INFO 14:14:41,512 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:41,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 14:14:41,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:14:41,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 14:14:41,517 HelpFormatter - Program Args: -T SelectVariants -R ../test8_0_REFERENCE_with_faidx/MSU7.fa -V ../test8_3_2_VariantFiltration/AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_raw_snp_indels_filtered.vcf -o ./AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_filtered_snp_only.vcf -selectType SNP
INFO 14:14:41,523 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 14:14:41,523 HelpFormatter - Date/Time: 2018/06/28 14:14:41
INFO 14:14:41,523 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:41,523 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:41,577 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:14:41,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 14:14:41,757 GenomeAnalysisEngine - Preparing for traversal
INFO 14:14:41,759 GenomeAnalysisEngine - Done preparing for traversal
INFO 14:14:41,759 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 14:14:41,759 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 14:14:41,760 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 14:14:51,830 SelectVariants - 458840 records processed.
INFO 14:14:53,434 ProgressMeter - done 583200.0 11.0 s 20.0 s 100.0% 11.0 s 0.0 s
INFO 14:14:53,435 ProgressMeter - Total runtime 11.68 secs, 0.19 min, 0.00 hours
WARN 14:14:54,307 RestStorageService - Error Response: PUT '/1QtH5ugL2ciyULpm5DIMwyYo3aru6Th6.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 402, x-amz-meta-md5-hash: 0e6f8f2d5089e8e09ab2f5ce17ff05fb, Content-Type: application/octet-stream, Content-MD5: Dm+PLVCJ6OCasvXOF/8F+w==, Date: Thu, 28 Jun 2018 12:14:53 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:A9etMJc7DAgs1PHUQvnaMAXitHU=, 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: 825D058C7990B8AF, x-amz-id-2: N1Ho7RXrXVTCN+R3CPI1SeRZkCfH+TmA7kbvDHyDNK6IPHlPiJ/+a2EeaxdmzAR1UyB4YZMEOAo=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 28 Jun 2018 13:13:41 GMT, Connection: close, Server: AmazonS3]
WARN 14:14:55,054 HttpMethodBase - Cookie rejected: "$Version="1"; aws-priv="eyJ2IjoxLCJldSI6MSwic3QiOjB9"; $Path="/"; $Domain=".aws.amazon.com"". Illegal domain attribute ".aws.amazon.com". Domain of origin: "aws.amazon.com"
WARN 14:14:55,056 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 3527 seconds. Retrying connection.
INFO 14:14:55,615 GATKRunReport - Uploaded run statistics report to AWS S3
[adiouf@node19 test8_3_3_SelectVariants]$ ls
AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_filtered_snp_only.vcf
AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_filtered_snp_only.vcf.idx
[adiouf@node19 test8_3_3_SelectVariants]$