Question: SAM-to-BAM error with custom reference
0
gravatar for christianwood7311
3.6 years ago by
United Kingdom
christianwood73110 wrote:

Dear Galaxy Biostar team,

I'm seem to be having a problem running Samtools SAM-to-BAM conversion on two BWA mapped paired end SAM files that have been associated with a custom reference genome so I can run SNP analysis with the GATK. The file size for the SAM files are from 10-20Gb in size and the genome file is 2.7Gb, may this be an issue? When I run the SAM-to-BAM tool using the custom reference genome located in the history on the aforementioned files I receive the following error after executing the process:

{
    "outputs": [],
    "implicit_collections": [],
    "jobs": [],
    "output_collections": []
}

This has occurred in the last few days and I'm slightly worried I've done something wrong in the processing of my data. Any help with this problem would be greatly appreciated.

 

Many thanks,

Christian

ADD COMMENTlink modified 3.6 years ago by aysam.guerler90 • written 3.6 years ago by christianwood73110

Hi Aysam,

I can share the history yes, would you be able to message me the address I should share it to please?

ADD REPLYlink written 3.6 years ago by christianwood73110

You may send the email to our mailing list at galaxy-dev@lists.galaxyproject.org or to me personally at aysam.guerler@gmail.com. Please CC me in either case.

ADD REPLYlink written 3.6 years ago by aysam.guerler90
0
gravatar for aysam.guerler
3.6 years ago by
United States
aysam.guerler90 wrote:

This issue was temporary and has been resolved now.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by aysam.guerler90
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