Question: Samtools mpileup ends abruptly without completing full analysis
0
gravatar for Richard
2.4 years ago by
Richard0
Richard0 wrote:

Hi all,

I'm trying to call SNPs/INDELs with Samtools mpileup however after ~20 minutes the programme stops abruptly about halfway through the genome but without an error message and at different points each time. For example:

 [mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
[bcfview] 100000 sites processed.
[afs] 0:95902.769 1:315.751 2:2273.980 3:252.098 4:1255.402
[bcfview] 200000 sites processed.
[afs] 0:95964.438 1:366.995 2:2113.553 3:266.025 4:1288.988
[bcfview] 300000 sites processed.
[afs] 0:95459.843 1:424.830 2:2691.948 3:277.845 4:1145.533
[bcfview] 400000 sites processed.
[afs] 0:96128.869 1:322.951 2:2383.096 3:218.602 4:946.481
[afs] 0:89965.151 1:309.198 2:2376.383 3:245.414 4:1090.854

I have tried to repeat the analysis with samples (and ref.fasta) I have successfully worked on in the past and they work fine. I have indexed the fasta file...

samtools mpileup -uf 'ref.fasta' 'input1.bam' 'input2.bam' | bcftools view -bvcg - > output.raw.bcf

Finally, I should point out the obvious fact that I'm a novice to this!

Thank you very much in advance for your help, Richard

software error • 805 views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.4 years ago by Richard0

Is your job running out of memory (or some other resource)?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax80k

I've never got an error message suggesting I have and when I look at the system monitor whilst the mpileup is running I'm only using ~5-10% of the available memory. Same with CPUs (~25% used). I think it's something to do with the bam files as some work and some lead to the 'crash' midway through the analysis.

ADD REPLYlink written 2.4 years ago by Richard0

Default mpileup will only output variants. Are you anticipating variants in all your bam files?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by pfs270
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