Question: Need help with "Reorder SAM/BAM" tool
0
gravatar for Guy Reeves
3.4 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI am trying to reorder a SAM file output from BWA. So I can use it in GATK.  

However I get the following error

 

## exit code=1; stdout=
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
[Tue Feb 10 02:59:23 CST 2015] net.sf.picard.sam.ReorderSam INPUT=/galaxy-repl/main/files/010/353/dataset_10353484.dat OUTPUT=/galaxy/main/scratch/tmptGtVr4.sam R

 

Any ideas?  Thanks Guy


 

Tool name: Reorder SAM/BAM
Tool version: 1.56.0
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/picard

 

error picard reorder-sam-bam • 1.4k views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by Guy Reeves1.0k
1
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Convert the dataset to BAM first (with SAMTools), then re-run the picard tool. 

I will follow up with our development team about why this is now required, and if intentional. 

Thanks for reporting the issue, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k

A ticket for the issue has been created and can be followed here: https://trello.com/c/juHlz9iw

ADD REPLYlink written 3.4 years ago by Jennifer Hillman Jackson25k

Hi I have now converted the dataset to BAM first (with SAMTools), then I tried the 'Reorder SAM/BAM <https: usegalaxy.org="" tool_runner?tool_id="toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_ReorderSam%2F1.56.0">’ tool but I got this error- I don´t know if it relevant but I used a reference file from the history.

exit code=1; stdout=

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch [Tue Feb 10 09:21:58 CST 2015] net.sf.picard.sam.ReorderSam INPUT=/galaxy-repl/main/files/010/362/dataset_10362504.dat OUTPUT=/galaxy/main/scratch/tmp8p75dE REFER

Thanks Guy I

ADD REPLYlink written 3.4 years ago by Guy Reeves1.0k

Hi - Would you please submit this as a bug report? Click on the green "bug" icon in the error dataset.

Please make certain that you undelete any error datasets and inputs (all - going back to data upload if necessary) before submitting.

Thanks, Jen, Galaxy team

ADD REPLYlink written 3.4 years ago by Jennifer Hillman Jackson25k

Done thanks for looking into this

ADD REPLYlink written 3.4 years ago by Guy Reeves1.0k

Hello, I just sent you the reply. There was a data input problem to the tool - please see the email for the description. Thanks, Jen

ADD REPLYlink written 3.4 years ago by Jennifer Hillman Jackson25k
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