Question: mpileup metadata problem in workflow
2
gravatar for abogutz
2.9 years ago by
abogutz30
Canada
abogutz30 wrote:

I've got a workflow that uses the old samtools mpileup (v0.0.1) on the main galaxy instance. The next step has been stalling due to metadata not being autodetected in the subsequent dataset. It seems to be happening regardless of the input .bam file. Is this a problem with galaxy? The workflow has worked in the past, probably last time about a month ago.

Thanks!

metadata mpileup samtools • 1.1k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by abogutz30
1

I am experiencing this as well. The error message:

"12 MPileup on data 7 and data 48 (log)

An error occurred setting the metadata for this dataset
Set it manually or retry auto-detection"

using "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1"

Thank you

ADD REPLYlink written 2.9 years ago by jrichardalbert30

Hi Can I ask in your output files vcf or bcf files?  Thanks Guy

ADD REPLYlink written 2.9 years ago by Guy Reeves1.0k
1

The output for this step is .bcf, but the specific file that receives the error message is the log file associated with the .bcf. 

ADD REPLYlink written 2.9 years ago by jrichardalbert30

 

Thanks for the info I get the same error on both usegalaxy.org and a cloudman instance regardless of what version of mpileup I use ( I tried 0.0.01, 0.0.02 and 2.0). But I have found a galaxy instance where everything works. So I suspect this is related to a recent galaxy update.

By the way bcftools viewer is installed 

Hopefully somebody will be able to help with this.

 

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Guy Reeves1.0k

I deleted my  comment

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Guy Reeves1.0k

HI I have the same problem but no resolution yet 

see

Cannot set metadata on .bcf output from mpileup

 

 

 

ADD REPLYlink written 2.9 years ago by Guy Reeves1.0k

I'd like to clarify this problem - it's definitely only a metadata problem, as I can cancel the step after the mpileup, resolve the metadata, then run the subsequent step successfully. Unfortunately this is an early step in a very long workflow, so restarting each step by hand would be quite unwieldy.

ADD REPLYlink written 2.9 years ago by abogutz30
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Does this problem occur with the latest version of the tool? It might be necessary to use run the most current version of a tool when using a newer version of Galaxy, as a small number will not be backwards compatible. If you need to use the older tool, consider using an older version of Galaxy. Just be aware that other issues may come up if you have also upgraded other tools. Backwards compatibility is a priority, but not always possible, and not all tools are authored by the same developers.

Hopefully upgrading the tool will resolve the problem. Our team will respond with additional information if there is more to share.

Thanks, Jen, Galaxy team

 

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
2

Update: the .1 and .2 version are presenting reported problems. A Trello ticket has been created to track the resolution. Please follow it here: https://trello.com/c/cYkUbipj

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson25k
1

Hi Jen,

I haven't seen any activity on the Trello ticket - is this metadata problem being worked on?

ADD REPLYlink written 2.8 years ago by abogutz30

Hi 

I was also checking I have had to give up using my old workflows and make new ones using Freebayes (which is very very good) but I think this could be a problem for many users on up to date instances. Thanks Guy

 

 

ADD REPLYlink written 2.8 years ago by Guy Reeves1.0k

Our team is still investigating. You may find that the tool fails directly now, as several users and recent testing has uncovered. This information was added to the ticket https://trello.com/c/cYkUbipj. When more is known, the ticket will update. Our apologies for the delay, but looking at this tool's issues is prioritized along with other pending resolutions and projects. 

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k
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