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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?
Jen Galaxy team
On 11/3/11 12:43 PM, Carlos Borroto wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: