bcftools error

[Morpse]

Hello,

The command
cat all.mpileup | bcftools view -bvcg - > all.var.raw.bcf

exits with the text below
[bcf_sync] incorrect number of fields (4 != 5) at 10:1696253
[afs] 0:38509.883 1:50.388 2:38.729

before exiting it outputs this text (this pattern starts at 100000)
[bcfview] 13600000 sites processed.
[afs] 0:99814.004 1:101.247 2:84.750
[bcfview] 13700000 sites processed.
[afs] 0:99786.086 1:107.189 2:106.725

all.mpileup was generated with the following command
samtools -verbose -uf reference.fasta all.bam > all.mpileup

Does anyone know what is causing this or how to fix it? I would like to be able to call both SNPs and indels with this.

Thank you

[Hkins552]

Same problem

I am having the same problem, which is strange as I've used this exact pipeline/command previously with no issues. Have you figured anything out?

[swbarnes2]

The "incorrect number of files" can happen if the file is truncated. I see it sometimes if I want to check on a big files while it's still being made by mpileup.

What's the purpose of the cat command, and the pipe?

[Mark.hz]

I ran into the same problem, either with or without nohup. Does anyone know how to fix? Now I am generating the raw bcf file and try to figure out what is wrong on that specific line.

[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?

[figo1019]

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?

Hi Mark.hz

Have you sorted out this problem as I am also facing the similar error while running the bcf file [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867.

Regards

[Mark.hz]

Hi Mark.hz

Have you sorted out this problem as I am also facing the similar error while running the bcf file [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867.

Regards

Truncated BAM file may cause this problem. You need to go back to validate your BAM files by Picard.

[figo1019]

Truncated BAM file may cause this problem. You need to go back to validate your BAM files by Picard.

Thank you for your reply

I ran the picard tool to validate I get an error
ERROR: Read groups is empty

Rest things are OK.

Does it make a huge difference ?

regards

[Mark.hz]

Thank you for your reply

I ran the picard tool to validate I get an error
ERROR: Read groups is empty

Rest things are OK.

Does it make a huge difference ?

regards

Strange. I don't think RG is the reason. Did the validation stop at the 1st error?