ERROR: [bcf_sync] incorrect number of fields..

[samhokin]

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

[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"

[zhkzhou]

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

[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

[silentio]

using -u when running samtools mpileup

[Sacrolfur]

Try to use both commands separately and write output here.

[Elsie]

Thanks Sacrolfur, I'll give that a try.

[Sacrolfur]

I had the same problem. I think the problen is that bcftools works with bcf-file but you don't specify for samtools to output bcf. So you should add to samtools mpileup command argument -g.

Hope this was helpful.

[Elsie]

Solved my own problem, simple typo in samples file I missed.

[Elsie]

I'm getting this error with this command
samtools mpileup -D -S -u -f hg19.fasta child.bam father.bam mother.bam | bcftools view -vcgT trioauto -s sample.txt - > samtoolsCLR.vcf
The resulting vcf file just has the INFO and FORMAT ## lines, then:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000
I am using the correct fa reference file.
My samples file looks like:
child.bam
father.bam
mother.bam

Any advice appreciated.

[mmartin]

The problem occurs when nohup is used with a Unix pipe.

I've just sent this reply to the samtools-help mailing list.

nohup merges stdout and stderr of the command that it runs. bcftools then
doesn't know what to do with the input data since it also contains messages
such as "[mpileup] 1 samples in 1 input files".

To avoid the problem, you can run the command like this:

nohup samtools mpileup ... 2> stderr.txt | bcftools ... - > out.raw.bcf &

But I strongly suggest you try the 'screen' program. It is less fragile and
much more powerful than nohup. This is the briefest introduction I could find: http://www.askbjoernhansen.com/2006/...ix_screen.html

[wangli]

I also had the problem when using nohup. Without nohup. it goes well.

[kweber2]

Make sure you're using the correct reference genome

In case anyone else encounters this same problem ("[bcf_sync] incorrect number of fields (6 != 5)..."), here's another possible solution:

I was having this problem with multiple files, but then I realized I was using the wrong reference fasta as the argument to the mpileup -f option. It wasn't the same reference fasta that was used to create the bam files. When I switched to the correct one, the problem went away.

[salturki]

I just had the same error and by adding '-u' option to 'samtools mplieup' part of the pipeline , this solved the issue in my case.

[Mark.hz]

I still got the error message without nohup: "[bcf_sync] incorrect number of fields (6 != 5) at 7:1396330564"