
I used the command to run demuxlet, and it took 3-4 days running smoothly, and today it gives me a message: demuxlet --sam SAMPLE.bam --vcf SAMPLE.vcf --field GT --out SAMPLE
Has anyone encountered this before? complete screenshot here:
NOTICE [2018/07/11 09:28:50] - Total number of gapped/noninformative reads : 283047021 NOTICE [2018/07/11 09:28:50] - Total number of base-QC-failed reads : 1195369 NOTICE [2018/07/11 09:28:50] - Total number of redundant reads : 32619271 NOTICE [2018/07/11 09:28:50] - Total number of pass-filtered reads : 23393737 NOTICE [2018/07/11 09:28:50] - Total number of pass-filtered reads overlapping with multiple SNPs : 10782274 NOTICE [2018/07/11 09:28:50] - Starting to prune out cells with too few reads... NOTICE [2018/07/11 09:28:50] - Finishing pruning out 0 cells with too few reads... NOTICE [2018/07/11 09:28:51] - Starting to identify best matching individual IDs [E::hts_open_format] Failed to open file /PATH/SAMPLE.single
FATAL ERROR - [E:cmd_cram_demuxlet.cpp:410 main] Cannot create /PATH/SAMPLE.single file
terminate called after throwing an instance of 'pException' what(): Exception was thrown Abort (core dumped)