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-...@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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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/