Question: BWA error [bwa_aln] 17bp reads: max_diff = 2
gravatar for eurioste
6 days ago by
eurioste30 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?

ADD COMMENTlink modified 6 days ago by Jennifer Hillman Jackson23k • written 6 days ago by eurioste30
gravatar for Jennifer Hillman Jackson
6 days ago by
United States
Jennifer Hillman Jackson23k wrote:


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:

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 COMMENTlink written 6 days ago by Jennifer Hillman Jackson23k

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).


ADD REPLYlink written 6 days ago by Jennifer Hillman Jackson23k
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