ERROR: [bcf_sync] incorrect number of fields..

[colindaven]

Actually, I think it wasn't truncated, but something added by nohup.

When I don't use nohup to run the mpileup command bcftools seems to work fine.

[brentp]

usually this happens if your bcf file is truncated.

[colindaven]

This is weird. I've used Samtools a lot before on bacterial references and never had this problem, yet on some human exomes it happens. Mpileup runs fine and then I repeatedly get

[bcf_sync] incorrect number of fields (0 != 5) at 0:0

Reinstalling/updating samtools and bcftools doesn't seem to help.

[Mark.hz]

Still have this problem when doing bcftools view for a bcf file (mpileup generated):[bcf_sync] incorrect number of fields (6 != 5) at 7:1396330564
Any help?

[Mark.hz]

I ran into this problem as well, using mpileup/bcftools (samtools-0.1.18) to call variants from 19 bam files.
I willl try to run it wiiltout nohup.

[sflink]

I get the same error message with a command like:

nohup samtools mpileup -uf ref.fa s1.bam s2.bam

but it runs fine without the 'nohup'. Have you tried the command sequence without the pipes?

[vinodhsri]

Has anyone encountered this error ('[bcf_sync] incorrect number of fields (0 != 5)') and found a solution already:


vcfutils.pl splitchr -l 50000000 ucsc.hg19.fasta.fai | xargs -i echo samtools mpileup -I -C50 -m3 -F0.0002 -DSuf ucsc.hg19.fasta -r {} -b bam.list | bcftools view -bcvg - /> part-{}.bcf

[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000
xargs: echo: terminated by signal 13

Appreciate your advice.

vsri