Question: ContEst sample contamination error
0
gravatar for MAPK
4.0 years ago by
MAPK1.5k
Washington University in St. Louis
MAPK1.5k wrote:

Hi Everyone, I am trying to run ContEst ( https://www.broadinstitute.org/cancer/cga/contest_run ) tool from GATK to identify contaminated samples. I keep getting this error below after finishing the run which only results into the header column in the output file. Can someone please explain the issue here?

INFO  12:14:47,154 TraversalEngine -   -> 1071322 reads (2.93% of total) failing DuplicateReadFilter 
WARN  12:14:48,879 RestStorageService - Error Response: PUT '/GATK_Run_Reports/Y0kZBwvQVniKPEBhGarKn0tcp24wtdpt.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1324, Content-MD5: HKZpqqhZe2yzyviG8jJdyg==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 1ca669aaa8597b6cb3caf886f2325dca, Date: Fri, 03 Jun 2016 02:14:47 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:QQGt8vQSt8iSEpKHKV7SGBXx3WA=, User-Agent: JetS3t/0.8.0 (Linux/2.6.32-573.26.1.el6.x86_64; amd64; en; JVM 1.6.0_30), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 72638CBABDCF9144, x-amz-id-2: cooKEVsyyyTQzQfXvwJmLNcm0o41aDNEB+x3ofyedhkxLPKa9tWvXmm2QLY8MY05PlioAASUMIw=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 03 Jun 2016 02:14:47 GMT, Connection: close, Server: AmazonS3]
contest • 1.2k views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum128k • written 4.0 years ago by MAPK1.5k
0
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

GATK try to push some stats on amazon. The new versions of gatk don't do this anymore. https://gatkforums.broadinstitute.org/gatk/discussion/9560/removal-of-phone-home

ADD COMMENTlink written 23 months ago by Pierre Lindenbaum128k
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