PacBio bam mpileup result in Segfault

[jackshen]

Hi, I'm new to this forum and I guess I would like to post this question here.

I had an aligned bam file with reads from 3 PacBio SMRT runs using blasr.
When I try to call snp between the bam and another bam file from illumina reads from the same library using "samtools mpileup -u". It raised an error with segmentation fault(core dump).

The error seems to originate from the pacbio bam file since doing mpileup with the illumina bam file alone, it finishes without error.

The pacbio bam file is sorted and when I try to index the bam, it also finishes without error. Later I tried mpileup without -u option, the text pileup finishes OK.

Could anyone give me some hints or directions to debug this issue?

Best,
jack

[Richard Finney]

How much memory does you machine have?
What version of samtools are you using?
What is your command line?
Can you "samtools view" the region you think it might be at when it bombs?

[jackshen]

How much memory does you machine have?
What version of samtools are you using?
What is your command line?
Can you "samtools view" the region you think it might be at when it bombs?

I'm using samtools Version: 0.1.17 (r973:277)

The following command is run under the headnode of our server. I monitored the mem usage to be less than 1% until segfault. The head node has 70GB of memory.

samtools mpileup -u -f ../hg19/hg19-EBV-fos-ecoli/hg19.fa directmap/PacBio_primary.bam > bcfpileup.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Segmentation fault (core dumped)

I did the samtools view into that region and there appears to be normal just like the rest of the reads.

[jackshen]

Anyone have any idea on this issue?

Or could someone tell me how to convert text mpileup into bcf file?

[mchaisso]

I'm always frustrated to see somebody answer a how-to question by suggesting somebody use a different method, but that's what I'm going to do here.

samtools mpileup is not designed to work with pacbio, and will probably give no result at best, and more likely something wrong.

It is much better to use the quiver software that you can download from github.

Anyone have any idea on this issue?

Or could someone tell me how to convert text mpileup into bcf file?