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Hello Carlos,
If what you want is a sorted SAM file, then the tool "Filter and Sort ->
Sort" may be a better choice. A SAM file is a tabular file.
If there is header data at the beginning of the SAM file, it can be
removed before running Sort with the tool "Filter and Sort -> Select"
(with a "not" matching regex). Although, you can choose to not include
header output as a BWA option.
Perhaps this will solve the immediate problem?
Best,
Jen
Galaxy team
On 11/3/11 12:43 PM, Carlos Borroto wrote:
Hi,
I'm running into this error:
"Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_),"
When using SAM-to-BAM tool on a locally install Galaxy using a SGE
cluster. I'm using the last version of galaxy-dist. I'm guessing I
have a problem with the configuration for the tmp folder. I have this
on "universe_wsgi.ini":
# Temporary files are stored in this directory.
new_file_path = /home/cborroto/galaxy_dist/database/tmp
But I don't see this directory being used and from the error looks
like /tmp in the node is used. I wonder if this is the problem, as I
don't know if there is enough space in the local /tmp directory at the
nodes? I ran the same tool in a subset of the same SAM file and it ran
fine.
Also, I see this in the description of the tool:
"This tool uses the SAMTools toolkit to produce an indexed BAM file
based on a sorted input SAM file."
But what I actually need is to sort a SAM file output from bwa, I
haven't found any other way than to converting it to BAM. Looking at
"sam_to_bam.py" I see the BAM file will also be sorted. Would it be
wrong to feed an unsorted SAM file into this tool?
Finally, just to be sure there is nothing wrong with the initial SAM
file, I ran "samtools view ..." and "samtools sort ..." on this file
manually outside of Galaxy and it ran fine.
Thanks in advance,
Carlos
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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