samtools segmentation fault pileup

[biochemMScstudent]

Hi, I am trying to create a pileup on samtools (v.0.1.8-20) from sorted bam files generated by CASAVA version 1.8 (Illumina GAIIe) but am getting a segmentation fault error. I removed duplicates using samtools rmdup, converted bam>sam, imported my FASTA reference genome, SAM file and BAM file and submitted the following job:

sqsub -r 12h --memperproc=20G -o Lane3-no-duplicates-pileup.txt samtools pileup -vcf hg19-name-fixed.fa Lane3-sorted-no-duplicates.bam

And the following error message was returned:

/var/spool/torque/mom_priv/jobs/5716617.krasched.SC: line 3: 13118 Segmentation fault samtools pileup -vcf hg19-name-fixed.fa Lane3-sorted-no-duplicates.bam

I don't think memory is an issue, I have indexed the bam file and reference FASTA file so I don't think that is the problem. I have also run a pileup directly on the bam file CASAVA produces (which also contained the indexed version) and I get the same segmentation fault. I have run pileups on sam files from the earlier version (1.7) of CASAVA with no problems, but when I try to do the same on bam files generated on the new version of CASAVA I get the error message shown above. If anyone can help me interpret that error message it would be greatly appreciated. Thanks!

[swbarnes2]

I don't see why you are converting to sams at all.

Pileup is deprecated in newer version of samtools, which means it's going to be harder to get help.

I'd try getting a newer samtools, and try mpileup before trying to make deprecated software work.