[Elsie]

Thanks Sacrolfur, I'll give that a try.

[Sacrolfur]

Try to use both commands separately and write output here.

[silentio]

using -u when running samtools mpileup

[simpson]

I got the same problem. I tried the verson 1.0, 0.1.19, 0.1.18 and none worked.
Any one can help to solve this problem.

Here are my command and error message:

samtools mpileup -ugf F.fna F.sorted.bam > F.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bcf_sync] incorrect number of fields (6 != 5) at 67:234
Segmentation fault

[zhkzhou]

I figure out it problem by update the bcftools from 0.1.17 to 1.1.

[frankenstain]

hello,all,I think I have solve this problem:
both nohup and ">" would add stdout and stderr to output file,which cause that problem。

so,
"samtools mpileup -ugf F.fna F.sorted.bam -o F.bcf"
instead of
"samtools mpileup -ugf F.fna F.sorted.bam > F.bcf"

[samhokin]

Same here, the bcftools that is compiled within samtools is old, and when I compiled a fresh version from github, this error vanished.