Hello Jessie,

This is a reply for both this question and the one you sent to me directly this afternoon.


First thing to double check is that the build assigned to the BAM file is correct, especially if older. The reference genome build used to generate the file must be exactly the same as used in Galaxy (chromosome names identical).

Next, a test on a smaller portion of the data, to determine if format is an issue, would be a good place to start. Cycling through BAM->SAM->BAM conversion would probably be informative. Or, running the tools line command, if that is an option for you.

Finally, it is possible that the files are simply too large (deep) to run on the public Galaxy instance. The Galaxy alternatives are to either set up a local instance or a cloud instance. Instructions are here:
http://getgalaxy.org

Hopefully this helps,

Best,

Jen
Galaxy team

On 10/3/11 7:31 AM, Golbus, Jessica wrote:
Hi-

I am currently working with one of Illumina's older Bam files and trying
to run SamTools Pileup. Unfortunately, the server has repeatedly timed
out on me and I am unable to run the program on my file. I was wondering
if other people are having trouble running Samtools on human genome .bam
files or whether this is secondary to the way the file is configured
(i.e. it was first run through Illumina's proprietary software and
provided as a .bam without an accompanying fastq file)?

Thanks for your help!

Jessie

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