Thanks for the quick response. The workaround you describe could work,
but I might run into trouble later on.
My interest is to develop a workflow for GATK, which have very strict
requirements on the input BAM file. One of which is that the sorting
have to be exactly the same as the reference. My reference is not
sorted lexicographically "chr1, chr10, chr11, ....", but instead is
sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to
do this with "Filter and Sort -> Sort". Also GATK needs the header for
the @RG tags, which I could resolve by just reintroducing the header
later on, but still it will be cumbersome.
I'll work on my galaxy/cluster configuration and see if I can find why
the SAM-to-BAM tool is failing.
On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote:
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
matching regex). Although, you can choose to not include header output as a
Perhaps this will solve the immediate problem?
On 11/3/11 12:43 PM, Carlos Borroto wrote:
> I'm running into this error:
> "Error sorting alignments from
> 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
> 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
> manually outside of Galaxy and it ran fine.
> Thanks in advance,
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