Question: BAM upload and manipulations involving new datatype "bam_native" present with error - follow for corrections
gravatar for chandrugcg_77
9 months ago by
chandrugcg_7710 wrote:

Dear Sir, File uploading after showing two files. Cufflink analysis showing paused for the analysis, Pls clarify

queued paused bamnative job bam • 364 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by chandrugcg_7710

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, 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_native datatype 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

ADD REPLYlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k

The fix is still in progress but better clarified. We are still testing and working through the issue.


ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I am only able to reproduce this issue when the uploaded BAM dataset is truncated. This might have occurred during upload. The complete BAM for this accession is nearly twice as large at the NCBI source.

Try loading directly from the source instead. The tool to use is NCBI SRA Tools > Extract reads in BAM format from NCBI SRA.

This use-case could be error trapped better. I'll suggest that to the developers on the ticket I referenced in my earlier comment.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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