INFO 15:38:22,350 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:38:22,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 15:38:22,352 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:38:22,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 15:38:22,355 HelpFormatter - Program Args: -R /data/kstamm/ref/GATK/bundle/1.2/human_g1k_v37.fasta -T PrintReads -o sub.BAM -I input.BAM -dcov 200 INFO 15:38:22,358 HelpFormatter - Executing as kstamm@etc on Linux 2.6.32-431.29.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01. INFO 15:38:22,358 HelpFormatter - Date/Time: 2014/12/15 15:38:22 INFO 15:38:22,358 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:38:22,358 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:38:22,842 GenomeAnalysisEngine - Strictness is SILENT INFO 15:38:22,904 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 200 INFO 15:38:22,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:38:22,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 15:38:22,981 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 15:38:22,985 GenomeAnalysisEngine - Done preparing for traversal INFO 15:38:22,985 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 15:38:22,986 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 15:38:22,986 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime INFO 15:38:22,987 ReadShardBalancer$1 - Loading BAM index data INFO 15:38:22,988 ReadShardBalancer$1 - Done loading BAM index data INFO 15:38:27,113 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6df76561 INFO 15:38:27,123 ProgressMeter - done 320398.0 4.0 s 12.0 s 98.5% 4.0 s 0.0 s INFO 15:38:27,124 ProgressMeter - Total runtime 4.14 secs, 0.07 min, 0.00 hours INFO 15:38:27,126 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 320426 total reads (0.00%) INFO 15:38:27,127 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 15:38:27,721 GATKRunReport - Uploaded run statistics report to AWS S3