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Question: AddOrReplaceReadGroups Fatal error
0
gravatar for Farbod
23 months ago by
Farbod • 10
Montreal
Farbod • 10 wrote:

Dear Biostars/Galaxy Friends, Hi

I am using AddOrReplaceReadGroups in online galaxy for two BAM files and all the options are on "Auto" mode (this is a part of a Coursera course assignment).

But I received this error:

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch -Xmx7680m -Xms256m ERROR: Option 'RGPU' is required. USAGE: AddOrReplaceReadGroups [options]

Please help me in this regard.

~ Best

NOTE: this is the pipeline I am running:

importing Data (6 fastq files) into Galaxy -> fastQC quality control for each -> fastq converting -> map with BWA for illumina to hg19 and BAM file creation ->AddOrReplaceReadGroups ->

bwa software error galaxy bam • 878 views
ADD COMMENT • link •
written 23 months ago by Farbod • 10
1

I can duplicate this at http://usegalaxy.org. The tool was recently updated and I do not see a default value for the PU tag on the form. I'll do some more testing and send more feedback soon as this may be a small bug.

Meanwhile, you could enter the value yourself to move forward, instead of using the auto default option (I didn't try that yet, but it will be part of my testing).

Thanks for reporting the problem, Jen, Galaxy team

ADD REPLY • link modified 23 months ago • written 23 months ago by Jennifer Hillman Jackson ♦ 25k
2
gravatar for Jennifer Hillman Jackson
23 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There does appear to be a bug. Adding in text for the tool form option Platform unit (PU) will avoid the error. I entered simply "Test" - but any single alphanumeric "word" is fine - do not include spaces. This can be done even when Auto-assign is used.

An issue has been created to track the bug and correction: https://github.com/galaxyproject/tools-devteam/issues/423

Thanks again for letting us know about the problem. Take care, Jen, Galaxy team
ADD COMMENT • link modified 23 months ago • written 23 months ago by Jennifer Hillman Jackson ♦ 25k
1

Dear Jennifer,

Hi. That really solve my problem after 90 days of receiving errors !

Thank you

~ Take care

ADD REPLY • link written 23 months ago by Farbod • 10
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