BuildBamIndex

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Robert Bremel

• November 08, 2022 20:27

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

Have run this script many times previously but problem occurred with the 4.3.0 update

After BwaAndMarkDuplicatesPipelineSpark need to SortSam and then to BuildBamIndex

Error log said the bam Index had been written couldn't find file anywhere

Fixed by adding and explicit --OUTPUT to create the file in the proper directory.  Sorry, didn't save the error log.

 

 

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  Anthony DiCi

  • November 09, 2022 16:23

  Hi Robert Bremel,

  Thank you for writing to the GATK forum! Please include your entire command line and program log so that we can properly troubleshoot this issue.

  I look forward to hearing back from you soon!

  Best,

  Anthony

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  Robert Bremel

  • November 09, 2022 16:38

   

   

  ./gatk BuildBamIndex --INPUT fname.bam

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  Anthony DiCi

  • November 18, 2022 15:40

  Hi Robert Bremel,

  Thank you for your previous response! It appears your copy and paste may have not been successful. Please include your entire program log/stack trace so that we can properly troubleshoot this issue.

  I look forward to hearing back from you soon!

  Best,

  Anthony

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  Anthony DiCi

  • November 28, 2022 16:19

  Hi Robert Bremel,

  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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