Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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 admin

    @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

Sign In or Register to comment.