INFO 13:02:01,866 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:02:01,869 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50 INFO 13:02:01,869 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 13:02:01,869 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 13:02:01,870 HelpFormatter - [Fri May 07 13:02:01 EDT 2021] Executing on Linux 3.10.0-1160.15.2.el7.x86_64 amd64 INFO 13:02:01,870 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_172-b11 INFO 13:02:01,873 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_400_6400064/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_400_6400064/SRR062634-realign-targets.intervals INFO 13:02:01,876 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 13:02:01,876 HelpFormatter - Date/Time: 2021/05/07 13:02:01 INFO 13:02:01,877 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:02:01,877 HelpFormatter - ------------------------------------------------------------------------------------ INFO 13:02:01,926 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 13:02:01,953 GenomeAnalysisEngine - Deflater: IntelDeflater INFO 13:02:01,953 GenomeAnalysisEngine - Inflater: IntelInflater INFO 13:02:01,954 GenomeAnalysisEngine - Strictness is SILENT INFO 13:02:03,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 13:02:03,508 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:02:03,642 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13 WARN 13:02:04,062 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation INFO 13:02:05,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 13:02:06,150 GenomeAnalysisEngine - Done preparing for traversal INFO 13:02:06,150 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:02:06,151 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 13:02:06,151 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 13:02:36,163 ProgressMeter - chr1:74779205 5.4575104E7 30.0 s 0.0 s 2.3% 21.5 m 21.0 m INFO 13:03:06,165 ProgressMeter - chr1:161823609 1.50110208E8 60.0 s 0.0 s 5.0% 19.9 m 18.9 m INFO 13:03:36,166 ProgressMeter - chr2:5990301 2.51004422E8 90.0 s 0.0 s 7.9% 18.9 m 17.4 m INFO 13:04:06,167 ProgressMeter - chr2:99372665 3.40641286E8 120.0 s 0.0 s 10.8% 18.5 m 16.5 m INFO 13:04:36,169 ProgressMeter - chr2:192494269 4.3904359E8 2.5 m 0.0 s 13.7% 18.2 m 15.7 m INFO 13:05:06,170 ProgressMeter - chr3:43401277 5.29881727E8 3.0 m 0.0 s 16.6% 18.1 m 15.1 m INFO 13:05:36,171 ProgressMeter - chr3:137421361 6.15504511E8 3.5 m 0.0 s 19.5% 17.9 m 14.4 m INFO 13:06:06,173 ProgressMeter - chr4:32087605 7.16577414E8 4.0 m 0.0 s 22.4% 17.8 m 13.8 m INFO 13:06:36,174 ProgressMeter - chr4:125290349 8.09409158E8 4.5 m 0.0 s 25.3% 17.8 m 13.3 m INFO 13:07:06,175 ProgressMeter - chr5:28205089 8.96568353E8 5.0 m 0.0 s 28.2% 17.7 m 12.7 m INFO 13:07:36,176 ProgressMeter - chr5:121255809 9.89629473E8 5.5 m 0.0 s 31.1% 17.7 m 12.2 m INFO 13:08:06,177 ProgressMeter - chr6:32798245 1.087265268E9 6.0 m 0.0 s 34.0% 17.6 m 11.6 m INFO 13:08:36,179 ProgressMeter - chr6:126229305 1.164925428E9 6.5 m 0.0 s 36.9% 17.6 m 11.1 m INFO 13:09:06,183 ProgressMeter - chr7:48606597 1.265083599E9 7.0 m 0.0 s 39.8% 17.6 m 10.6 m INFO 13:09:36,184 ProgressMeter - chr7:142344913 1.373201615E9 7.5 m 0.0 s 42.7% 17.6 m 10.1 m INFO 13:10:06,185 ProgressMeter - chr8:75756517 1.466700292E9 8.0 m 0.0 s 45.6% 17.5 m 9.5 m INFO 13:10:36,186 ProgressMeter - chr9:23864565 1.559360976E9 8.5 m 0.0 s 48.5% 17.5 m 9.0 m INFO 13:11:06,187 ProgressMeter - chr9:115865865 1.636775376E9 9.0 m 0.0 s 51.4% 17.5 m 8.5 m INFO 13:11:36,188 ProgressMeter - chr10:71167149 1.744466477E9 9.5 m 0.0 s 54.3% 17.5 m 8.0 m INFO 13:12:06,189 ProgressMeter - chr11:30398925 1.833846875E9 10.0 m 0.0 s 57.2% 17.5 m 7.5 m INFO 13:12:36,190 ProgressMeter - chr11:122479001 1.913948251E9 10.5 m 0.0 s 60.0% 17.5 m 7.0 m INFO 13:13:06,191 ProgressMeter - chr12:81463837 2.022476409E9 11.0 m 0.0 s 62.9% 17.5 m 6.5 m INFO 13:13:36,192 ProgressMeter - chr13:41479185 2.113923366E9 11.5 m 0.0 s 65.8% 17.5 m 6.0 m INFO 13:14:06,194 ProgressMeter - chr14:20701257 2.211625166E9 12.0 m 0.0 s 68.8% 17.5 m 5.5 m INFO 13:14:36,195 ProgressMeter - chr15:5548301 2.298451028E9 12.5 m 0.0 s 71.6% 17.5 m 5.0 m INFO 13:15:06,196 ProgressMeter - chr15:99573741 2.393642068E9 13.0 m 0.0 s 74.5% 17.4 m 4.4 m INFO 13:15:36,197 ProgressMeter - chr17:1226001 2.490780562E9 13.5 m 0.0 s 77.5% 17.4 m 3.9 m INFO 13:16:06,198 ProgressMeter - chr18:11506105 2.576593907E9 14.0 m 0.0 s 80.4% 17.4 m 3.4 m INFO 13:16:36,200 ProgressMeter - chr19:24086849 2.674432536E9 14.5 m 0.0 s 83.3% 17.4 m 2.9 m INFO 13:17:06,201 ProgressMeter - chr20:56982557 2.76806276E9 15.0 m 0.0 s 86.1% 17.4 m 2.4 m INFO 13:17:36,202 ProgressMeter - chr22:41527033 2.836028686E9 15.5 m 0.0 s 89.1% 17.4 m 114.0 s INFO 13:18:06,203 ProgressMeter - chrX:85207357 2.957888178E9 16.0 m 0.0 s 92.0% 17.4 m 83.0 s INFO 13:18:36,204 ProgressMeter - chrY:23689569 3.042543985E9 16.5 m 0.0 s 94.9% 17.4 m 52.0 s INFO 13:19:06,206 ProgressMeter - chr19_GL949746v1_alt:720001 3.149865314E9 17.0 m 0.0 s 97.9% 17.4 m 21.0 s INFO 13:19:36,208 ProgressMeter - HLA-DRB1*16:02:01:11001 3.217335912E9 17.5 m 0.0 s 100.0% 17.5 m 0.0 s INFO 13:19:38,904 ProgressMeter - done 3.217346917E9 17.5 m 0.0 s 100.0% 17.5 m 0.0 s INFO 13:19:38,905 ProgressMeter - Total runtime 1052.75 secs, 17.55 min, 0.29 hours INFO 13:19:38,909 MicroScheduler - 94 reads were filtered out during the traversal out of approximately 824 total reads (11.41%) INFO 13:19:38,910 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 13:19:38,910 MicroScheduler - -> 8 reads (0.97% of total) failing BadMateFilter INFO 13:19:38,910 MicroScheduler - -> 4 reads (0.49% of total) failing DuplicateReadFilter INFO 13:19:38,910 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 13:19:38,910 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 13:19:38,911 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 13:19:38,911 MicroScheduler - -> 81 reads (9.83% of total) failing MappingQualityZeroFilter INFO 13:19:38,911 MicroScheduler - -> 1 reads (0.12% of total) failing NotPrimaryAlignmentFilter INFO 13:19:38,911 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter INFO 13:19:38,911 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter ------------------------------------------------------------------------------------------ Done. ------------------------------------------------------------------------------------------