samtools error file
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
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Hello.
I might be a problem with your BAM file.
The EOF error is a known bug in some versions of samtools: see this thread.
Thanks. I will try to use lower version.
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.