riboPicker / Bugs / #12 Segmentation Fault bwa64

#12 Segmentation Fault bwa64 Edit

Status: open

Owner: nobody

Labels: None

Updated: 2014-03-25

Created: 2014-03-25

Creator: Anonymous

Private: No

Wondering if there is a way to determine what is causing the segfault in bwa64. I have attempted to run the bwa command with different flags and am coming up with the same error.

This is what I see:

bwa64 bwasw -A -f tmp.tsv -z 1 /data/ribodb/rrnadb LA1224mod_1.fastq
[bsw2_aln] read 99010 sequences (10000010 bp)...
Segmentation fault

Memory should not be an issue as the machine I am running the command on is a 48 core server with 1TB of RAM.

I have tested with the -S command setting the value quite high and all that happens is the segmentation fault occurs after more sequences read in.

Is this version of bwa having issues with number of sequences? This should not be an issue I would think.

Discussion

Anonymous - 2014-03-25

Description has changed:

Diff:

--- old +++ new @@ -2,7 +2,7 @@ This is what I see: -# bwa64 bwasw -A -f tmp.tsv -z 1 /data/ribodb/rrnadb LA1224mod_1.fastq +bwa64 bwasw -A -f tmp.tsv -z 1 /data/ribodb/rrnadb LA1224mod_1.fastq [bsw2_aln] read 99010 sequences (10000010 bp)... Segmentation fault
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Anonymous

Segmentation Fault bwa64

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#12 Segmentation Fault bwa64 Edit

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