Question: samtools error file
0
gravatar for fufuyou
4.0 years ago by
fufuyou110
United States
fufuyou110 wrote:

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 files 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 • 3.7k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum124k • written 4.0 years ago by fufuyou110
1

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

ADD REPLYlink written 4.0 years ago by harold.smith.tarheel4.5k
2

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.

ADD REPLYlink written 4.0 years ago by Devon Ryan92k

Thanks. I will try to use lower version.

ADD REPLYlink written 4.0 years ago by fufuyou110

Hello.

I might be a problem with your BAM file.

ADD REPLYlink written 4.0 years ago by Leandro Lima930
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