INFO 11:48:18,648 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:48:18,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 11:48:18,650 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:48:18,650 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:48:18,654 HelpFormatter - Program Args: -T IndelRealigner -R ../test8_0_REFERENCE_with_faidx/MSU7.fa -I ../test6_sortsam/AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed.bam -targetIntervals ../test8_1_RealignerTargetCreator/AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed.intervals -o ./AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realigned.bam -fixMisencodedQuals
INFO 11:48:18,663 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 11:48:18,663 HelpFormatter - Date/Time: 2018/06/27 11:48:18
INFO 11:48:18,663 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:48:18,664 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:48:18,823 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:48:18,900 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:48:18,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:48:18,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 11:48:19,005 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:48:19,010 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:48:19,011 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:48:19,011 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:48:19,011 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 11:48:19,258 ReadShardBalancer$1 - Loading BAM index data
INFO 11:48:19,259 ReadShardBalancer$1 - Done loading BAM index data
INFO 11:48:49,232 ProgressMeter - Chr3:20153069 1323612.0 30.0 s 22.0 s 26.5% 113.0 s 83.0 s
INFO 11:49:19,234 ProgressMeter - Chr6:30199454 3046364.0 60.0 s 19.0 s 56.3% 106.0 s 46.0 s
INFO 11:49:49,235 ProgressMeter - Chr11:2246958 4664477.0 90.0 s 19.0 s 85.0% 105.0 s 15.0 s
INFO 11:50:05,165 ProgressMeter - done 5550596.0 106.0 s 19.0 s 100.0% 106.0 s 0.0 s
INFO 11:50:05,169 ProgressMeter - Total runtime 106.16 secs, 1.77 min, 0.03 hours
INFO 11:50:05,173 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 5550596 total reads (0.00%)
INFO 11:50:05,173 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
WARN 11:50:06,478 RestStorageService - Error Response: PUT '/9PBNINWa0fvLMZBWHCG5o3XeDjbsF5fD.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 413, x-amz-meta-md5-hash: b112180d4b42250c70a41841dd105fb3, Content-Type: application/octet-stream, Content-MD5: sRIYDUtCJQxwpBhB3RBfsw==, Date: Wed, 27 Jun 2018 09:50:05 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:goSgEKXZ2PbB6Y59Js5nNP77eEE=, User-Agent: JetS3t/0.8.1 (Linux/3.10.0-693.11.6.el7.x86_64; amd64; fr; JVM 1.8.0_65), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: E4CB663BBC5693B5, x-amz-id-2: dzDVWBIHQqk1b85YzgaQH5eWzKUzYqPZLaPTRaSL+XpYWkstKTRXtiFsetTm9jCwJqNML5ruPwE=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 27 Jun 2018 10:48:57 GMT, Connection: close, Server: AmazonS3]
WARN 11:50:07,227 HttpMethodBase - Cookie rejected: "$Version="1"; aws-priv="eyJ2IjoxLCJldSI6MSwic3QiOjB9"; $Path="/"; $Domain=".aws.amazon.com"". Illegal domain attribute ".aws.amazon.com". Domain of origin: "aws.amazon.com"
WARN 11:50:07,233 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 3530 seconds. Retrying connection.
INFO 11:50:07,933 GATKRunReport - Uploaded run statistics report to AWS S3
[adiouf@node19 test8_2_IndelRealigner]$ ls
AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realigned.bai AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realigned.bam
[adiouf@node19 test8_2_IndelRealigner]$