Sortie 9 : sdtout de VariantFiltration - Dioufamad/SNPs_Calling GitHub Wiki

INFO  11:02:44,218 HelpFormatter - Executing as [email protected] on Linux 3.10.0-693.11.6.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_65-b17. 
INFO  11:02:44,218 HelpFormatter - Date/Time: 2018/06/28 11:02:44 
INFO  11:02:44,219 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  11:02:44,219 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  11:02:44,273 GenomeAnalysisEngine - Strictness is SILENT 
INFO  11:02:44,344 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  11:02:44,470 GenomeAnalysisEngine - Preparing for traversal 
INFO  11:02:44,472 GenomeAnalysisEngine - Done preparing for traversal 
INFO  11:02:44,472 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  11:02:44,472 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  11:02:44,472 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  11:02:57,734 ProgressMeter -            done    583200.0    13.0 s      22.0 s      100.0%    13.0 s       0.0 s 
INFO  11:02:57,735 ProgressMeter - Total runtime 13.26 secs, 0.22 min, 0.00 hours 
WARN  11:02:58,602 RestStorageService - Error Response: PUT '/liZEceyuQEHdCc3nEH5x7fvFWjwHa1hW.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 405, x-amz-meta-md5-hash: a15a41efd2317e68b717187bb3de57f4, Content-Type: application/octet-stream, Content-MD5: oVpB79Ixfmi3Fxh7s95X9A==, Date: Thu, 28 Jun 2018 09:02:57 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:BLN09DwnEdISRP5pYl1oDOpo0uI=, User-Agent: JetS3t/0.8.1 (Linux/3.10.0-693.11.6.el7.x86_64; amd64; fr; JVM 1.8.0_65), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 5FF7146348DFBFD5, x-amz-id-2: Ln+wAQKJItm2ny9PtedPGxDkDD24n+LMKqsQcKpBKAvfR8Tz+5y6JYcJ6H22RandpEMJOF6nqF8=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 28 Jun 2018 10:01:47 GMT, Connection: close, Server: AmazonS3] 
WARN  11:02:59,341 HttpMethodBase - Cookie rejected: "$Version="1"; aws-priv="eyJ2IjoxLCJldSI6MSwic3QiOjB9"; $Path="/"; $Domain=".aws.amazon.com"". Illegal domain attribute ".aws.amazon.com". Domain of origin: "aws.amazon.com" 
WARN  11:02:59,343 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 3527 seconds. Retrying connection. 
INFO  11:02:59,923 GATKRunReport - Uploaded run statistics report to AWS S3 
[adiouf@node19 test8_3_2_VariantFiltration]$ ls
AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_raw_snp_indels_filtered.vcf
AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_raw_snp_indels_filtered.vcf.idx