INFO 11:15:32,005 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:15:32,007 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 11:15:32,007 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:15:32,008 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:15:32,011 HelpFormatter - Program Args: -T RealignerTargetCreator -R ../test8_0_REFERENCE_with_faidx/MSU7.fa -I ../test6_sortsam/AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed.bam -o ./AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed.intervals -fixMisencodedQuals
INFO 11:15:32,017 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 11:15:32,017 HelpFormatter - Date/Time: 2018/06/27 11:15:32
INFO 11:15:32,017 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:15:32,017 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:15:32,063 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:15:32,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:15:32,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:15:32,157 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:15:32,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:15:32,310 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:15:32,311 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:15:32,311 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:15:32,311 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:16:02,315 ProgressMeter - Chr2:5301633 4.8562955E7 30.0 s 0.0 s 12.9% 3.9 m 3.4 m
INFO 11:16:32,317 ProgressMeter - Chr3:18995357 9.8197229E7 60.0 s 0.0 s 26.2% 3.8 m 2.8 m
INFO 11:17:02,318 ProgressMeter - Chr5:5760985 1.5687547E8 90.0 s 0.0 s 41.8% 3.6 m 2.1 m
INFO 11:17:32,321 ProgressMeter - Chr6:23215145 2.04282864E8 120.0 s 0.0 s 54.5% 3.7 m 100.0 s
INFO 11:18:02,325 ProgressMeter - Chr8:8407193 2.5043452E8 2.5 m 0.0 s 66.8% 3.7 m 74.0 s
INFO 11:18:32,328 ProgressMeter - Chr10:17352357 3.10835926E8 3.0 m 0.0 s 82.9% 3.6 m 37.0 s
INFO 11:19:02,331 ProgressMeter - Chr12:23517641 3.69224703E8 3.5 m 0.0 s 98.4% 3.6 m 3.0 s
INFO 11:19:06,913 ProgressMeter - done 3.75096285E8 3.6 m 0.0 s 100.0% 3.6 m 0.0 s
INFO 11:19:06,913 ProgressMeter - Total runtime 214.60 secs, 3.58 min, 0.06 hours
INFO 11:19:06,916 MicroScheduler - 1162672 reads were filtered out during the traversal out of approximately 5573073 total reads (20.86%)
INFO 11:19:06,917 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 11:19:06,917 MicroScheduler - -> 406 reads (0.01% of total) failing BadMateFilter
INFO 11:19:06,917 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 11:19:06,917 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 11:19:06,918 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 11:19:06,918 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 11:19:06,918 MicroScheduler - -> 1160521 reads (20.82% of total) failing MappingQualityZeroFilter
INFO 11:19:06,918 MicroScheduler - -> 1745 reads (0.03% of total) failing NotPrimaryAlignmentFilter
INFO 11:19:06,918 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter
INFO 11:19:06,919 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
WARN 11:19:07,797 RestStorageService - Error Response: PUT '/CLi6J7GSFzGxBVGmy2CgJAG2VPFqQKr8.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 418, x-amz-meta-md5-hash: ca58fe2a019147bac1f6cd092117d90f, Content-Type: application/octet-stream, Content-MD5: ylj+KgGRR7rB9s0JIRfZDw==, Date: Wed, 27 Jun 2018 09:19:07 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:UVs6qjqcTClIHBXZLYroQKqxpIE=, 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: 178398585A400B3B, x-amz-id-2: LG0wfDsoWi/xgAbVs+XYhMVYd0dYj/WvROOOYGfQSvIKiptL9Q0V9jsLxntql569T7CGtXh1Uoc=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 27 Jun 2018 10:17:59 GMT, Connection: close, Server: AmazonS3]
WARN 11:19:08,539 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 11:19:08,542 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 3531 seconds. Retrying connection.
INFO 11:19:09,088 GATKRunReport - Uploaded run statistics report to AWS S3