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Question: data manager problem - building Bowtie Index for hg19
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gravatar for k.z.sutton
3.7 years ago by
k.z.sutton • 0
United Kingdom
k.z.sutton • 0 wrote:

I am testing out the process of setting up a local galaxy host - for analysis of clinical exome samples. Basic install is fine and runs ok. But I am having issues building local reference genomes.

I have trying to use the Bowtie Index builder (rev. 5515ee3559f0). This works fine for SacCer2, but when I attempt the build on hg19 it fails.

The builder does not return any apparent error messages. However, when I attempt to use the reference (hg19) in Bowtie2 it returns an error due to no index being present. When I check the tool_data file it appears that the files have not transferred from the working directory (the files appear to form correctly there during the builder run).

I am running on OSX, using SQLite. The computer is a 2012 Macbook Pro with 8Gb of ram and over 500Gb of hard drive space - so should be ok?

Has anyone encountered a similar problem and identified a solution?

cheers,

Keith

 

 
data managers bowtie galaxy • 1.2k views
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modified 3.7 years ago • written 3.7 years ago by k.z.sutton • 0
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Just to confirm, the data manager job for this does not have any error or warning messages and is green (successful)? Have you tried restarting the server?

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for k.z.sutton
3.7 years ago by
k.z.sutton • 0
United Kingdom
k.z.sutton • 0 wrote:

Yes, pane is green at end of index build and the ref genome appears as an option in bowtie2 - but the alignment in bowtie2 fails at start due to no index file. I did do a Server restart- didn't help. Also done a couple of clean installs of galaxy to make sure it wasn't any other tool/dependency interfering.

As an appendum I have just run a successful(?) BWA run which completed both the reference build and also the alignment for a full fastq seq dataset. A (?) as I need to finish installing a bunch of tools/dependencies to check it against what I get out of galaxy main.

keith
ADD COMMENT • link written 3.7 years ago by k.z.sutton • 0
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