gatk4-4.2.4.0-0 Fixmate Error

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Abrish

• January 26, 2022 10:25
• Edited

I would be grateful If I could get help regarding this error.

 shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Mon Jan 24 14:04:00 CET 2022] Executing as shazia@shazia-PT on Linux 5.13.0-27-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.4.0
INFO 2022-01-24 14:04:00 FixMateInformation Output will be sorted by queryname
INFO 2022-01-24 14:04:00 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
[Mon Jan 24 14:04:00 CET 2022] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1106771968
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Found two records that are paired, not supplementary, and first of the pair: E00591:309:H7L2KCCX2:7:1101:10003:12947
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.advance(SamPairUtil.java:454)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:501)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:388)
at picard.sam.FixMateInformation.doWork(FixMateInformation.java:224)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

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  Genevieve Brandt (she/her)

  • January 24, 2022 21:39

  Hi Abrish,

  This looks like an issue with your reads in the BAM file. I found some hits on google containing explanations and possible solutions. There's more out there too if you search htsjdk.samtools.SAMException: Found two records that are paired, not supplementary, and first of the pair: E00591:309:H7L2KCCX2:7:1101:10003:12947.

  1. https://github.com/broadinstitute/picard/issues/201#issuecomment-486693195
  2. https://support.bioconductor.org/p/74023/

  Best,

  Genevieve

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  Abrish

  • January 25, 2022 06:36

  Ok, Thank you so much. I will check.

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