RmDup fails to build index file

Question: RmDup fails to build index file

3.5 years ago by

United States

hkedskes • 20 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 • 1.6k views

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modified 3.2 years ago by Guy Reeves • 1.0k • written 3.5 years ago by hkedskes • 20

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

ADD REPLY • link written 3.4 years ago by alons • 0

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

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

selecting version "1.x" from the upper right corner menu "Versions" on the tool form itself
confirming proper inputs
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 COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.2 years ago by mikie5120 • 0

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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

Thanks so much!

ADD REPLY • link written 3.2 years ago by moroch • 0

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.2 years ago by

moroch • 0

Spain

moroch • 0 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 COMMENT • link written 3.2 years ago by moroch • 0

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much!

ADD REPLY • link written 3.2 years ago by moroch • 0

3.2 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

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 COMMENT • link modified 3.2 years ago • written 3.2 years ago by Guy Reeves • 1.0k

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