Need help with "Reorder SAM/BAM" tool

Question: Need help with "Reorder SAM/BAM" tool

3.8 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k 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 • 1.6k views

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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by Guy Reeves • 1.0k

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

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 REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Done thanks for looking into this

ADD REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

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 REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

exit code=1; stdout=

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