INFO  13:19:43,693 HelpFormatter - ------------------------------------------------------------------------------------ 
INFO  13:19:43,695 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50 
INFO  13:19:43,696 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  13:19:43,697 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  13:19:43,697 HelpFormatter - [Fri May 07 13:19:43 EDT 2021] Executing on Linux 3.10.0-1160.15.2.el7.x86_64 amd64 
INFO  13:19:43,697 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_172-b11 
INFO  13:19:43,700 HelpFormatter - Program Args: -T IndelRealigner -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -known /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz -targetIntervals /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-realign-targets.intervals -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup.bam -o /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_400_6400064/SRR062634-sort-rg-dedup-realigned.bam --filter_bases_not_stored 
INFO  13:19:43,704 HelpFormatter - Executing as yshen16@scc-mc2.scc.bu.edu on Linux 3.10.0-1160.15.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_172-b11. 
INFO  13:19:43,704 HelpFormatter - Date/Time: 2021/05/07 13:19:43 
INFO  13:19:43,704 HelpFormatter - ------------------------------------------------------------------------------------ 
INFO  13:19:43,704 HelpFormatter - ------------------------------------------------------------------------------------ 
INFO  13:19:43,777 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/pkg.7/gatk/3.8-1/install/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so 
INFO  13:19:43,798 GenomeAnalysisEngine - Deflater: IntelDeflater 
INFO  13:19:43,798 GenomeAnalysisEngine - Inflater: IntelInflater 
INFO  13:19:43,799 GenomeAnalysisEngine - Strictness is SILENT 
INFO  13:19:45,128 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  13:19:45,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  13:19:45,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13 
WARN  13:19:45,647 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation 
INFO  13:19:46,814 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  13:19:46,818 GenomeAnalysisEngine - Done preparing for traversal 
INFO  13:19:46,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  13:19:46,819 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  13:19:46,819 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime 
INFO  13:19:47,825 ReadShardBalancer$1 - Loading BAM index data 
INFO  13:19:47,826 ReadShardBalancer$1 - Done loading BAM index data 
INFO  13:20:01,210 ProgressMeter -            done       803.0    14.0 s       5.0 h       99.9%    14.0 s       0.0 s 
INFO  13:20:01,211 ProgressMeter - Total runtime 14.39 secs, 0.24 min, 0.00 hours 
INFO  13:20:01,214 MicroScheduler - 24 reads were filtered out during the traversal out of approximately 827 total reads (2.90%) 
INFO  13:20:01,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  13:20:01,215 MicroScheduler -   -> 24 reads (2.90% of total) failing MalformedReadFilter 
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Done. ------------------------------------------------------------------------------------------