[tahamasoodi]

Hi,

I'm getting the same error message. How it can be sorted out?

samtools: bam_plcmd.c:612: group_smpl: Assertion `id >= 0 && id < m->n' failed

[rubi]

Hi vinodhsri,

Did you manage to solve the [bcf_sync] incorrect number of fields (0 != 5) problem?

I'm facing the same problem myself.

Thanks,
rubi

[vinodhsri]

[bcf_sync] incorrect number of fields Error:

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

[aatu18]

Hi,

How did you solve this error, samtools: bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed ? I am repeatedly getting this error! I have a merged and sorted bam file, which I am using to call SNPs using bcftools. i merged multiple sorted bam files using a "rg.txt" file I created..

Where should I look first ?

Thanks for any help!

aarti

[jamminbeh]

How can I implement the -I option? I've tried:

/u/local/apps/samtools/0.1.11/samtools mpileup -I -uf hg19.fa accepted_hits.bam

and

/u/local/apps/samtools/0.1.11/samtools mpileup -ufI hg19.fa accepted_hits.bam

and I still get the same error:

[bcf_sync] incorrect number of fields (8 != 5). Corrupted file?

[Hkins552]

Is there anyway to avoid using the -I option? I would still like to call the INDELs on my file. My error is:

[bcf_sync] incorrect number of fields (6 != 5) at 0:33736084
[afs] 0:27544.812 1:16105.314 2:36880.874

[Haiqing]

I think I just removed these @RG header from SAM file(I do not use the read groups in my case).

[oudacontrol]

How did you fix the read group issue? I am getting the same error: "bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed" ...

[Haiqing]

Thanks! It works now!

BTW, I also tried the old "pileup" for SNP/INDEL call with my deep sequencing data (50000+). Somehow, the pileup out only count 8000 read depth (column eight of the pileup output) for the first reference base. And then add one more read for every next base(like 8001 for second reference base, 8002 for third reference base, and so on). Any suggestions(I already give the -d60000 option to increase the max read depth. It works for mpileup, but not for pileup)? Thanks.

[lh3]

You have read groups undefined in the header

[Haiqing]

Another error message when do the first step for SNP call using samtools:
samtools mpileup -uf reference.fna sample.sort.bam |bcftools view -bvcg - > var.raw.bcf
[mpileup] 1 samples in 1 input files
samtools: bam_plcmd.c:596: group_smpl: Assertion `id >= 0 && id < m->n' failed.
Aborted
:-(

Any suggestions?

[Haiqing]

Hi! lh3,

I got similar error:
[bcf_sync] incorrect number of fields (0 != 5). Corrupted file?
[afs] 0:0.000

What does this mean?

Thanks

[gaffa]

I am also getting this error. I wonder if it would be possible to somehow sort out positions with excessively many indels before running mpileup.

[bair]

No, your results are truncated.

Yes, you are right. I get more variants with -I option on chr:MT.

[lh3]

No, your results are truncated.