Error running GATK

When I run this command:

java -jar /storage/app/GATK_3.3/GenomeAnalysisTK.jar -R /storage/data/gabriel/ucsc/hg19/hg19.fasta -T UnifiedGenotyper -I SRR493939.valid.bam -o teste2.vcf

This error happens:

WARN 04:34:22,257 RestStorageService - Error Response: PUT '/DAXKr9W5oe2LWMJhFdSveQd50kAK6tex.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 393, Content-MD5: 33uF1RoVpa9w9uTWFUxP0g==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: df7b85d51a15a5af70f6e4d6154c4fd2, Date: Tue, 25 Nov 2014 06:34:20 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:agZvhjUckV8Jnth+aubQX9KViUo=, User-Agent: JetS3t/0.8.1 (Linux/3.13.0-30-generic; amd64; en; JVM 1.7.0_65), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: B6DD058B64A98870, x-amz-id-2: ADKbyes3Qb8ovjofT4tKpP3gV3yPuc9v5C157qzTkfII2q3U2ZwEpUgzy0eIOz+J, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 25 Nov 2014 14:39:19 GMT, Connection: close, Server: AmazonS3]
WARN 04:34:22,846 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 29096 seconds. Retrying connection.

Can someone help me?

Best Answers

Answers

  • Sheila, I have already asked for a key last November 26th, do you know how many days do I have to wait to get it ??
    Thanks,

    Gabriel

  • alejandraalejandra spainMember

    I have a similar error:
    WARN 16:32:30,139 RestStorageService - Error Response: PUT '/dpqv1h9anwH8rEeFvfadgeK1Q5rh51bi.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 401, Content-MD5: vvkPMOrtqAaqPaS//VEYhg==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: bef90f30eaeda806aa3da4bffd511886, Date: Tue, 24 Nov 2015 16:32:29 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:YKhF46BYWD0DFZUXE2t60LYOhzs=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-431.20.3.el6.x86_64; amd64; en; JVM 1.7.0_91), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: F99C8DFABB482962, x-amz-id-2: 5MtxwF+QRjN53jt+qml1KbZz3Q6YeoBhaqfN5Kko042C9DvALOZ9doEF3tRiJOMqxrn/SvPoYS4=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 24 Nov 2015 16:17:21 GMT, Connection: close, Server: AmazonS3]
    WARN 16:32:30,354 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately -909 seconds. Retrying connection.
    INFO 16:32:31,015 GATKRunReport - Uploaded run statistics report to AWS S3

    when I run: java -jar /usr/local/Modules/modulefiles/tools/gatk/3.4.0/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ../../../mapping/hg38/hg38.fa -I duplicates.bam -o M3060_intervalListFromRTC.intervals

    if I don't get a key and just ignore the warning, does it mean that the output is wrong? or with the key the output will be better?
    or with this warning the RealignerTargetCreator didn't complete the analysis?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @alejandra
    Hi,

    The error message doesn't mean the run failed. Your results will be fine. You can either ignore the warning or request a key to disable the system so you don't get the error message.

    -Sheila

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