Question: RmDup fails to build index file
2
gravatar for hkedskes
3.1 years ago by
hkedskes20
United States
hkedskes20 wrote:

We tried to run RmDup from NGS: SAMtools on https://usegalaxy.org/

However, we get the following error:

Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/galaxy-repl/main/jobdir/009/599/9599227/__dataset_19916105_metadata_temp_file_SEcbID.bai' Fatal error: Exit code 134 (Error) Samtools-htslib-API

Other tools we tried with the BAM files worked fine

 

software error • 1.3k views
ADD COMMENTlink modified 2.8 years ago by Guy Reeves1.0k • written 3.1 years ago by hkedskes20

Hi hkedskes, I've just run into the same error, have you managed to solve it somehow?

ADD REPLYlink written 2.9 years ago by alons0
1
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Temporary work-around on http://usegalaxy.org:

Use the prior version of the tool wrapper (v 1.2). Do this by

  1. selecting version "1.x" from the upper right corner menu "Versions" on the tool form itself
  2. confirming proper inputs
  3. re-running the job.

This information and future updates are in Trello ticket tracking this issue https://trello.com/c/cmvVu5EF

Thanks, Jen, Galaxy team

 

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k

Hi, I am also having this issue and I would like to try your workaround.

Can you point out how I can specify it as version 1.x? I don't see "Versions" option, can you point out step by step where I can find this "Versions" option? Thank you 

ADD REPLYlink written 2.8 years ago by mikie51200

If a tool has more than one version on the server (http://usegalaxy.org does for this one), you can switch by using the "Versions" button at the top of the tool form. This is what it looks like:

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k

Hi! I have tried V1.0.0 and still get the same error. Any updates on this issue? 

Thanks so much! 

 

ADD REPLYlink written 2.8 years ago by moroch0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Did you sort the input BAM file by coordinates first, using "SortSam". Right now that is requrired, even for output that may appear to be already coordinate sorted (Tophat is one example). Our team is investigating why. But this may get you going now. Just add the sort set to your workflow (and hide it, delete intermediate datasets, whatever works to manage disk space/quota).

For all - if errors come up with Picard or SAMtools - try a "SortSam" as a first pass solution. Upload BAM datasets are automatically sorted, but intermediate analysis datasets may not have the sorting exactly how SAM/Picard are expecting it. This has been manifesting as a range of errors and some messages can be cryptic (meaning, not obviously resolved by this additional processing step). We are working to make this more clear across the application.

If something else is going on, please let us know. I may ask for you to share a history (privately - there are specific instructions for that - no need to share with the entire forum). But, any resolution we can share in general terms.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for moroch
2.8 years ago by
moroch0
Spain
moroch0 wrote:

Hi! I have the same problem. Did sort my BAM file with "SortSam" but I keep getting an error for rmDup:

Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/galaxy-repl/main/jobdir/010/229/10229605/__dataset_20961387_metadata_temp_file_qnHT6E.bai'

 

Any ideas on something else I should try?

Thanks!!! 
 

 

 

 

ADD COMMENTlink written 2.8 years ago by moroch0
1

Since this question was originally asked, this tool has presented with problems for other users. I believe that this is still undergoing investigation and resolution on http://usegalaxy.org. Please follow this Trello ticket for updates: https://trello.com/c/cmvVu5EF

If you would like to send in a bug report from the error dataset for us to double check that this is the same issue, please submit one through the Galaxy user interface by clicking on the "green bug" icon within the error dataset. Please be sure to leave all inputs and the error dataset undeleted.

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k

Thank you very much!

ADD REPLYlink written 2.8 years ago by moroch0
0
gravatar for Guy Reeves
2.8 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi 

I wonder if an alliterative temporary work around is to use picard> markDuplicates as an alternative path to the same route.  Note that that RmDup works in a slightly different way, but markDuplicates should work for many users I guess.

The only down side i have found with this program is that it is rather memory intensive and it can exceed user limits if they are set.

Thanks Guy

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Guy Reeves1.0k
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