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Mutect Error / warning message

rnaharrnahar SingaporeMember

Hi
I see a warning message (mentioned below) at the end of every mutect run - could someone tell me what it means and if it really affects the mutect run ?

WARN 13:40:19,000 RestStorageService - Error Response: PUT '/GATK_Run_Reports/ATv75XCLzx6dlIqoQfSoVHT34uGT58BE.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 400, Content-MD5: iBOLwuniyHaSqZwJL5Dy5A==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 88138bc2e9e2c87692a99c092f90f2e4, Date: Tue, 29 Jul 2014 05:40:17 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:BNzzu1dX1hGy38yNCjTGxKEV6Lk=, 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: 5411B079C3E90B86, x-amz-id-2: TMNJEETV91DLxw505rJv7bGyo9NxW6ZOon6OvppoNZoJIVX9495ulNyIcw2FpF9G, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 29 Jul 2014 05:40:18 GMT, Connection: close, Server: AmazonS3]

thanks
Rahul

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Answers

  • rnaharrnahar SingaporeMember

    Ok thanks Geraldine - would there be a difference in output if I use mutect newer version compared to the older version 1.1.4 (which I am using) ?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    There should not be any significant difference in the results. The main changes that were made since version 1.1.4 are that the newest release is now built on GATK version 3.1, which includes various bug fixes to parts of the engine that MuTect uses. Note that the newest version runs on Java 7 (whereas the old one ran on Java 6) so you will need to upgrade your version of Java.

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