4 weeks ago by
The BAM datasets with problematic indexes are those that were loaded to Galaxy as
unsorted.bam. I see that you used autodetect in the Upload tools. I fairly certain that these should have been sorted upon Upload and that the function should be fixed. I'm following up on that -- ran a test yesterday using test data and it produced the same output. This 1) confirmed action was still was reproducible (it is) and that 2) re-sorting repairs the formatting correctly (test workflow: unsorted bam > Upload tool with autodetect used for database >
unsorted.bam instead of
bam result > coordinate sort >
bam result produced and full functionality restored).
The solution for you now is to also coordinate-sort any BAM data that has the datatype
unsorted.bam currently assigned. This will allow you to use the BAM data with tools (most expected sorted inputs) and will make the index available for download. Use the tool Picard > SortSam with the option for coordinate sort order. To avoid data duplication, once the data are sorted, the originals can be permanently deleted and quota space will be recovered.
Thanks for reporting the issue! I'll link back the ticket once created. Jen, Galaxy team