Question: Unable to download Bam_index
0
gravatar for uc2009105230
17 days ago by
uc20091052300 wrote:

Hi,

I've been trying to download the Bam_index from my files but I am getting this message:

Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #408aab5596824675b4b745a06b952dd4

Can you please help?

Thank you!

Tania

bam_index download • 62 views
ADD COMMENTlink modified 14 days ago • written 17 days ago by uc20091052300
0
gravatar for Jennifer Hillman Jackson
15 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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

ADD COMMENTlink written 15 days ago by Jennifer Hillman Jackson25k

Update:

The Upload tool no longer coordinate-sorts BAM data by default. Tools will perform the sort during execution (when a coordinate-sorted input is required). For uploaded unsorted BAMs, we'll be fixing the index download. Full details in this ticket: https://github.com/galaxyproject/galaxy/issues/6945

ADD REPLYlink written 15 days ago by Jennifer Hillman Jackson25k
0
gravatar for uc2009105230
15 days ago by
uc20091052300 wrote:

Dear Jennifer,

Thank you so much for your help! Nevertheless, I cannot use any tool in my current history as this message shows up: "The previously selected dataset has been deleted". However, I can view the entire data when I click on it (is not showing as deleted) - please see image attached. Could you please help me on this?

Thank you! Tania Dataset shows up but I'm not able to run any tool

ADD COMMENTlink written 15 days ago by uc20091052300

Hi - I am looking at the history named "All data" and the datasets appear to be intact (not deleted). I can't see your image -- could you post it somewhere public (https://imgur.com is one option) and link it back here? Or better, send an email with a share link to the history, the steps to reproduce, and the image(s) to galaxy-bugs@lists.galaxyproject.org. This is an internal mailing list that reaches the administrators of the https://usegalaxy.org public Galaxy server. We can review from there. Jen

ADD REPLYlink written 15 days ago by Jennifer Hillman Jackson25k
0
gravatar for uc2009105230
14 days ago by
uc20091052300 wrote:

I just sent the email with the link to my history. Thank you for your help!

ADD COMMENTlink written 14 days ago by uc20091052300
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