SortSam - Question about I/O error

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Henry

• October 27, 2022 08:20

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

v.4.2.0.0

b) Exact command used:

java -Xmx32g -jar /mnt/garnet/Tools/WGS_Analysis/Program/GATK/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar SortSam -I data.sam -O data.bam -SO coordinate

 

 c) Entire program log:

I think I/O error depends on the how many data are open or read.

when I faced this issue, I allocated more memory at the java options such as "-xmx " or "-xmG". 

I wonder how many memories are allocated by using gatk SortSam local package

I want to know default memory usage during run the analysis.

0

• 

  Anthony DiCi

  • October 31, 2022 13:41

  Hi Henry,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  Please reply with your entire program log, including any exceptions/errors you've encountered. From that, we should be better able to diagnose the error's origin.

  SortSam (Picard) 

  I look forward to hearing back from you!

  Best,

  Anthony

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• 

  Anthony DiCi

  • November 08, 2022 16:17

  Hi Henry,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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