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Question: BWA error [bwa_aln] 17bp reads: max_diff = 2
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gravatar for eurioste
10 months ago by
eurioste • 40
eurioste • 40 wrote:

I wish to align single end fastq sample using "Map with BWA" tool. The reads were trimmed several times with "Trim Galore" to remove specific adaptor sequences. The reads are 20-50 bp long. I'm using default parameters, except for the read group setting.

But the run quickly fails at start giving the following error:

Fatal error: Exit code 1 () 
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3 
[bwa_aln] 64bp reads: max_diff = 4 
[bwa_aln] 93bp reads: max_diff = 5 
[bwa_aln] 124bp reads: max_diff = 6 
[bwa_aln] 157bp reads: max_diff = 7 
[bwa_aln] 190b

Why is this happening?
alignment bwa software error • 380 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by eurioste • 40
2
gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I took a closer look at your job/error server-side and it looks like a transient cluster error. Please try a rerun now to see if that resolves the problem. If the rerun fails, please send in a bug report, this is how: https://galaxyproject.org/issues/#usage-problem-reporting

We are looking into if there is more going on. If so, we will get back to you. But you can try a rerun now and don't need to wait.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

Update: The problem seems to be related to the hg19canon indexes for this specific tool, possibly on only one cluster.

Test reruns using hg19canon also failed for me. Using just hg19 worked ok as well as for hg19female. Perhaps one of those would be acceptable? If you choose hg19, you can always filter the resulting BAM dataset later to remove non-canonical hits (temporary workaround, we will fix what is going wrong, just don't know exactly what or when that will be yet).

Thanks!

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

Hello, I'm having a similar problem again, even while using the work around suggested, which was working until now:

Fatal error: Exit code 134 () 
[bwa_aln] 17bp reads: max_diff = 2 
[bwa_aln] 38bp reads: max_diff = 3 
[bwa_aln] 64bp reads: max_diff = 4 
[bwa_aln] 93bp reads: max_diff = 5 
[bwa_aln] 124bp reads: max_diff = 6 
[bwa_aln] 157bp reads: max_diff = 7 
[bwa_aln] 19
ADD REPLY • link modified 9 months ago • written 9 months ago by eurioste • 40
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