ContEst sample contamination error
1
0
Entering edit mode
7.7 years ago
MAPK ★ 2.1k

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 • 1.8k views
ADD COMMENT
0
Entering edit mode
5.7 years ago

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 COMMENT

Login before adding your answer.

Traffic: 1937 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6