samtools error file

Question

[fufuyou]

Hi everyone,

I use samtools for calling SNP. I running many samples with the same code. Most of samples is normal. I met some error files from a few samples. Could you tell me what it happened?

My code is

samtools mpileup -u -g -f /depot/tmengist/data/ref/Sb_ref/Sb21b.fa SSSS.realn.bam | bcftools call -mv > SSSS.samtools.raw.vcf

The error is

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_plp_destroy] memory leak: 353. Continue anyway.

Thanks
Fuyou

[harold.smith.tarheel]

The EOF error is a known bug in some versions of samtools: see this thread.

[Devon Ryan]

It's only a bug if you're piping into samtools (the error gets printed due to bam_hdr_read() trying to seek to the end of the file to check for a magic number there...which obviously doesn't work with pipes). In this case it's a broken BAM file.

[fufuyou]

Thanks. I will try to use lower version.

[Leandro Lima]

Hello.

I might be a problem with your BAM file.