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zeeev / wham

Structural variant detection and association testing
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Floating Point Exception #40

Closed akkellogg closed 8 years ago

akkellogg commented 8 years ago

Hello,

I'm having a problem running WHAM on some smaller BAM files. Every time I try to run it the WHAM.err file returns the following:

INFO: WHAM-BAM will using the following fasta: ../ABL1_cds.fasta INFO: OpenMP will roughly use 24 threads INFO: target bams: S2.bam INFO: gathering stats for each bam file.

At which point it exits out and prints "Floating Point Exception" to the terminal.

The reads are aligned with BWA-MEM, and duplicates marked with Picard. Any idea what would be causing this issue? My BAM file is relatively small, could this be causing the problem?

Thanks for your help.

-Ana

zeeev commented 8 years ago

@akkellogg Sorry for the late reply, i'm just returning from holiday. What type of data are you working with? Exome or genome?

akkellogg commented 8 years ago

@zeeev We think we pinpointed the problem. We were aligning the reads to a custom reference and we think the issue was with that reference, since aligning to a different reference seems to have solved the problem.