Question: BAM upload and manipulations involving new datatype "bam_native" present with error - follow for corrections
9 months ago by
chandrugcg_77 • 10
chandrugcg_77 • 10 wrote:
Dear Sir, File uploading after showing two files. Cufflink analysis showing paused for the analysis, Pls clarify
ADD COMMENT • link •modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by chandrugcg_77 • 10
The problem is with the BAM upload. The BAM is actually uploaded but is in an error state related to a newly introduced datatype (bam_native), triggering downstream tools to pause before the metadata state is in a non-error state.
A few reports have also come in about the same issue through bug reports at Galaxy Main https://usegalaxy.org, but the problem is not necessarily server-specific (we don't know yet). This server was updated to the new version of Galaxy (
18.01) in the last week, with more changes made Friday, and even more changes and fixes will occur before that is published as we work out any final issues.
Others facing this same issue with BAM upload or BAM manipulations involving the
bam_nativedatatype can follow this post for updates. And if the use-case is novel (not related to upload), please share which tool is presenting a problem as we'll want to capture that as well in our tests/fixes.
More feedback soon. Thanks for reporting the problem!
Jen, Galaxy team
The fix is still in progress but better clarified. We are still testing and working through the issue.