INFO 13:01:11,180 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:01:11,182 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50 INFO 13:01:11,182 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 13:01:11,182 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 13:01:11,182 HelpFormatter - [Fri May 07 13:01:11 EDT 2021] Executing on Linux 3.10.0-1160.15.2.el7.x86_64 amd64 INFO 13:01:11,183 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_172-b11 INFO 13:01:11,185 HelpFormatter - Program Args: -T RealignerTargetCreator -R /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.fasta -I /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg-dedup.bam -known /project/scv/examples/bioinformatics/gatk/ref/Homo_sapiens_assembly38.known_indels.vcf.gz -o /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-realign-targets.intervals INFO 13:01:11,188 HelpFormatter - Executing as yshen16@scc-pi1.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 13:01:11,189 HelpFormatter - Date/Time: 2021/05/07 13:01:11 INFO 13:01:11,189 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:01:11,189 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:01:11,215 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 13:01:11,243 GenomeAnalysisEngine - Deflater: IntelDeflater INFO 13:01:11,243 GenomeAnalysisEngine - Inflater: IntelInflater INFO 13:01:11,243 GenomeAnalysisEngine - Strictness is SILENT INFO 13:01:12,821 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 13:01:12,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:01:12,927 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10 WARN 13:01:13,269 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation INFO 13:01:14,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 13:01:15,529 GenomeAnalysisEngine - Done preparing for traversal INFO 13:01:15,530 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:01:15,531 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 13:01:15,531 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 13:01:45,534 ProgressMeter - chr1:67811045 5.1462144E7 30.0 s 0.0 s 2.1% 23.7 m 23.2 m INFO 13:02:15,536 ProgressMeter - chr1:156763609 1.50110208E8 60.0 s 0.0 s 4.9% 20.5 m 19.5 m INFO 13:02:45,537 ProgressMeter - chr1:248956393 2.25902592E8 90.0 s 0.0 s 7.7% 19.4 m 17.9 m INFO 13:03:15,539 ProgressMeter - chr2:90539653 3.21504774E8 120.0 s 0.0 s 10.6% 19.0 m 17.0 m INFO 13:03:45,540 ProgressMeter - chr2:182567693 4.16695814E8 2.5 m 0.0 s 13.4% 18.6 m 16.1 m INFO 13:04:15,542 ProgressMeter - chr3:31643773 5.22001023E8 3.0 m 0.0 s 16.2% 18.5 m 15.5 m INFO 13:04:45,543 ProgressMeter - chr3:122540589 5.79738239E8 3.5 m 0.0 s 19.1% 18.3 m 14.8 m INFO 13:05:15,545 ProgressMeter - chr4:12409701 6.8944551E8 4.0 m 0.0 s 21.8% 18.3 m 14.3 m INFO 13:05:45,546 ProgressMeter - chr4:103658233 7.77067142E8 4.5 m 0.0 s 24.7% 18.3 m 13.8 m INFO 13:06:15,551 ProgressMeter - chr5:7352553 8.85034017E8 5.0 m 0.0 s 27.6% 18.1 m 13.1 m INFO 13:06:45,552 ProgressMeter - chr5:100781981 9.77882145E8 5.5 m 0.0 s 30.5% 18.0 m 12.5 m INFO 13:07:15,553 ProgressMeter - chr6:13264865 1.072191988E9 6.0 m 0.0 s 33.4% 18.0 m 12.0 m INFO 13:07:45,555 ProgressMeter - chr6:107248881 1.162697204E9 6.5 m 0.0 s 36.3% 17.9 m 11.4 m INFO 13:08:15,560 ProgressMeter - chr7:30047129 1.260954831E9 7.0 m 0.0 s 39.2% 17.8 m 10.8 m INFO 13:08:45,561 ProgressMeter - chr7:124690921 1.352918223E9 7.5 m 0.0 s 42.2% 17.8 m 10.3 m INFO 13:09:15,562 ProgressMeter - chr8:61719969 1.446269444E9 8.0 m 0.0 s 45.2% 17.7 m 9.7 m INFO 13:09:45,564 ProgressMeter - chr9:10458957 1.546466768E9 8.5 m 0.0 s 48.1% 17.7 m 9.2 m INFO 13:10:15,565 ProgressMeter - chr9:105535865 1.617114576E9 9.0 m 0.0 s 51.0% 17.6 m 8.6 m INFO 13:10:45,566 ProgressMeter - chr10:60977157 1.732375085E9 9.5 m 0.0 s 54.0% 17.6 m 8.1 m INFO 13:11:15,568 ProgressMeter - chr11:23031309 1.830586459E9 10.0 m 0.0 s 56.9% 17.6 m 7.6 m INFO 13:11:45,569 ProgressMeter - chr11:117732201 1.913948251E9 10.5 m 0.0 s 59.9% 17.5 m 7.0 m INFO 13:12:15,570 ProgressMeter - chr12:77543313 2.006731385E9 11.0 m 0.0 s 62.8% 17.5 m 6.5 m INFO 13:12:45,572 ProgressMeter - chr13:37974185 2.113923366E9 11.5 m 0.0 s 65.7% 17.5 m 6.0 m INFO 13:13:15,573 ProgressMeter - chr14:12122301 2.19140731E9 12.0 m 0.0 s 68.5% 17.5 m 5.5 m INFO 13:13:45,574 ProgressMeter - chr14:104845297 2.294118606E9 12.5 m 0.0 s 71.4% 17.5 m 5.0 m INFO 13:14:15,575 ProgressMeter - chr15:95653305 2.391528532E9 13.0 m 0.0 s 74.4% 17.5 m 4.5 m INFO 13:14:45,577 ProgressMeter - chr16:88315917 2.472515433E9 13.5 m 0.0 s 77.4% 17.5 m 4.0 m INFO 13:15:15,578 ProgressMeter - chr18:9034401 2.574038003E9 14.0 m 0.0 s 80.3% 17.4 m 3.4 m INFO 13:15:45,579 ProgressMeter - chr19:23244049 2.674432536E9 14.5 m 0.0 s 83.2% 17.4 m 2.9 m INFO 13:16:15,581 ProgressMeter - chr20:60973229 2.753448232E9 15.0 m 0.0 s 86.2% 17.4 m 2.4 m INFO 13:16:45,582 ProgressMeter - chr22:47268633 2.836028686E9 15.5 m 0.0 s 89.2% 17.4 m 112.0 s INFO 13:17:15,583 ProgressMeter - chrX:93588725 2.934983346E9 16.0 m 0.0 s 92.3% 17.3 m 80.0 s INFO 13:17:45,584 ProgressMeter - chrY:34249629 3.042380145E9 16.5 m 0.0 s 95.3% 17.3 m 49.0 s INFO 13:18:15,586 ProgressMeter - chr7_KI270899v1_alt:64101 3.16298831E9 17.0 m 0.0 s 98.3% 17.3 m 17.0 s INFO 13:18:44,262 ProgressMeter - done 3.217346917E9 17.5 m 0.0 s 100.0% 17.5 m 0.0 s INFO 13:18:44,263 ProgressMeter - Total runtime 1048.73 secs, 17.48 min, 0.29 hours INFO 13:18:44,266 MicroScheduler - 51 reads were filtered out during the traversal out of approximately 415 total reads (12.29%) INFO 13:18:44,266 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 13:18:44,266 MicroScheduler - -> 3 reads (0.72% of total) failing BadMateFilter INFO 13:18:44,267 MicroScheduler - -> 2 reads (0.48% of total) failing DuplicateReadFilter INFO 13:18:44,267 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 13:18:44,267 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 13:18:44,267 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 13:18:44,267 MicroScheduler - -> 45 reads (10.84% of total) failing MappingQualityZeroFilter INFO 13:18:44,267 MicroScheduler - -> 1 reads (0.24% of total) failing NotPrimaryAlignmentFilter INFO 13:18:44,268 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter INFO 13:18:44,268 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter ------------------------------------------------------------------------------------------ Done. ------------------------------------------------------------------------------------------