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


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 • 581 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by yuvalmalka790
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k

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:

Thank you very much for reporting the problem! Jen

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour