Two related issues:

We tried to run BWA for Illumina on two groomed files (fastqsanger)  and
got the following error message.

* *

*24: Map with BWA for Illumina on data 6 and data 5: mapped reads*


An error occurred with this dataset: *BWA Version: 0.5.9-r16 The alignment
failed. Error aligning sequence. [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

We have done this many times before on the public server.  However, this is
a new local instance and we just uploaded the files for “hg19 indexed for
bwa” (from the TopHat website) which put it into the pull down menu.

Along those same lines.  I thought that a .fa file put into history, could
be used and would be indexed automatically in bowtie and bwa (maybe tophat
as well, haven’t used that one yet).  With bowtie, having the
WholeGenomeFasta file from the UCSC seems to work, but not with bwa.

Does anybody know if it should work with bwa as well?

Any help is much appreciated.

Thank you,
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