Samtools mpileup ends abruptly without completing full analysis

Question

[Richard]

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

[GenoMax]

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

[Richard]

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.

[pfs]

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