samtools error file
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6.9 years ago
fufuyou ▴ 110

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

SNP samtools • 4.4k views
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1
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The EOF error is a known bug in some versions of samtools: see this thread.

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2
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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.

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Thanks. I will try to use lower version.

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Hello.

I might be a problem with your BAM file.

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