Galaxy BWA Segmentation Fault

[fladje]

Hi,

In the past I've successfully aligned PE Illumina MiSeq reads using BWA in Galaxy but lately some of my alignments have started failing. All samples go through the same pipeline, most align but a few stop after a segmentation fault in BWA. I confess I'm new at this Bioinformatics thing, and I can't seem to find a solution on my own.. Anybody know what I might be doing wrong?

Any help would be appreciated!

Hilde

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The alignment failed.
Error generating alignments. [bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (2402, 5234, 8910)
[infer_isize] low and high boundaries: 151 and 21926 for estimating avg and std
[infer_isize] inferred external isize from 251269 pairs: 5940.068 +/- 4124.607
[infer_isize] skewness: 0.511; kurtosis: -0.744; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 23222 (4.19 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.37 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3297 out of 10352 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 188377 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2241.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.37 sec
[bwa_sai2sam_pe_core] print alignments... 1.76 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (2595, 7186, 11297)
[infer_isize] low and high boundaries: 151 and 28701 for estimating avg and std
[infer_isize] inferred external isize from 84557 pairs: 7236.733 +/- 4785.357
[infer_isize] skewness: 0.066; kurtosis: -1.262; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 27144 (4.16 sigma)
[bwa_sai2sam_pe_core] time elapses: 0.38 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 482 out of 3212 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 40389 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 532.50 sec
[bwa_sai2sam_pe_core] refine gapped alignments... /bin/sh: line 1: 28068 Segmentation fault bwa sampe /tmp/3030216.cyberstar.psu.edu/tmprNNXwj/tmpXybcjA /tmp/3030216.cyberstar.psu.edu/tmpq3YCcl/tmpKvAb8e /tmp/3030216.cyberstar.psu.edu/tmpq3YCcl/tmpvUAE3E /galaxy/main_pool/pool3/files/005/540/dataset_5540834.dat /galaxy/main_pool/pool3/files/005/540/dataset_5540837.dat >> /galaxy/main_pool/pool2/tmp/job_working_directory/004/860/4860532/galaxy_dataset_5540842.dat

[GenoMax]

Is this happening on the main PSU galaxy site or is this a local mirror of galaxy?

[fladje]

Thanks for your reply! I'm using the main website. How would that influence analysis? A lack of CPU power on the local install?

[JackieBadger]

I wouldn't do any large alignments via the main site...It's very easy to install a local instance.
Plus it would be even quicker just to use BWA from the command line in Linux

[fladje]

Quicker, yes, but the command line usually results in a lot of hair-pulling here haha. I've just installed a local client, but I have analyzed far greater datasets without BWA issues so I wonder if that would solve the problem?

[GenoMax]

If this issue was with the main PSU site then have you tried emailing the tech support at Galaxy ([email protected])? They are generally very helpful.

[fladje]

BWA is not available on the local client so I'm trying a different aligner now, but running into some issues with the Fastq joiner instead. Thanks for the email address! I'll definitely follow up with them.