Hi,

When you say "uploaded the files for “hg19 indexed for bwa", do you mean that these indexes were loaded into the history as datasets? If so, that won't work. Instead, for a local install, adding the data as a buillt-in index is better. Instructions are here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

You can also user our version, and get the loc file too, from the rsync server:
http://wiki.galaxyproject.org/Admin/Data%20Integration
See "Get the data"

A fasta file in the history used as Custom reference genome is another option, but this would mean extra processing for each run. With such a large database, the option above would be preferred, especially if you are having problems (perhaps memory issues?). Still, here are custom reference genome instructions that including troubleshooting help:
http://wiki.galaxyproject.org/Learn/CustomGenomes

I am assuming that you have already made the upgrades to the advanced configuration, but if not, instructions are here:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

Next time, you will want to send local install questions to the galaxy-dev@bx.psu.edu mailing list (best list to reach dev community):
http://wiki.galaxyproject.org/MailingLists

Hopefully this helps,

Jen
Galaxy team

On 5/24/13 10:55 AM, Seattle Oneeechan wrote:

Hi,

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

error

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 [bwa_aln]

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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