Question: Problem in converting Bam to Bai files
0
gravatar for yuvalmalka79
3 months ago by
yuvalmalka790 wrote:

Hi,

In last sessions, I had problems with conversion of Bam files to Bai (error message). Could it be a bug? Thanks, Yuval.

rna-seq bam • 115 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson23k • written 3 months ago by yuvalmalka790
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The job likely ran out of memory during execution. BAM datasets over 25-45 GB (content matters) approach the maximum size for data conversions/upload.

There is usually no need to do this conversion within Galaxy. Tools within Galaxy do not use the file.bam.bai as an input specified independently (a selected BAM dataset is internally linked to the BAM index and entered as a single BAM input).

Should you instead want the index file to work with outside of Galaxy, directly download it from the primary BAM dataset. Click on the disc icon for the BAM dataset, and you will find multiple choices, where both the BAM and BAM index is included.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson23k

Update: I retested the function on a smaller dataset and it is missing a dependency, triggering an error. Once fixed, please be aware that the size of your data might still be a factor and while the conversion function is available, it is usually not needed. The function to download a .bam.bai dataset is working as expected.

Please follow this ticket for progress on the bam-to-bai conversion bug fix: https://github.com/galaxyproject/usegalaxy-playbook/issues/36

Thank you very much for reporting the problem! Jen

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k
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