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Warning message from Mutect

JojoTanJojoTan SingaporeMember

Dear All,

I was running Mutect recently and I had this warning message at the end of the run.

WARN 23:35:58,735 RestStorageService - Error Response: PUT '/GATK_Run_Reports/nWCfXwuU0VtIYEk6rprnFDHtkJTGL7DV.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 401, Content-MD5: 83Z1d2So8+OPduJ7mIfn1Q==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: f376757764a8f3e38f76e27b9887e7d5, Date: Fri, 20 Jun 2014 15:35:57 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:PhhcmE8R1qrQY1UKNvTSnLMeRIw=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-358.2.1.el6.x86_64; amd64; en; JVM 1.6.0_24), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 534C83C0DB8C022A, x-amz-id-2: UclW27FDSEsRGmN0Qo0hKHgB2QJAHABCjj30jAzYhA7A9u4p0eKGas5sVntavYB1, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 20 Jun 2014 15:35:58 GMT, Connection: close, Server: AmazonS3]

What does this warning means? And does this mean that I will have to re-run the job or will the job be completed successfully despite the warning message?

Thank you for you help.

Joanna

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Best Answer

Answers

  • JojoTanJojoTan SingaporeMember

    Hi @Geraldine_VdAuwera‌

    We tried running many mutect jobs but some of the mutect jobs hang and has been running for several days to weeks.
    We then tried to re-run the hanged mutect jobs, some of the jobs completed. However, there are some jobs that continued to hang despite us trying to re-run them.

    Could the hanging of the mutect jobs be a consequence of the logging and reporting function of the GATK engine as we are still using the older version?

    Thank you very much and hope to hear from you soon.

    Best regards,
    Joanna

  • bruxbrux ItalyMember

    Hi,
    I'm running muTect-1.1.4 and GenomeAnalysisTK-3.2-2, but I got the same warning message...

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    @brux, can you please post the full output?

  • anishanish Member
    edited September 2014

    Hi,

    I get the same error as well. The MuTect stops running after analyzing chr1 or chr2, which ran for about 2 days. And the samples I used are obtained from exome sequencing (each sample is about 8GB). So it should not take that long.

    This is the Warning Message I get:

    WARN 12:30:42,788 RestStorageService - Error Response: PUT '/GATK_Run_Reports/T8Pf4hDHny5zRtpv2EWzBRZGrHF3RJZJ.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1079, Content-MD5: LP33hXO/PNalyaLjgOCZaA==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 2cfdf78573bf3cd6a5c9a2e380e09968, Date: Wed, 13 Aug 2014 16:30:42 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:khw1J1N58DXtKQ4gC5kbqKnqkLE=, User-Agent: JetS3t/0.8.1 (Linux/3.0.80-0.7-default; amd64; en; JVM 1.7.0_05), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 70EA9C2C947AEA85, x-amz-id-2: m2It2TSi3wAwpnfs1gY/a7MSBUgCs2qPLIKnKRPFcOTrkGBRfTld1nhYF17gOpKA, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 13 Aug 2014 16:30:42 GMT, Connection: close, Server: AmazonS3]

    • ja -set /bl2/achakka/jafiles/1670927
  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Hi @anish,

    The warning you get is unrelated to the MuTect failure. That's just the Phone Home system (see GATK FAQs) trying and failing to report your run failure for our logs. If you post the complete console output I can help you find what is the actual error causing the failure.

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