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Question: Error message when using the ValidateSamFile tool (Picard) in summary mode
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gravatar for nhs
2.6 years ago by
nhs • 0
European Union
nhs • 0 wrote:

Hi

After the update the Picard tool "ValidateSamFile" in the summary output mode returned the following error (verbose works fine).Do I need to adjust any settings?

Thanks..

236 ValidateSamFile on data 232: BAM validation summary empty formattxtdatabasehg38 Warning: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch ERROR: 'MAX_OUTPUT=100' is not a valid value for Type. USAGE: ValidateSamFile [options] Documentation: http://broadinstitute.github.io/picard/command-line-overv
software error galaxy bam • 754 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by nhs • 0
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am able to reproduce the error. An issue ticket has been created here that you can follow for the correction: https://github.com/galaxyproject/tools-devteam/issues/369

Thanks for reporting the problem. Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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