nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 nyx5299 INFO 13:14:44,931 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:14:44,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 INFO 13:14:44,933 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:14:44,933 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:14:44,937 HelpFormatter - Program Args: -T BaseRecalibrator -R ../../genomes/dpse-all-gene-r3.1.fasta -I ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.realigned.bam -knownSites ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf -o ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.recal.table -nct 12 INFO 13:14:44,938 HelpFormatter - Date/Time: 2013/12/02 13:14:44 INFO 13:14:44,938 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:14:44,938 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:14:45,773 ArgumentTypeDescriptor - Dynamically determined type of ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf to be VCF INFO 13:14:46,414 GenomeAnalysisEngine - Strictness is SILENT INFO 13:14:47,132 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 13:14:47,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:14:47,500 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.36 INFO 13:14:47,592 RMDTrackBuilder - Loading Tribble index from disk for file ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf WARN 13:14:47,734 RMDTrackBuilder - Index file /scratch/lsa_flux/kraigrs/Machado_Dpse/scripts/shell/../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf.idx is out of date (index older than input file), deleting and updating the index file INFO 13:14:47,737 RMDTrackBuilder - Creating Tribble index in memory for file ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf INFO 13:14:48,653 RMDTrackBuilder - Writing Tribble index to disk for file /scratch/lsa_flux/kraigrs/Machado_Dpse/scripts/shell/../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.raw_variants_highQual.vcf.idx INFO 13:14:52,398 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 12 CPU thread(s) for each of 1 data thread(s), of 12 processors available on this machine INFO 13:14:52,619 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 13:14:52,623 GenomeAnalysisEngine - Done preparing for traversal INFO 13:14:52,623 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:14:52,623 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 13:14:52,711 BaseRecalibrator - The covariates being used here: INFO 13:14:52,711 BaseRecalibrator - ReadGroupCovariate INFO 13:14:52,711 BaseRecalibrator - QualityScoreCovariate INFO 13:14:52,711 BaseRecalibrator - ContextCovariate INFO 13:14:52,711 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 13:14:52,711 BaseRecalibrator - CycleCovariate INFO 13:14:52,714 ReadShardBalancer$1 - Loading BAM index data INFO 13:14:52,715 ReadShardBalancer$1 - Done loading BAM index data INFO 13:15:22,697 ProgressMeter - FBgn0263302:62930 2.23e+06 30.0 s 13.0 s 8.4% 6.0 m 5.5 m INFO 13:15:52,701 ProgressMeter - FBgn0078676:10017 4.65e+06 60.0 s 12.0 s 17.5% 5.7 m 4.7 m INFO 13:16:22,703 ProgressMeter - FBgn0071294:552 7.11e+06 90.0 s 12.0 s 26.8% 5.6 m 4.1 m INFO 13:16:52,705 ProgressMeter - FBgn0081817:5315 9.53e+06 120.0 s 12.0 s 36.0% 5.6 m 3.6 m INFO 13:17:22,707 ProgressMeter - FBgn0245200:21267 1.19e+07 2.5 m 12.0 s 45.1% 5.5 m 3.0 m INFO 13:17:52,708 ProgressMeter - FBgn0250015:286 1.43e+07 3.0 m 12.0 s 54.0% 5.6 m 2.6 m INFO 13:18:22,709 ProgressMeter - FBgn0079189:2996 1.67e+07 3.5 m 12.0 s 63.3% 5.5 m 2.0 m INFO 13:18:52,711 ProgressMeter - FBgn0074644:22894 1.91e+07 4.0 m 12.0 s 72.6% 5.5 m 90.0 s INFO 13:19:22,712 ProgressMeter - FBgn0243733:6879 2.15e+07 4.5 m 12.0 s 81.5% 5.5 m 61.0 s INFO 13:19:52,713 ProgressMeter - FBgn0079236:2717 2.39e+07 5.0 m 12.0 s 90.7% 5.5 m 30.0 s INFO 13:20:22,748 ProgressMeter - FBgn0072080:1146 2.64e+07 5.5 m 12.0 s 99.9% 5.5 m 0.0 s INFO 13:20:52,749 ProgressMeter - FBgn0077946:649 2.64e+07 6.0 m 13.0 s 100.0% 6.0 m 0.0 s INFO 13:21:22,751 ProgressMeter - FBgn0077946:649 2.64e+07 6.5 m 14.0 s 100.0% 6.5 m 0.0 s INFO 13:21:52,752 ProgressMeter - FBgn0077946:649 2.64e+07 7.0 m 15.0 s 100.0% 7.0 m 0.0 s INFO 13:22:22,754 ProgressMeter - FBgn0077946:649 2.64e+07 7.5 m 17.0 s 100.0% 7.5 m 0.0 s INFO 13:22:52,755 ProgressMeter - FBgn0077946:649 2.64e+07 8.0 m 18.0 s 100.0% 8.0 m 0.0 s INFO 13:23:22,757 ProgressMeter - FBgn0077946:649 2.64e+07 8.5 m 19.0 s 100.0% 8.5 m 0.0 s INFO 13:23:52,758 ProgressMeter - FBgn0077946:649 2.64e+07 9.0 m 20.0 s 100.0% 9.0 m 0.0 s INFO 13:24:04,002 BaseRecalibrator - Calculating quantized quality scores... INFO 13:24:04,058 BaseRecalibrator - Writing recalibration report... INFO 13:24:05,151 BaseRecalibrator - ...done! INFO 13:24:05,151 BaseRecalibrator - BaseRecalibrator was able to recalibrate 26400640 reads INFO 13:24:05,152 ProgressMeter - done 2.64e+07 9.2 m 20.0 s 100.0% 9.2 m 0.0 s INFO 13:24:05,153 ProgressMeter - Total runtime 552.53 secs, 9.21 min, 0.15 hours INFO 13:24:05,153 MicroScheduler - 205209395 reads were filtered out during the traversal out of approximately 231648926 total reads (88.59%) INFO 13:24:05,153 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter INFO 13:24:05,153 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 13:24:05,153 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 13:24:05,153 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 13:24:05,154 MicroScheduler - -> 205209395 reads (88.59% of total) failing MappingQualityZeroFilter INFO 13:24:05,154 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 13:24:05,154 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter INFO 13:24:38,396 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:24:38,398 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 INFO 13:24:38,398 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:24:38,398 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:24:38,402 HelpFormatter - Program Args: -T PrintReads -R ../../genomes/dpse-all-gene-r3.1.fasta -I ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.realigned.bam -BQSR ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.recal.table -o ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.recal.bam -nct 12 INFO 13:24:38,402 HelpFormatter - Date/Time: 2013/12/02 13:24:38 INFO 13:24:38,402 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:24:38,402 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:24:39,004 GenomeAnalysisEngine - Strictness is SILENT INFO 13:24:40,015 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 13:24:40,047 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 13:24:40,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:24:40,197 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14 INFO 13:24:40,333 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 12 CPU thread(s) for each of 1 data thread(s), of 12 processors available on this machine INFO 13:24:40,427 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 13:24:40,431 GenomeAnalysisEngine - Done preparing for traversal INFO 13:24:40,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:24:40,432 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 13:24:40,570 ReadShardBalancer$1 - Loading BAM index data INFO 13:24:40,571 ReadShardBalancer$1 - Done loading BAM index data INFO 13:25:10,435 ProgressMeter - FBgn0262506:28658 8.05e+05 30.0 s 37.0 s 2.8% 17.8 m 17.3 m INFO 13:25:40,437 ProgressMeter - FBgn0081872:777 1.64e+06 60.0 s 36.0 s 5.6% 17.8 m 16.8 m INFO 13:26:10,438 ProgressMeter - FBgn0263302:201682 2.39e+06 90.0 s 37.0 s 8.6% 17.4 m 15.9 m INFO 13:26:40,439 ProgressMeter - FBgn0079044:1151 3.30e+06 120.0 s 36.0 s 11.5% 17.4 m 15.4 m INFO 13:27:10,441 ProgressMeter - FBgn0247929:70854 4.11e+06 2.5 m 36.0 s 14.5% 17.2 m 14.7 m INFO 13:27:40,442 ProgressMeter - FBgn0078676:650 4.98e+06 3.0 m 36.0 s 17.5% 17.2 m 14.2 m INFO 13:28:10,444 ProgressMeter - FBgn0079324:448 5.83e+06 3.5 m 36.0 s 20.5% 17.1 m 13.6 m INFO 13:28:40,445 ProgressMeter - FBgn0245358:55576 6.66e+06 4.0 m 36.0 s 23.5% 17.0 m 13.0 m INFO 13:29:10,446 ProgressMeter - FBgn0076949:20903 7.51e+06 4.5 m 35.0 s 26.4% 17.1 m 12.6 m INFO 13:29:40,446 ProgressMeter - FBgn0081865:1356 8.36e+06 5.0 m 35.0 s 29.3% 17.1 m 12.1 m INFO 13:30:10,452 ProgressMeter - FBgn0263807:22359 9.19e+06 5.5 m 35.0 s 32.3% 17.0 m 11.5 m INFO 13:30:40,453 ProgressMeter - FBgn0074333:1035 1.00e+07 6.0 m 35.0 s 35.3% 17.0 m 11.0 m INFO 13:31:10,454 ProgressMeter - FBgn0076357:1611 1.09e+07 6.5 m 35.0 s 38.2% 17.0 m 10.5 m INFO 13:31:40,457 ProgressMeter - FBgn0077976:2485 1.17e+07 7.0 m 35.0 s 41.1% 17.0 m 10.0 m INFO 13:32:10,458 ProgressMeter - FBgn0070826:3259 1.25e+07 7.5 m 35.0 s 44.1% 17.0 m 9.5 m INFO 13:32:40,459 ProgressMeter - FBgn0077745:1561 1.34e+07 8.0 m 35.0 s 47.0% 17.0 m 9.0 m INFO 13:33:20,460 ProgressMeter - FBgn0077549:8582 1.45e+07 8.7 m 35.0 s 50.9% 17.0 m 8.4 m INFO 13:34:00,461 ProgressMeter - FBgn0080859:1650 1.56e+07 9.3 m 35.0 s 55.0% 17.0 m 7.6 m INFO 13:34:30,462 ProgressMeter - FBgn0074595:239 1.64e+07 9.8 m 35.0 s 58.0% 17.0 m 7.1 m INFO 13:35:00,463 ProgressMeter - FBgn0074092:1679 1.73e+07 10.3 m 35.0 s 60.9% 17.0 m 6.6 m INFO 13:35:30,464 ProgressMeter - FBgn0248178:4765 1.81e+07 10.8 m 35.0 s 63.9% 17.0 m 6.1 m INFO 13:36:00,464 ProgressMeter - FBgn0243730:6920 1.89e+07 11.3 m 35.0 s 66.8% 17.0 m 5.6 m INFO 13:36:30,465 ProgressMeter - FBgn0080659:1627 1.98e+07 11.8 m 35.0 s 69.7% 17.0 m 5.1 m INFO 13:37:00,466 ProgressMeter - FBgn0074349:31961 2.06e+07 12.3 m 35.0 s 72.8% 16.9 m 4.6 m INFO 13:37:30,467 ProgressMeter - FBgn0248374:1394 2.14e+07 12.8 m 35.0 s 75.9% 16.9 m 4.1 m INFO 13:38:00,468 ProgressMeter - FBgn0075831:1982 2.23e+07 13.3 m 35.0 s 78.8% 16.9 m 3.6 m INFO 13:38:30,469 ProgressMeter - FBgn0244196:8683 2.31e+07 13.8 m 35.0 s 81.7% 16.9 m 3.1 m INFO 13:39:00,470 ProgressMeter - FBgn0076393:9483 2.40e+07 14.3 m 35.0 s 84.6% 16.9 m 2.6 m INFO 13:39:30,471 ProgressMeter - FBgn0074325:1114 2.48e+07 14.8 m 35.0 s 87.5% 16.9 m 2.1 m INFO 13:40:00,472 ProgressMeter - FBgn0265173:3119 2.57e+07 15.3 m 35.0 s 90.6% 16.9 m 95.0 s INFO 13:40:30,473 ProgressMeter - FBgn0072467:3667 2.65e+07 15.8 m 35.0 s 93.6% 16.9 m 65.0 s INFO 13:41:00,474 ProgressMeter - FBgn0082095:48882 2.73e+07 16.3 m 35.0 s 96.5% 16.9 m 35.0 s INFO 13:41:40,475 ProgressMeter - FBgn0082054:8344 2.84e+07 17.0 m 35.0 s 100.0% 17.0 m 0.0 s INFO 13:42:20,571 ProgressMeter - FBgn0082054:8344 2.84e+07 17.7 m 37.0 s 100.0% 17.7 m 0.0 s INFO 13:42:50,572 ProgressMeter - FBgn0082054:8344 2.84e+07 18.2 m 38.0 s 100.0% 18.2 m 0.0 s INFO 13:43:20,573 ProgressMeter - FBgn0082054:8344 2.84e+07 18.7 m 39.0 s 100.0% 18.7 m 0.0 s INFO 13:43:50,574 ProgressMeter - FBgn0082054:8344 2.84e+07 19.2 m 40.0 s 100.0% 19.2 m 0.0 s INFO 13:44:30,575 ProgressMeter - FBgn0082054:8344 2.84e+07 19.8 m 41.0 s 100.0% 19.8 m 0.0 s INFO 13:45:00,841 ProgressMeter - FBgn0082054:8344 2.84e+07 20.3 m 43.0 s 100.0% 20.3 m 0.0 s INFO 13:45:30,922 ProgressMeter - FBgn0082054:8344 2.84e+07 20.8 m 44.0 s 100.0% 20.8 m 0.0 s INFO 13:46:00,923 ProgressMeter - FBgn0082054:8344 2.84e+07 21.3 m 45.0 s 100.0% 21.3 m 0.0 s INFO 13:46:30,924 ProgressMeter - FBgn0082054:8344 2.84e+07 21.8 m 46.0 s 100.0% 21.8 m 0.0 s INFO 13:47:00,924 ProgressMeter - FBgn0082054:8344 2.84e+07 22.3 m 47.0 s 100.0% 22.3 m 0.0 s INFO 13:47:30,925 ProgressMeter - FBgn0082054:8344 2.84e+07 22.8 m 48.0 s 100.0% 22.8 m 0.0 s INFO 13:48:00,926 ProgressMeter - FBgn0082054:8344 2.84e+07 23.3 m 49.0 s 100.0% 23.3 m 0.0 s INFO 13:48:30,927 ProgressMeter - FBgn0082054:8344 2.84e+07 23.8 m 50.0 s 100.0% 23.8 m 0.0 s INFO 13:49:00,928 ProgressMeter - FBgn0082054:8344 2.84e+07 24.3 m 51.0 s 100.0% 24.3 m 0.0 s INFO 13:49:30,935 ProgressMeter - FBgn0082054:8344 2.84e+07 24.8 m 52.0 s 100.0% 24.8 m 0.0 s INFO 13:50:00,936 ProgressMeter - FBgn0082054:8344 2.84e+07 25.3 m 53.0 s 100.0% 25.3 m 0.0 s INFO 13:50:30,949 ProgressMeter - FBgn0082054:8344 2.84e+07 25.8 m 54.0 s 100.0% 25.8 m 0.0 s INFO 13:51:00,950 ProgressMeter - FBgn0082054:8344 2.84e+07 26.3 m 55.0 s 100.0% 26.3 m 0.0 s INFO 13:51:30,951 ProgressMeter - FBgn0082054:8344 2.84e+07 26.8 m 56.0 s 100.0% 26.8 m 0.0 s INFO 13:52:00,952 ProgressMeter - FBgn0082054:8344 2.84e+07 27.3 m 57.0 s 100.0% 27.3 m 0.0 s INFO 13:52:31,005 ProgressMeter - FBgn0082054:8344 2.84e+07 27.8 m 58.0 s 100.0% 27.8 m 0.0 s INFO 13:53:01,006 ProgressMeter - FBgn0082054:8344 2.84e+07 28.3 m 59.0 s 100.0% 28.3 m 0.0 s INFO 13:53:31,007 ProgressMeter - FBgn0082054:8344 2.84e+07 28.8 m 61.0 s 100.0% 28.8 m 0.0 s INFO 13:54:01,008 ProgressMeter - FBgn0082054:8344 2.84e+07 29.3 m 62.0 s 100.0% 29.3 m 0.0 s INFO 13:54:31,041 ProgressMeter - FBgn0082054:8344 2.84e+07 29.8 m 63.0 s 100.0% 29.8 m 0.0 s INFO 13:55:01,042 ProgressMeter - FBgn0082054:8344 2.84e+07 30.3 m 64.0 s 100.0% 30.3 m 0.0 s INFO 13:55:31,043 ProgressMeter - FBgn0082054:8344 2.84e+07 30.8 m 65.0 s 100.0% 30.8 m 0.0 s INFO 13:56:01,044 ProgressMeter - FBgn0082054:8344 2.84e+07 31.3 m 66.0 s 100.0% 31.3 m 0.0 s INFO 13:56:31,092 ProgressMeter - FBgn0082054:8344 2.84e+07 31.8 m 67.0 s 100.0% 31.8 m 0.0 s INFO 13:57:01,093 ProgressMeter - FBgn0082054:8344 2.84e+07 32.3 m 68.0 s 100.0% 32.3 m 0.0 s INFO 13:57:31,094 ProgressMeter - FBgn0082054:8344 2.84e+07 32.8 m 69.0 s 100.0% 32.8 m 0.0 s INFO 13:58:01,149 ProgressMeter - FBgn0082054:8344 2.84e+07 33.3 m 70.0 s 100.0% 33.3 m 0.0 s INFO 13:58:31,150 ProgressMeter - FBgn0082054:8344 2.84e+07 33.8 m 71.0 s 100.0% 33.8 m 0.0 s INFO 13:59:01,151 ProgressMeter - FBgn0082054:8344 2.84e+07 34.3 m 72.0 s 100.0% 34.3 m 0.0 s INFO 13:59:31,196 ProgressMeter - FBgn0082054:8344 2.84e+07 34.8 m 73.0 s 100.0% 34.8 m 0.0 s INFO 14:00:01,197 ProgressMeter - FBgn0082054:8344 2.84e+07 35.3 m 74.0 s 100.0% 35.3 m 0.0 s INFO 14:00:31,376 ProgressMeter - FBgn0082054:8344 2.84e+07 35.8 m 75.0 s 100.0% 35.8 m 0.0 s INFO 14:01:01,377 ProgressMeter - FBgn0082054:8344 2.84e+07 36.3 m 76.0 s 100.0% 36.3 m 0.0 s INFO 14:01:31,378 ProgressMeter - FBgn0082054:8344 2.84e+07 36.8 m 77.0 s 100.0% 36.8 m 0.0 s INFO 14:02:01,379 ProgressMeter - FBgn0082054:8344 2.84e+07 37.3 m 78.0 s 100.0% 37.3 m 0.0 s INFO 14:02:31,398 ProgressMeter - FBgn0082054:8344 2.84e+07 37.8 m 80.0 s 100.0% 37.8 m 0.0 s INFO 14:03:01,399 ProgressMeter - FBgn0082054:8344 2.84e+07 38.3 m 81.0 s 100.0% 38.3 m 0.0 s INFO 14:03:31,400 ProgressMeter - FBgn0082054:8344 2.84e+07 38.8 m 82.0 s 100.0% 38.8 m 0.0 s INFO 14:04:01,407 ProgressMeter - FBgn0082054:8344 2.84e+07 39.3 m 83.0 s 100.0% 39.3 m 0.0 s INFO 14:04:31,408 ProgressMeter - FBgn0082054:8344 2.84e+07 39.8 m 84.0 s 100.0% 39.8 m 0.0 s INFO 14:05:01,409 ProgressMeter - FBgn0082054:8344 2.84e+07 40.3 m 85.0 s 100.0% 40.3 m 0.0 s INFO 14:05:31,410 ProgressMeter - FBgn0082054:8344 2.84e+07 40.8 m 86.0 s 100.0% 40.8 m 0.0 s INFO 14:06:01,427 ProgressMeter - FBgn0082054:8344 2.84e+07 41.3 m 87.0 s 100.0% 41.3 m 0.0 s INFO 14:06:31,428 ProgressMeter - FBgn0082054:8344 2.84e+07 41.8 m 88.0 s 100.0% 41.8 m 0.0 s INFO 14:07:01,463 ProgressMeter - FBgn0082054:8344 2.84e+07 42.4 m 89.0 s 100.0% 42.4 m 0.0 s INFO 14:07:31,464 ProgressMeter - FBgn0082054:8344 2.84e+07 42.9 m 90.0 s 100.0% 42.9 m 0.0 s INFO 14:08:01,487 ProgressMeter - FBgn0082054:8344 2.84e+07 43.4 m 91.0 s 100.0% 43.4 m 0.0 s INFO 14:08:31,488 ProgressMeter - FBgn0082054:8344 2.84e+07 43.9 m 92.0 s 100.0% 43.9 m 0.0 s INFO 14:09:01,489 ProgressMeter - FBgn0082054:8344 2.84e+07 44.4 m 93.0 s 100.0% 44.4 m 0.0 s INFO 14:09:31,490 ProgressMeter - FBgn0082054:8344 2.84e+07 44.9 m 94.0 s 100.0% 44.9 m 0.0 s INFO 14:10:01,491 ProgressMeter - FBgn0082054:8344 2.84e+07 45.4 m 95.0 s 100.0% 45.4 m 0.0 s INFO 14:10:31,492 ProgressMeter - FBgn0082054:8344 2.84e+07 45.9 m 96.0 s 100.0% 45.9 m 0.0 s INFO 14:11:01,493 ProgressMeter - FBgn0082054:8344 2.84e+07 46.4 m 98.0 s 100.0% 46.4 m 0.0 s INFO 14:11:31,494 ProgressMeter - FBgn0082054:8344 2.84e+07 46.9 m 99.0 s 100.0% 46.9 m 0.0 s INFO 14:12:01,494 ProgressMeter - FBgn0082054:8344 2.84e+07 47.4 m 100.0 s 100.0% 47.4 m 0.0 s INFO 14:12:31,495 ProgressMeter - FBgn0082054:8344 2.84e+07 47.9 m 101.0 s 100.0% 47.9 m 0.0 s INFO 14:13:01,509 ProgressMeter - FBgn0082054:8344 2.84e+07 48.4 m 102.0 s 100.0% 48.4 m 0.0 s INFO 14:13:31,510 ProgressMeter - FBgn0082054:8344 2.84e+07 48.9 m 103.0 s 100.0% 48.9 m 0.0 s INFO 14:14:01,510 ProgressMeter - FBgn0082054:8344 2.84e+07 49.4 m 104.0 s 100.0% 49.4 m 0.0 s INFO 14:14:31,511 ProgressMeter - FBgn0082054:8344 2.84e+07 49.9 m 105.0 s 100.0% 49.9 m 0.0 s INFO 14:15:01,512 ProgressMeter - FBgn0082054:8344 2.84e+07 50.4 m 106.0 s 100.0% 50.4 m 0.0 s INFO 14:15:31,513 ProgressMeter - FBgn0082054:8344 2.84e+07 50.9 m 107.0 s 100.0% 50.9 m 0.0 s INFO 14:16:01,514 ProgressMeter - FBgn0082054:8344 2.84e+07 51.4 m 108.0 s 100.0% 51.4 m 0.0 s INFO 14:16:31,515 ProgressMeter - FBgn0082054:8344 2.84e+07 51.9 m 109.0 s 100.0% 51.9 m 0.0 s INFO 14:17:01,516 ProgressMeter - FBgn0082054:8344 2.84e+07 52.4 m 110.0 s 100.0% 52.4 m 0.0 s INFO 14:17:31,517 ProgressMeter - FBgn0082054:8344 2.84e+07 52.9 m 111.0 s 100.0% 52.9 m 0.0 s INFO 14:18:01,518 ProgressMeter - FBgn0082054:8344 2.84e+07 53.4 m 112.0 s 100.0% 53.4 m 0.0 s INFO 14:18:31,519 ProgressMeter - FBgn0082054:8344 2.84e+07 53.9 m 113.0 s 100.0% 53.9 m 0.0 s INFO 14:19:01,520 ProgressMeter - FBgn0082054:8344 2.84e+07 54.4 m 114.0 s 100.0% 54.4 m 0.0 s INFO 14:19:41,521 ProgressMeter - FBgn0082054:8344 2.84e+07 55.0 m 116.0 s 100.0% 55.0 m 0.0 s INFO 14:20:21,522 ProgressMeter - FBgn0082054:8344 2.84e+07 55.7 m 117.0 s 100.0% 55.7 m 0.0 s INFO 14:20:51,523 ProgressMeter - FBgn0082054:8344 2.84e+07 56.2 m 118.0 s 100.0% 56.2 m 0.0 s INFO 14:21:21,524 ProgressMeter - FBgn0082054:8344 2.84e+07 56.7 m 119.0 s 100.0% 56.7 m 0.0 s INFO 14:22:01,525 ProgressMeter - FBgn0082054:8344 2.84e+07 57.4 m 2.0 m 100.0% 57.4 m 0.0 s INFO 14:22:41,526 ProgressMeter - FBgn0082054:8344 2.84e+07 58.0 m 2.0 m 100.0% 58.0 m 0.0 s INFO 14:23:11,527 ProgressMeter - FBgn0082054:8344 2.84e+07 58.5 m 2.1 m 100.0% 58.5 m 0.0 s INFO 14:23:51,528 ProgressMeter - FBgn0082054:8344 2.84e+07 59.2 m 2.1 m 100.0% 59.2 m 0.0 s INFO 14:24:31,529 ProgressMeter - FBgn0082054:8344 2.84e+07 59.9 m 2.1 m 100.0% 59.9 m 0.0 s INFO 14:25:01,530 ProgressMeter - FBgn0082054:8344 2.84e+07 60.4 m 2.1 m 100.0% 60.4 m 0.0 s INFO 14:25:41,531 ProgressMeter - FBgn0082054:8344 2.84e+07 61.0 m 2.2 m 100.0% 61.0 m 0.0 s INFO 14:26:11,746 ProgressMeter - FBgn0082054:8344 2.84e+07 61.5 m 2.2 m 100.0% 61.5 m 0.0 s INFO 14:26:41,747 ProgressMeter - FBgn0082054:8344 2.84e+07 62.0 m 2.2 m 100.0% 62.0 m 0.0 s INFO 14:27:11,748 ProgressMeter - FBgn0082054:8344 2.84e+07 62.5 m 2.2 m 100.0% 62.5 m 0.0 s INFO 14:27:41,801 ProgressMeter - FBgn0082054:8344 2.84e+07 63.0 m 2.2 m 100.0% 63.0 m 0.0 s INFO 14:28:11,802 ProgressMeter - FBgn0082054:8344 2.84e+07 63.5 m 2.2 m 100.0% 63.5 m 0.0 s INFO 14:28:41,856 ProgressMeter - FBgn0082054:8344 2.84e+07 64.0 m 2.3 m 100.0% 64.0 m 0.0 s INFO 14:29:11,857 ProgressMeter - FBgn0082054:8344 2.84e+07 64.5 m 2.3 m 100.0% 64.5 m 0.0 s INFO 14:29:41,864 ProgressMeter - FBgn0082054:8344 2.84e+07 65.0 m 2.3 m 100.0% 65.0 m 0.0 s INFO 14:30:11,865 ProgressMeter - FBgn0082054:8344 2.84e+07 65.5 m 2.3 m 100.0% 65.5 m 0.0 s INFO 14:30:41,866 ProgressMeter - FBgn0082054:8344 2.84e+07 66.0 m 2.3 m 100.0% 66.0 m 0.0 s INFO 14:31:11,867 ProgressMeter - FBgn0082054:8344 2.84e+07 66.5 m 2.3 m 100.0% 66.5 m 0.0 s INFO 14:31:41,868 ProgressMeter - FBgn0082054:8344 2.84e+07 67.0 m 2.4 m 100.0% 67.0 m 0.0 s INFO 14:32:11,869 ProgressMeter - FBgn0082054:8344 2.84e+07 67.5 m 2.4 m 100.0% 67.5 m 0.0 s INFO 14:32:41,870 ProgressMeter - FBgn0082054:8344 2.84e+07 68.0 m 2.4 m 100.0% 68.0 m 0.0 s INFO 14:33:11,871 ProgressMeter - FBgn0082054:8344 2.84e+07 68.5 m 2.4 m 100.0% 68.5 m 0.0 s INFO 14:33:41,919 ProgressMeter - FBgn0082054:8344 2.84e+07 69.0 m 2.4 m 100.0% 69.0 m 0.0 s INFO 14:34:11,920 ProgressMeter - FBgn0082054:8344 2.84e+07 69.5 m 2.5 m 100.0% 69.5 m 0.0 s INFO 14:34:41,921 ProgressMeter - FBgn0082054:8344 2.84e+07 70.0 m 2.5 m 100.0% 70.0 m 0.0 s INFO 14:35:12,148 ProgressMeter - FBgn0082054:8344 2.84e+07 70.5 m 2.5 m 100.0% 70.5 m 0.0 s INFO 14:35:42,149 ProgressMeter - FBgn0082054:8344 2.84e+07 71.0 m 2.5 m 100.0% 71.0 m 0.0 s INFO 14:36:12,150 ProgressMeter - FBgn0082054:8344 2.84e+07 71.5 m 2.5 m 100.0% 71.5 m 0.0 s INFO 14:36:42,207 ProgressMeter - FBgn0082054:8344 2.84e+07 72.0 m 2.5 m 100.0% 72.0 m 0.0 s INFO 14:37:12,207 ProgressMeter - FBgn0082054:8344 2.84e+07 72.5 m 2.6 m 100.0% 72.5 m 0.0 s INFO 14:37:42,263 ProgressMeter - FBgn0082054:8344 2.84e+07 73.0 m 2.6 m 100.0% 73.0 m 0.0 s INFO 14:38:12,264 ProgressMeter - FBgn0082054:8344 2.84e+07 73.5 m 2.6 m 100.0% 73.5 m 0.0 s INFO 14:38:42,265 ProgressMeter - FBgn0082054:8344 2.84e+07 74.0 m 2.6 m 100.0% 74.0 m 0.0 s INFO 14:39:12,280 ProgressMeter - FBgn0082054:8344 2.84e+07 74.5 m 2.6 m 100.0% 74.5 m 0.0 s INFO 14:39:42,281 ProgressMeter - FBgn0082054:8344 2.84e+07 75.0 m 2.6 m 100.0% 75.0 m 0.0 s INFO 14:40:12,282 ProgressMeter - FBgn0082054:8344 2.84e+07 75.5 m 2.7 m 100.0% 75.5 m 0.0 s INFO 14:40:42,283 ProgressMeter - FBgn0082054:8344 2.84e+07 76.0 m 2.7 m 100.0% 76.0 m 0.0 s INFO 14:41:12,400 ProgressMeter - FBgn0082054:8344 2.84e+07 76.5 m 2.7 m 100.0% 76.5 m 0.0 s INFO 14:41:42,401 ProgressMeter - FBgn0082054:8344 2.84e+07 77.0 m 2.7 m 100.0% 77.0 m 0.0 s INFO 14:42:12,402 ProgressMeter - FBgn0082054:8344 2.84e+07 77.5 m 2.7 m 100.0% 77.5 m 0.0 s INFO 14:42:42,403 ProgressMeter - FBgn0082054:8344 2.84e+07 78.0 m 2.8 m 100.0% 78.0 m 0.0 s INFO 14:43:12,415 ProgressMeter - FBgn0082054:8344 2.84e+07 78.5 m 2.8 m 100.0% 78.5 m 0.0 s INFO 14:43:42,416 ProgressMeter - FBgn0082054:8344 2.84e+07 79.0 m 2.8 m 100.0% 79.0 m 0.0 s INFO 14:44:12,417 ProgressMeter - FBgn0082054:8344 2.84e+07 79.5 m 2.8 m 100.0% 79.5 m 0.0 s INFO 14:44:42,418 ProgressMeter - FBgn0082054:8344 2.84e+07 80.0 m 2.8 m 100.0% 80.0 m 0.0 s INFO 14:45:12,419 ProgressMeter - FBgn0082054:8344 2.84e+07 80.5 m 2.8 m 100.0% 80.5 m 0.0 s INFO 14:45:42,419 ProgressMeter - FBgn0082054:8344 2.84e+07 81.0 m 2.9 m 100.0% 81.0 m 0.0 s INFO 14:46:12,420 ProgressMeter - FBgn0082054:8344 2.84e+07 81.5 m 2.9 m 100.0% 81.5 m 0.0 s INFO 14:46:42,421 ProgressMeter - FBgn0082054:8344 2.84e+07 82.0 m 2.9 m 100.0% 82.0 m 0.0 s INFO 14:47:12,422 ProgressMeter - FBgn0082054:8344 2.84e+07 82.5 m 2.9 m 100.0% 82.5 m 0.0 s INFO 14:47:42,423 ProgressMeter - FBgn0082054:8344 2.84e+07 83.0 m 2.9 m 100.0% 83.0 m 0.0 s INFO 14:48:12,424 ProgressMeter - FBgn0082054:8344 2.84e+07 83.5 m 2.9 m 100.0% 83.5 m 0.0 s INFO 14:48:42,425 ProgressMeter - FBgn0082054:8344 2.84e+07 84.0 m 3.0 m 100.0% 84.0 m 0.0 s INFO 14:49:12,426 ProgressMeter - FBgn0082054:8344 2.84e+07 84.5 m 3.0 m 100.0% 84.5 m 0.0 s INFO 14:49:42,427 ProgressMeter - FBgn0082054:8344 2.84e+07 85.0 m 3.0 m 100.0% 85.0 m 0.0 s INFO 14:50:12,428 ProgressMeter - FBgn0082054:8344 2.84e+07 85.5 m 3.0 m 100.0% 85.5 m 0.0 s INFO 14:50:42,429 ProgressMeter - FBgn0082054:8344 2.84e+07 86.0 m 3.0 m 100.0% 86.0 m 0.0 s INFO 14:51:22,430 ProgressMeter - FBgn0082054:8344 2.84e+07 86.7 m 3.1 m 100.0% 86.7 m 0.0 s INFO 14:51:52,449 ProgressMeter - FBgn0082054:8344 2.84e+07 87.2 m 3.1 m 100.0% 87.2 m 0.0 s INFO 14:52:22,450 ProgressMeter - FBgn0082054:8344 2.84e+07 87.7 m 3.1 m 100.0% 87.7 m 0.0 s INFO 14:52:52,451 ProgressMeter - FBgn0082054:8344 2.84e+07 88.2 m 3.1 m 100.0% 88.2 m 0.0 s INFO 14:53:22,468 ProgressMeter - FBgn0082054:8344 2.84e+07 88.7 m 3.1 m 100.0% 88.7 m 0.0 s INFO 14:53:52,469 ProgressMeter - FBgn0082054:8344 2.84e+07 89.2 m 3.1 m 100.0% 89.2 m 0.0 s INFO 14:54:22,470 ProgressMeter - FBgn0082054:8344 2.84e+07 89.7 m 3.2 m 100.0% 89.7 m 0.0 s INFO 14:54:52,471 ProgressMeter - FBgn0082054:8344 2.84e+07 90.2 m 3.2 m 100.0% 90.2 m 0.0 s INFO 14:55:22,472 ProgressMeter - FBgn0082054:8344 2.84e+07 90.7 m 3.2 m 100.0% 90.7 m 0.0 s INFO 14:55:52,473 ProgressMeter - FBgn0082054:8344 2.84e+07 91.2 m 3.2 m 100.0% 91.2 m 0.0 s INFO 14:56:22,651 ProgressMeter - FBgn0082054:8344 2.84e+07 91.7 m 3.2 m 100.0% 91.7 m 0.0 s INFO 14:56:52,652 ProgressMeter - FBgn0082054:8344 2.84e+07 92.2 m 3.3 m 100.0% 92.2 m 0.0 s INFO 14:57:22,671 ProgressMeter - FBgn0082054:8344 2.84e+07 92.7 m 3.3 m 100.0% 92.7 m 0.0 s INFO 14:57:52,672 ProgressMeter - FBgn0082054:8344 2.84e+07 93.2 m 3.3 m 100.0% 93.2 m 0.0 s INFO 14:58:22,673 ProgressMeter - FBgn0082054:8344 2.84e+07 93.7 m 3.3 m 100.0% 93.7 m 0.0 s INFO 14:58:52,674 ProgressMeter - FBgn0082054:8344 2.84e+07 94.2 m 3.3 m 100.0% 94.2 m 0.0 s INFO 14:59:22,689 ProgressMeter - FBgn0082054:8344 2.84e+07 94.7 m 3.3 m 100.0% 94.7 m 0.0 s INFO 14:59:52,690 ProgressMeter - FBgn0082054:8344 2.84e+07 95.2 m 3.4 m 100.0% 95.2 m 0.0 s INFO 15:00:22,691 ProgressMeter - FBgn0082054:8344 2.84e+07 95.7 m 3.4 m 100.0% 95.7 m 0.0 s INFO 15:00:52,777 ProgressMeter - FBgn0082054:8344 2.84e+07 96.2 m 3.4 m 100.0% 96.2 m 0.0 s INFO 15:01:22,778 ProgressMeter - FBgn0082054:8344 2.84e+07 96.7 m 3.4 m 100.0% 96.7 m 0.0 s INFO 15:01:52,779 ProgressMeter - FBgn0082054:8344 2.84e+07 97.2 m 3.4 m 100.0% 97.2 m 0.0 s INFO 15:02:22,780 ProgressMeter - FBgn0082054:8344 2.84e+07 97.7 m 3.4 m 100.0% 97.7 m 0.0 s INFO 15:02:52,781 ProgressMeter - FBgn0082054:8344 2.84e+07 98.2 m 3.5 m 100.0% 98.2 m 0.0 s INFO 15:03:22,782 ProgressMeter - FBgn0082054:8344 2.84e+07 98.7 m 3.5 m 100.0% 98.7 m 0.0 s INFO 15:03:52,783 ProgressMeter - FBgn0082054:8344 2.84e+07 99.2 m 3.5 m 100.0% 99.2 m 0.0 s INFO 15:04:22,784 ProgressMeter - FBgn0082054:8344 2.84e+07 99.7 m 3.5 m 100.0% 99.7 m 0.0 s INFO 15:04:52,785 ProgressMeter - FBgn0082054:8344 2.84e+07 100.2 m 3.5 m 100.0% 100.2 m 0.0 s INFO 15:05:22,786 ProgressMeter - FBgn0082054:8344 2.84e+07 100.7 m 3.5 m 100.0% 100.7 m 0.0 s INFO 15:05:52,787 ProgressMeter - FBgn0082054:8344 2.84e+07 101.2 m 3.6 m 100.0% 101.2 m 0.0 s INFO 15:06:22,788 ProgressMeter - FBgn0082054:8344 2.84e+07 101.7 m 3.6 m 100.0% 101.7 m 0.0 s INFO 15:06:52,789 ProgressMeter - FBgn0082054:8344 2.84e+07 102.2 m 3.6 m 100.0% 102.2 m 0.0 s INFO 15:07:32,790 ProgressMeter - FBgn0082054:8344 2.84e+07 102.9 m 3.6 m 100.0% 102.9 m 0.0 s INFO 15:08:12,849 ProgressMeter - FBgn0082054:8344 2.84e+07 103.5 m 3.6 m 100.0% 103.5 m 0.0 s INFO 15:08:42,880 ProgressMeter - FBgn0082054:8344 2.84e+07 104.0 m 3.7 m 100.0% 104.0 m 0.0 s INFO 15:09:12,881 ProgressMeter - FBgn0082054:8344 2.84e+07 104.5 m 3.7 m 100.0% 104.5 m 0.0 s INFO 15:09:42,882 ProgressMeter - FBgn0082054:8344 2.84e+07 105.0 m 3.7 m 100.0% 105.0 m 0.0 s INFO 15:10:12,935 ProgressMeter - FBgn0082054:8344 2.84e+07 105.5 m 3.7 m 100.0% 105.5 m 0.0 s INFO 15:10:42,936 ProgressMeter - FBgn0082054:8344 2.84e+07 106.0 m 3.7 m 100.0% 106.0 m 0.0 s INFO 15:11:12,947 ProgressMeter - FBgn0082054:8344 2.84e+07 106.5 m 3.8 m 100.0% 106.5 m 0.0 s INFO 15:11:42,948 ProgressMeter - FBgn0082054:8344 2.84e+07 107.0 m 3.8 m 100.0% 107.0 m 0.0 s INFO 15:12:12,949 ProgressMeter - FBgn0082054:8344 2.84e+07 107.5 m 3.8 m 100.0% 107.5 m 0.0 s INFO 15:12:42,950 ProgressMeter - FBgn0082054:8344 2.84e+07 108.0 m 3.8 m 100.0% 108.0 m 0.0 s INFO 15:12:57,954 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@9b46a1a INFO 15:12:58,290 ProgressMeter - done 2.32e+08 108.3 m 28.0 s 100.0% 108.3 m 0.0 s INFO 15:12:58,290 ProgressMeter - Total runtime 6497.86 secs, 108.30 min, 1.80 hours INFO 15:12:58,291 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 231648926 total reads (0.00%) INFO 15:12:58,291 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 15:13:31,535 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:13:31,538 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 INFO 15:13:31,538 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:13:31,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 15:13:31,542 HelpFormatter - Program Args: -T ReduceReads -R ../../genomes/dpse-all-gene-r3.1.fasta -I ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.recal.bam -o ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.reduced.bam INFO 15:13:31,542 HelpFormatter - Date/Time: 2013/12/02 15:13:31 INFO 15:13:31,542 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:13:31,542 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:13:32,167 GenomeAnalysisEngine - Strictness is SILENT INFO 15:13:32,948 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 40 INFO 15:13:32,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:13:33,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14 INFO 15:13:33,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 15:13:33,409 GenomeAnalysisEngine - Done preparing for traversal INFO 15:13:33,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 15:13:33,410 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 15:13:33,567 ReadShardBalancer$1 - Loading BAM index data INFO 15:13:33,569 ReadShardBalancer$1 - Done loading BAM index data INFO 15:14:03,414 ProgressMeter - FBgn0249570:5986 1.44e+06 30.0 s 20.0 s 4.9% 10.1 m 9.6 m INFO 15:14:33,663 ProgressMeter - FBgn0077653:608 2.88e+06 60.0 s 20.0 s 10.1% 9.9 m 8.9 m INFO 15:15:04,274 ProgressMeter - FBgn0245390:76 4.40e+06 90.0 s 20.0 s 15.4% 9.7 m 8.2 m INFO 15:15:34,276 ProgressMeter - FBgn0244948:7711 5.90e+06 120.0 s 20.0 s 20.7% 9.7 m 7.7 m INFO 15:16:04,279 ProgressMeter - FBgn0070929:9798 7.47e+06 2.5 m 20.0 s 26.2% 9.5 m 7.0 m INFO 15:16:34,282 ProgressMeter - FBgn0012710:5388 8.88e+06 3.0 m 20.0 s 31.2% 9.6 m 6.6 m INFO 15:17:04,302 ProgressMeter - FBgn0246904:811 1.05e+07 3.5 m 20.0 s 37.0% 9.5 m 6.0 m INFO 15:17:34,303 ProgressMeter - FBgn0245627:2134 1.19e+07 4.0 m 20.0 s 41.7% 9.6 m 5.6 m INFO 15:18:04,304 ProgressMeter - FBgn0247088:14069 1.34e+07 4.5 m 20.0 s 47.1% 9.5 m 5.0 m INFO 15:18:34,376 ProgressMeter - FBgn0245503:930 1.49e+07 5.0 m 20.0 s 52.6% 9.5 m 4.5 m INFO 15:19:04,378 ProgressMeter - FBgn0247038:811 1.64e+07 5.5 m 20.0 s 58.0% 9.5 m 4.0 m INFO 15:19:34,379 ProgressMeter - FBgn0245748:10171 1.80e+07 6.0 m 20.0 s 63.6% 9.4 m 3.4 m INFO 15:20:04,381 ProgressMeter - FBgn0245798:73 1.95e+07 6.5 m 20.0 s 68.8% 9.4 m 2.9 m INFO 15:20:34,382 ProgressMeter - FBgn0075973:8050 2.10e+07 7.0 m 20.0 s 74.4% 9.4 m 2.4 m INFO 15:21:04,384 ProgressMeter - FBgn0082089:73 2.26e+07 7.5 m 19.0 s 79.8% 9.4 m 113.0 s INFO 15:21:34,385 ProgressMeter - FBgn0247461:15604 2.41e+07 8.0 m 19.0 s 85.2% 9.4 m 83.0 s INFO 15:22:04,386 ProgressMeter - FBgn0248490:13963 2.57e+07 8.5 m 19.0 s 90.9% 9.4 m 51.0 s INFO 15:22:34,388 ProgressMeter - FBgn0261900:8104 2.73e+07 9.0 m 19.0 s 96.2% 9.4 m 21.0 s INFO 15:23:04,392 ProgressMeter - FBgn0077946:640 2.84e+07 9.5 m 20.0 s 100.0% 9.5 m 0.0 s INFO 15:23:34,393 ProgressMeter - FBgn0077946:640 2.84e+07 10.0 m 21.0 s 100.0% 10.0 m 0.0 s INFO 15:24:04,395 ProgressMeter - FBgn0077946:640 2.84e+07 10.5 m 22.0 s 100.0% 10.5 m 0.0 s INFO 15:24:34,396 ProgressMeter - FBgn0077946:640 2.84e+07 11.0 m 23.0 s 100.0% 11.0 m 0.0 s INFO 15:25:04,397 ProgressMeter - FBgn0077946:640 2.84e+07 11.5 m 24.0 s 100.0% 11.5 m 0.0 s INFO 15:25:34,399 ProgressMeter - FBgn0077946:640 2.84e+07 12.0 m 25.0 s 100.0% 12.0 m 0.0 s INFO 15:26:04,400 ProgressMeter - FBgn0077946:640 2.84e+07 12.5 m 26.0 s 100.0% 12.5 m 0.0 s INFO 15:26:34,402 ProgressMeter - FBgn0077946:640 2.84e+07 13.0 m 27.0 s 100.0% 13.0 m 0.0 s INFO 15:27:04,403 ProgressMeter - FBgn0077946:640 2.84e+07 13.5 m 28.0 s 100.0% 13.5 m 0.0 s INFO 15:27:34,404 ProgressMeter - FBgn0077946:640 2.84e+07 14.0 m 29.0 s 100.0% 14.0 m 0.0 s INFO 15:28:04,406 ProgressMeter - FBgn0077946:640 2.84e+07 14.5 m 30.0 s 100.0% 14.5 m 0.0 s INFO 15:28:34,407 ProgressMeter - FBgn0082054:8344 2.84e+07 15.0 m 31.0 s 100.0% 15.0 m 0.0 s INFO 15:29:04,408 ProgressMeter - FBgn0082054:8344 2.84e+07 15.5 m 32.0 s 100.0% 15.5 m 0.0 s INFO 15:29:34,410 ProgressMeter - FBgn0082054:8344 2.84e+07 16.0 m 33.0 s 100.0% 16.0 m 0.0 s INFO 15:30:04,411 ProgressMeter - FBgn0082054:8344 2.84e+07 16.5 m 34.0 s 100.0% 16.5 m 0.0 s INFO 15:30:34,413 ProgressMeter - FBgn0082054:8344 2.84e+07 17.0 m 35.0 s 100.0% 17.0 m 0.0 s INFO 15:30:41,657 ProgressMeter - done 2.84e+07 17.1 m 36.0 s 100.0% 17.1 m 0.0 s INFO 15:30:41,658 ProgressMeter - Total runtime 1028.25 secs, 17.14 min, 0.29 hours INFO 15:30:41,658 MicroScheduler - 203276418 reads were filtered out during the traversal out of approximately 231648926 total reads (87.75%) INFO 15:30:41,659 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 15:30:41,659 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter INFO 15:30:41,659 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 15:30:41,659 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 15:30:41,659 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 15:30:41,659 MicroScheduler - -> 203276418 reads (87.75% of total) failing UnmappedReadFilter INFO 15:31:14,868 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:31:14,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 INFO 15:31:14,871 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 15:31:14,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 15:31:14,875 HelpFormatter - Program Args: -T HaplotypeCaller -R ../../genomes/dpse-all-gene-r3.1.fasta -I ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.group.picard.reduced.bam -o ../../data/Dpse_TL.dpse-all-gene-r3.1.bowtie2_very_sensitive.merged.sorted.rmdup.GATK.vcf -nct 12 INFO 15:31:14,875 HelpFormatter - Date/Time: 2013/12/02 15:31:14 INFO 15:31:14,875 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:31:14,876 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:31:15,482 GenomeAnalysisEngine - Strictness is SILENT INFO 15:31:16,074 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 15:31:16,081 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:31:16,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17 INFO 15:31:16,265 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 15:31:16,423 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 12 CPU thread(s) for each of 1 data thread(s), of 12 processors available on this machine INFO 15:31:16,602 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 15:31:16,649 GenomeAnalysisEngine - Done preparing for traversal INFO 15:31:16,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 15:31:16,650 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining INFO 15:31:17,518 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 15:31:46,653 ProgressMeter - FBgn0072796:17624 2.24e+05 30.0 s 2.2 m 0.4% 2.0 h 119.8 m INFO 15:32:16,655 ProgressMeter - FBgn0072201:3600 4.61e+05 60.0 s 2.2 m 0.8% 2.1 h 2.1 h INFO 15:32:46,656 ProgressMeter - FBgn0249065:5203 7.17e+05 90.0 s 2.1 m 1.2% 2.0 h 119.2 m INFO 15:33:16,657 ProgressMeter - FBgn0072402:4146 9.73e+05 120.0 s 2.1 m 1.7% 119.0 m 117.0 m INFO 15:33:56,658 ProgressMeter - FBgn0079437:5275 1.27e+06 2.7 m 2.1 m 2.2% 2.0 h 118.4 m INFO 15:34:36,659 ProgressMeter - FBgn0247076:9094 1.68e+06 3.3 m 119.0 s 2.9% 114.9 m 111.5 m INFO 15:35:16,660 ProgressMeter - FBgn0077532:30545 2.00e+06 4.0 m 120.0 s 3.5% 114.6 m 110.6 m INFO 15:35:56,661 ProgressMeter - FBgn0074587:703 2.40e+06 4.7 m 116.0 s 4.1% 113.1 m 108.5 m INFO 15:36:36,662 ProgressMeter - FBgn0079125:2798 2.64e+06 5.3 m 2.0 m 4.5% 117.3 m 112.0 m INFO 15:37:06,663 ProgressMeter - FBgn0074002:4231 2.96e+06 5.8 m 118.0 s 5.1% 114.3 m 108.4 m INFO 15:37:36,664 ProgressMeter - FBgn0075469:13110 3.27e+06 6.3 m 116.0 s 5.7% 112.0 m 105.7 m INFO 15:38:06,666 ProgressMeter - FBgn0070325:6585 3.42e+06 6.8 m 119.0 s 5.9% 115.8 m 108.9 m INFO 15:38:36,667 ProgressMeter - FBgn0072989:5176 3.82e+06 7.3 m 115.0 s 6.6% 111.4 m 104.1 m INFO 15:39:06,668 ProgressMeter - FBgn0079389:2506 3.99e+06 7.8 m 117.0 s 6.9% 113.9 m 106.1 m INFO 15:39:36,669 ProgressMeter - FBgn0079973:1458 4.27e+06 8.3 m 117.0 s 7.3% 113.4 m 105.1 m INFO 15:40:06,670 ProgressMeter - FBgn0245196:20056 4.51e+06 8.8 m 117.0 s 7.8% 113.3 m 104.5 m INFO 15:40:36,671 ProgressMeter - FBgn0263302:16723 4.80e+06 9.3 m 116.0 s 8.3% 112.6 m 103.3 m INFO 15:41:06,671 ProgressMeter - FBgn0263362:13887 5.14e+06 9.8 m 114.0 s 8.9% 110.9 m 101.0 m INFO 15:41:36,673 ProgressMeter - FBgn0074080:4400 5.43e+06 10.3 m 114.0 s 9.4% 110.4 m 100.0 m INFO 15:42:06,674 ProgressMeter - FBgn0075621:3398 5.75e+06 10.8 m 113.0 s 9.9% 109.4 m 98.6 m INFO 15:42:36,675 ProgressMeter - FBgn0078736:6853 5.95e+06 11.3 m 114.0 s 10.2% 110.6 m 99.2 m INFO 15:43:16,676 ProgressMeter - FBgn0244549:43612 6.25e+06 12.0 m 115.0 s 10.8% 110.8 m 98.8 m INFO 15:43:56,677 ProgressMeter - FBgn0081023:5604 6.49e+06 12.7 m 117.0 s 11.2% 113.3 m 100.6 m INFO 15:44:26,677 ProgressMeter - FBgn0249149:6120 6.70e+06 13.2 m 117.0 s 11.5% 114.0 m 100.9 m INFO 15:44:56,678 ProgressMeter - FBgn0249416:712 6.98e+06 13.7 m 117.0 s 12.0% 113.8 m 100.1 m INFO 15:45:26,679 ProgressMeter - FBgn0076945:12022 7.28e+06 14.2 m 116.0 s 12.5% 112.9 m 98.7 m INFO 15:46:06,680 ProgressMeter - FBgn0244695:1225 7.53e+06 14.8 m 118.0 s 13.0% 114.4 m 99.6 m INFO 15:46:46,681 ProgressMeter - FBgn0081281:4769 7.82e+06 15.5 m 118.0 s 13.5% 115.1 m 99.6 m INFO 15:47:16,681 ProgressMeter - FBgn0245579:29729 7.99e+06 16.0 m 120.0 s 13.8% 115.9 m 99.9 m INFO 15:47:46,682 ProgressMeter - FBgn0077065:5682 8.29e+06 16.5 m 119.0 s 14.3% 115.5 m 99.0 m INFO 15:48:16,683 ProgressMeter - FBgn0076088:17022 8.58e+06 17.0 m 118.0 s 14.8% 114.8 m 97.8 m INFO 15:48:46,684 ProgressMeter - FBgn0079187:2833 8.97e+06 17.5 m 117.0 s 15.5% 113.3 m 95.8 m INFO 15:49:26,685 ProgressMeter - FBgn0081507:3280 9.29e+06 18.2 m 117.0 s 16.0% 113.5 m 95.4 m INFO 15:50:06,686 ProgressMeter - FBgn0079305:48470 9.60e+06 18.8 m 117.0 s 16.6% 113.4 m 94.6 m INFO 15:50:36,686 ProgressMeter - FBgn0250466:3400 9.85e+06 19.3 m 117.0 s 17.0% 114.0 m 94.7 m INFO 15:51:06,687 ProgressMeter - FBgn0250466:3400 9.85e+06 19.8 m 120.0 s 17.0% 117.0 m 97.1 m INFO 15:51:36,688 ProgressMeter - FBgn0243941:1095 9.90e+06 20.3 m 2.1 m 17.0% 119.3 m 99.0 m INFO 15:52:16,689 ProgressMeter - FBgn0080661:2354 1.02e+07 21.0 m 2.1 m 17.5% 119.7 m 98.7 m INFO 15:52:46,689 ProgressMeter - FBgn0077222:3171 1.03e+07 21.5 m 2.1 m 17.7% 2.0 h 99.7 m INFO 15:53:16,690 ProgressMeter - FBgn0249392:18813 1.05e+07 22.0 m 2.1 m 18.1% 2.0 h 99.6 m INFO 15:53:46,691 ProgressMeter - FBgn0263173:61860 1.06e+07 22.5 m 2.1 m 18.4% 2.0 h 99.8 m INFO 15:54:16,692 ProgressMeter - FBgn0073593:1422 1.09e+07 23.0 m 2.1 m 18.7% 2.0 h 99.7 m INFO 15:54:56,693 ProgressMeter - FBgn0074440:1440 1.10e+07 23.7 m 2.2 m 18.9% 2.1 h 101.7 m INFO 15:55:36,694 ProgressMeter - FBgn0072459:4519 1.14e+07 24.3 m 2.1 m 19.6% 2.1 h 99.7 m INFO 15:56:06,695 ProgressMeter - FBgn0246703:13301 1.16e+07 24.8 m 2.1 m 20.0% 2.1 h 99.6 m INFO 15:56:36,695 ProgressMeter - FBgn0079846:6907 1.18e+07 25.3 m 2.2 m 20.2% 2.1 h 99.8 m INFO 15:57:06,696 ProgressMeter - FBgn0078407:4655 1.19e+07 25.8 m 2.2 m 20.5% 2.1 h 100.5 m INFO 15:57:36,697 ProgressMeter - FBgn0080534:9267 1.21e+07 26.3 m 2.2 m 20.8% 2.1 h 100.1 m INFO 15:58:16,698 ProgressMeter - FBgn0077879:1345 1.25e+07 27.0 m 2.2 m 21.4% 2.1 h 99.0 m INFO 15:58:56,699 ProgressMeter - FBgn0249473:1642 1.27e+07 27.7 m 2.2 m 21.9% 2.1 h 98.5 m INFO 15:59:36,700 ProgressMeter - FBgn0243937:4792 1.30e+07 28.3 m 2.2 m 22.3% 2.1 h 98.6 m INFO 16:00:06,700 ProgressMeter - FBgn0249485:6400 1.31e+07 28.8 m 2.2 m 22.5% 2.1 h 99.3 m INFO 16:00:36,701 ProgressMeter - FBgn0246445:1200 1.32e+07 29.3 m 2.2 m 22.7% 2.2 h 100.1 m INFO 16:01:06,702 ProgressMeter - FBgn0081371:17820 1.35e+07 29.8 m 2.2 m 23.3% 2.1 h 98.3 m INFO 16:01:36,703 ProgressMeter - FBgn0077610:78184 1.37e+07 30.3 m 2.2 m 23.7% 2.1 h 97.9 m INFO 16:02:16,704 ProgressMeter - FBgn0075408:14123 1.39e+07 31.0 m 2.2 m 24.0% 2.2 h 98.1 m INFO 16:02:46,704 ProgressMeter - FBgn0243929:4166 1.42e+07 31.5 m 2.2 m 24.4% 2.1 h 97.5 m INFO 16:03:16,705 ProgressMeter - FBgn0083529:1407 1.43e+07 32.0 m 2.2 m 24.7% 2.2 h 97.5 m INFO 16:03:46,706 ProgressMeter - FBgn0244275:19244 1.46e+07 32.5 m 2.2 m 25.2% 2.1 h 96.3 m INFO 16:04:16,707 ProgressMeter - FBgn0247105:13071 1.48e+07 33.0 m 2.2 m 25.6% 2.2 h 96.0 m INFO 16:04:46,708 ProgressMeter - FBgn0070413:7446 1.50e+07 33.5 m 2.2 m 25.9% 2.2 h 96.0 m INFO 16:05:26,709 ProgressMeter - FBgn0070929:10298 1.52e+07 34.2 m 2.2 m 26.2% 2.2 h 96.0 m INFO 16:06:06,710 ProgressMeter - FBgn0074765:2284 1.53e+07 34.8 m 2.3 m 26.4% 2.2 h 97.1 m INFO 16:06:46,711 ProgressMeter - FBgn0244629:270 1.56e+07 35.5 m 2.3 m 26.8% 2.2 h 97.0 m INFO 16:07:16,711 ProgressMeter - FBgn0078914:38855 1.58e+07 36.0 m 2.3 m 27.2% 2.2 h 96.2 m INFO 16:07:46,712 ProgressMeter - FBgn0245476:907 1.60e+07 36.5 m 2.3 m 27.5% 2.2 h 96.2 m INFO 16:08:16,713 ProgressMeter - FBgn0077996:1468 1.63e+07 37.0 m 2.3 m 28.0% 2.2 h 95.2 m INFO 16:08:46,714 ProgressMeter - FBgn0073599:5460 1.64e+07 37.5 m 2.3 m 28.2% 2.2 h 95.5 m INFO 16:09:16,715 ProgressMeter - FBgn0075462:3338 1.65e+07 38.0 m 2.3 m 28.5% 2.2 h 95.5 m INFO 16:09:56,717 ProgressMeter - FBgn0082009:2544 1.68e+07 38.7 m 2.3 m 28.8% 2.2 h 95.4 m INFO 16:10:26,718 ProgressMeter - FBgn0079379:5859 1.69e+07 39.2 m 2.3 m 29.0% 2.2 h 95.7 m INFO 16:10:56,719 ProgressMeter - FBgn0070511:34682 1.70e+07 39.7 m 2.3 m 29.3% 2.3 h 95.9 m INFO 16:11:36,720 ProgressMeter - FBgn0249175:5729 1.72e+07 40.3 m 2.3 m 29.6% 2.3 h 96.1 m INFO 16:12:06,720 ProgressMeter - FBgn0243834:726 1.74e+07 40.8 m 2.3 m 30.0% 2.3 h 95.5 m INFO 16:12:36,721 ProgressMeter - FBgn0082037:2328 1.76e+07 41.3 m 2.3 m 30.4% 2.3 h 94.8 m INFO 16:13:06,722 ProgressMeter - FBgn0071982:28598 1.80e+07 41.8 m 2.3 m 31.0% 2.3 h 93.2 m INFO 16:13:46,723 ProgressMeter - FBgn0080708:3054 1.82e+07 42.5 m 2.3 m 31.4% 2.3 h 92.9 m INFO 16:14:26,724 ProgressMeter - FBgn0074176:17047 1.85e+07 43.2 m 2.3 m 31.9% 2.3 h 92.2 m INFO 16:14:56,724 ProgressMeter - FBgn0077426:2861 1.89e+07 43.7 m 2.3 m 32.5% 2.2 h 90.7 m INFO 16:15:26,725 ProgressMeter - FBgn0246832:2000 1.91e+07 44.2 m 2.3 m 33.0% 2.2 h 89.8 m INFO 16:15:56,726 ProgressMeter - FBgn0250467:297 1.93e+07 44.7 m 2.3 m 33.2% 2.2 h 89.9 m INFO 16:16:26,727 ProgressMeter - FBgn0246887:3784 1.94e+07 45.2 m 2.3 m 33.4% 2.3 h 90.1 m INFO 16:16:56,728 ProgressMeter - FBgn0248416:14871 1.97e+07 45.7 m 2.3 m 33.9% 2.2 h 89.2 m INFO 16:17:26,729 ProgressMeter - FBgn0081376:31923 2.00e+07 46.2 m 2.3 m 34.4% 2.2 h 88.0 m INFO 16:18:06,730 ProgressMeter - FBgn0246476:7503 2.03e+07 46.8 m 2.3 m 34.9% 2.2 h 87.2 m INFO 16:18:36,730 ProgressMeter - FBgn0078094:5863 2.06e+07 47.3 m 2.3 m 35.5% 2.2 h 86.0 m INFO 16:19:06,731 ProgressMeter - FBgn0249496:2284 2.09e+07 47.8 m 2.3 m 35.9% 2.2 h 85.3 m INFO 16:19:36,732 ProgressMeter - FBgn0078123:1786 2.11e+07 48.3 m 2.3 m 36.2% 2.2 h 85.0 m INFO 16:20:06,733 ProgressMeter - FBgn0243821:1304 2.14e+07 48.8 m 2.3 m 36.8% 2.2 h 84.0 m INFO 16:20:46,734 ProgressMeter - FBgn0079845:10992 2.17e+07 49.5 m 2.3 m 37.4% 2.2 h 83.0 m INFO 16:21:26,735 ProgressMeter - FBgn0075542:4390 2.19e+07 50.2 m 2.3 m 37.6% 2.2 h 83.1 m INFO 16:21:56,735 ProgressMeter - FBgn0247098:7871 2.20e+07 50.7 m 2.3 m 37.9% 2.2 h 83.0 m INFO 16:22:26,736 ProgressMeter - FBgn0077331:15824 2.23e+07 51.2 m 2.3 m 38.4% 2.2 h 82.2 m INFO 16:22:56,737 ProgressMeter - FBgn0264582:10471 2.24e+07 51.7 m 2.3 m 38.5% 2.2 h 82.4 m INFO 16:23:26,745 ProgressMeter - FBgn0250503:2047 2.26e+07 52.2 m 2.3 m 38.8% 2.2 h 82.2 m INFO 16:23:56,746 ProgressMeter - FBgn0079927:15210 2.28e+07 52.7 m 2.3 m 39.2% 2.2 h 81.7 m INFO 16:24:26,747 ProgressMeter - FBgn0073337:71656 2.31e+07 53.2 m 2.3 m 39.8% 2.2 h 80.3 m INFO 16:24:56,748 ProgressMeter - FBgn0248620:749 2.32e+07 53.7 m 2.3 m 40.0% 2.2 h 80.5 m INFO 16:25:26,749 ProgressMeter - FBgn0244622:29562 2.34e+07 54.2 m 2.3 m 40.3% 2.2 h 80.3 m INFO 16:25:56,750 ProgressMeter - FBgn0070119:1865 2.37e+07 54.7 m 2.3 m 40.8% 2.2 h 79.3 m INFO 16:26:26,751 ProgressMeter - FBgn0245525:7959 2.39e+07 55.2 m 2.3 m 41.2% 2.2 h 78.8 m INFO 16:26:56,752 ProgressMeter - FBgn0263373:68835 2.42e+07 55.7 m 2.3 m 41.9% 2.2 h 77.3 m INFO 16:27:26,753 ProgressMeter - FBgn0248838:48756 2.47e+07 56.2 m 2.3 m 42.6% 2.2 h 75.7 m INFO 16:27:56,771 ProgressMeter - FBgn0247374:14236 2.49e+07 56.7 m 2.3 m 42.8% 2.2 h 75.6 m INFO 16:28:26,772 ProgressMeter - FBgn0247958:1626 2.52e+07 57.2 m 2.3 m 43.4% 2.2 h 74.6 m INFO 16:29:06,773 ProgressMeter - FBgn0082011:571 2.53e+07 57.8 m 2.3 m 43.6% 2.2 h 74.7 m INFO 16:29:36,774 ProgressMeter - FBgn0263148:34493 2.55e+07 58.3 m 2.3 m 44.0% 2.2 h 74.2 m INFO 16:30:06,774 ProgressMeter - FBgn0246066:2234 2.56e+07 58.8 m 2.3 m 44.1% 2.2 h 74.5 m INFO 16:30:36,775 ProgressMeter - FBgn0243719:16271 2.58e+07 59.3 m 2.3 m 44.4% 2.2 h 74.4 m INFO 16:31:06,776 ProgressMeter - FBgn0244685:2004 2.62e+07 59.8 m 2.3 m 45.0% 2.2 h 73.0 m INFO 16:31:36,777 ProgressMeter - FBgn0263147:12902 2.64e+07 60.3 m 2.3 m 45.5% 2.2 h 72.1 m INFO 16:32:06,778 ProgressMeter - FBgn0249030:682 2.66e+07 60.8 m 2.3 m 45.8% 2.2 h 72.0 m INFO 16:32:36,779 ProgressMeter - FBgn0245369:18475 2.66e+07 61.3 m 2.3 m 45.9% 2.2 h 72.4 m INFO 16:33:06,782 ProgressMeter - FBgn0076192:9422 2.67e+07 61.8 m 2.3 m 46.0% 2.2 h 72.5 m INFO 16:33:36,783 ProgressMeter - FBgn0075191:6114 2.70e+07 62.3 m 2.3 m 46.4% 2.2 h 72.0 m INFO 16:34:06,784 ProgressMeter - FBgn0249393:1099 2.73e+07 62.8 m 2.3 m 47.0% 2.2 h 70.7 m INFO 16:34:36,785 ProgressMeter - FBgn0250007:7865 2.76e+07 63.3 m 2.3 m 47.6% 2.2 h 69.8 m INFO 16:35:06,786 ProgressMeter - FBgn0079976:6754 2.78e+07 63.8 m 2.3 m 47.9% 2.2 h 69.4 m INFO 16:35:36,787 ProgressMeter - FBgn0249268:2039 2.80e+07 64.3 m 2.3 m 48.2% 2.2 h 69.1 m INFO 16:36:06,788 ProgressMeter - FBgn0074177:2749 2.82e+07 64.8 m 2.3 m 48.6% 2.2 h 68.7 m INFO 16:36:36,789 ProgressMeter - FBgn0244131:255 2.85e+07 65.3 m 2.3 m 49.0% 2.2 h 68.0 m INFO 16:37:16,790 ProgressMeter - FBgn0243696:1474 2.89e+07 66.0 m 2.3 m 49.7% 2.2 h 66.8 m INFO 16:37:46,790 ProgressMeter - FBgn0080009:18097 2.91e+07 66.5 m 2.3 m 50.1% 2.2 h 66.1 m INFO 16:38:16,791 ProgressMeter - FBgn0078875:5570 2.94e+07 67.0 m 2.3 m 50.6% 2.2 h 65.4 m INFO 16:38:46,792 ProgressMeter - FBgn0077421:10012 2.96e+07 67.5 m 2.3 m 51.0% 2.2 h 64.8 m INFO 16:39:16,793 ProgressMeter - FBgn0246487:837 2.99e+07 68.0 m 2.3 m 51.5% 2.2 h 64.1 m INFO 16:39:46,794 ProgressMeter - FBgn0076617:9803 3.01e+07 68.5 m 2.3 m 51.9% 2.2 h 63.6 m INFO 16:40:26,795 ProgressMeter - FBgn0250517:2158 3.03e+07 69.2 m 2.3 m 52.1% 2.2 h 63.6 m INFO 16:40:56,796 ProgressMeter - FBgn0075594:11562 3.05e+07 69.7 m 2.3 m 52.5% 2.2 h 63.0 m INFO 16:41:26,796 ProgressMeter - FBgn0076619:787 3.06e+07 70.2 m 2.3 m 52.6% 2.2 h 63.1 m INFO 16:41:56,797 ProgressMeter - FBgn0261031:739 3.08e+07 70.7 m 2.3 m 53.1% 2.2 h 62.4 m INFO 16:42:26,798 ProgressMeter - FBgn0248632:1783 3.10e+07 71.2 m 2.3 m 53.3% 2.2 h 62.4 m INFO 16:42:56,799 ProgressMeter - FBgn0080758:586 3.11e+07 71.7 m 2.3 m 53.5% 2.2 h 62.2 m INFO 16:43:36,800 ProgressMeter - FBgn0080133:138803 3.15e+07 72.3 m 2.3 m 54.4% 2.2 h 60.7 m INFO 16:44:06,800 ProgressMeter - FBgn0245222:4122 3.18e+07 72.8 m 2.3 m 54.8% 2.2 h 60.1 m INFO 16:44:36,801 ProgressMeter - FBgn0247253:1532 3.20e+07 73.3 m 2.3 m 55.0% 2.2 h 59.9 m INFO 16:45:06,802 ProgressMeter - FBgn0070466:36929 3.22e+07 73.8 m 2.3 m 55.5% 2.2 h 59.3 m INFO 16:45:36,803 ProgressMeter - FBgn0248579:12346 3.25e+07 74.3 m 2.3 m 56.0% 2.2 h 58.3 m INFO 16:46:06,804 ProgressMeter - FBgn0250459:2313 3.28e+07 74.8 m 2.3 m 56.5% 2.2 h 57.7 m INFO 16:46:46,805 ProgressMeter - FBgn0244347:634 3.31e+07 75.5 m 2.3 m 57.0% 2.2 h 57.0 m INFO 16:47:16,805 ProgressMeter - FBgn0070451:1507 3.34e+07 76.0 m 2.3 m 57.5% 2.2 h 56.2 m INFO 16:47:46,806 ProgressMeter - FBgn0075426:1997 3.36e+07 76.5 m 2.3 m 57.9% 2.2 h 55.7 m INFO 16:48:16,807 ProgressMeter - FBgn0247171:20266 3.39e+07 77.0 m 2.3 m 58.4% 2.2 h 55.0 m INFO 16:48:46,808 ProgressMeter - FBgn0249657:10896 3.40e+07 77.5 m 2.3 m 58.6% 2.2 h 54.8 m INFO 16:49:26,809 ProgressMeter - FBgn0264769:67377 3.43e+07 78.2 m 2.3 m 59.2% 2.2 h 53.9 m INFO 16:49:56,810 ProgressMeter - FBgn0078787:4404 3.46e+07 78.7 m 2.3 m 59.6% 2.2 h 53.4 m INFO 16:50:36,811 ProgressMeter - FBgn0246739:15456 3.50e+07 79.3 m 2.3 m 60.3% 2.2 h 52.2 m INFO 16:51:16,812 ProgressMeter - FBgn0249468:1800 3.54e+07 80.0 m 2.3 m 60.9% 2.2 h 51.4 m INFO 16:51:56,813 ProgressMeter - FBgn0071965:545 3.56e+07 80.7 m 2.3 m 61.3% 2.2 h 50.9 m INFO 16:52:36,814 ProgressMeter - FBgn0243650:927 3.59e+07 81.3 m 2.3 m 61.8% 2.2 h 50.2 m INFO 16:53:16,815 ProgressMeter - FBgn0073720:5113 3.61e+07 82.0 m 2.3 m 62.2% 2.2 h 49.8 m INFO 16:53:46,816 ProgressMeter - FBgn0081304:12867 3.65e+07 82.5 m 2.3 m 62.8% 2.2 h 48.8 m INFO 16:54:16,816 ProgressMeter - FBgn0248892:1461 3.67e+07 83.0 m 2.3 m 63.2% 2.2 h 48.4 m INFO 16:54:46,817 ProgressMeter - FBgn0080478:1925 3.70e+07 83.5 m 2.3 m 63.6% 2.2 h 47.7 m INFO 16:55:16,818 ProgressMeter - FBgn0243664:1725 3.72e+07 84.0 m 2.3 m 64.1% 2.2 h 47.1 m INFO 16:55:56,819 ProgressMeter - FBgn0244702:3900 3.73e+07 84.7 m 2.3 m 64.2% 2.2 h 47.2 m INFO 16:56:26,820 ProgressMeter - FBgn0247423:7785 3.75e+07 85.2 m 2.3 m 64.5% 2.2 h 46.9 m INFO 16:56:56,820 ProgressMeter - FBgn0248853:13955 3.77e+07 85.7 m 2.3 m 64.9% 2.2 h 46.4 m INFO 16:57:26,821 ProgressMeter - FBgn0249478:1755 3.79e+07 86.2 m 2.3 m 65.2% 2.2 h 46.0 m INFO 16:57:56,822 ProgressMeter - FBgn0246091:29993 3.81e+07 86.7 m 2.3 m 65.6% 2.2 h 45.5 m INFO 16:58:26,823 ProgressMeter - FBgn0250321:24163 3.83e+07 87.2 m 2.3 m 66.0% 2.2 h 44.8 m INFO 16:58:56,830 ProgressMeter - FBgn0071287:5748 3.85e+07 87.7 m 2.3 m 66.3% 2.2 h 44.5 m INFO 16:59:26,831 ProgressMeter - FBgn0248668:2558 3.88e+07 88.2 m 2.3 m 66.8% 2.2 h 43.9 m INFO 16:59:56,832 ProgressMeter - FBgn0075968:4290 3.91e+07 88.7 m 2.3 m 67.3% 2.2 h 43.2 m INFO 17:00:36,833 ProgressMeter - FBgn0244176:2132 3.95e+07 89.3 m 2.3 m 67.9% 2.2 h 42.1 m INFO 17:01:16,834 ProgressMeter - FBgn0081461:4438 3.98e+07 90.0 m 2.3 m 68.5% 2.2 h 41.4 m INFO 17:01:46,835 ProgressMeter - FBgn0072490:468 4.00e+07 90.5 m 2.3 m 68.8% 2.2 h 41.0 m INFO 17:02:16,835 ProgressMeter - FBgn0082041:1195 4.03e+07 91.0 m 2.3 m 69.3% 2.2 h 40.2 m INFO 17:02:46,836 ProgressMeter - FBgn0071799:29413 4.06e+07 91.5 m 2.3 m 70.0% 2.2 h 39.3 m INFO 17:03:16,837 ProgressMeter - FBgn0077635:3561 4.08e+07 92.0 m 2.3 m 70.3% 2.2 h 38.9 m INFO 17:03:46,838 ProgressMeter - FBgn0070851:11581 4.11e+07 92.5 m 2.2 m 70.8% 2.2 h 38.1 m INFO 17:04:16,839 ProgressMeter - FBgn0248117:3312 4.13e+07 93.0 m 2.2 m 71.2% 2.2 h 37.7 m INFO 17:04:46,840 ProgressMeter - FBgn0245410:8769 4.16e+07 93.5 m 2.2 m 71.6% 2.2 h 37.0 m INFO 17:05:16,841 ProgressMeter - FBgn0076634:11205 4.19e+07 94.0 m 2.2 m 72.1% 2.2 h 36.4 m INFO 17:05:56,842 ProgressMeter - FBgn0244012:18285 4.22e+07 94.7 m 2.2 m 72.6% 2.2 h 35.7 m INFO 17:06:26,842 ProgressMeter - FBgn0265241:583 4.25e+07 95.2 m 2.2 m 73.1% 2.2 h 35.0 m INFO 17:06:56,843 ProgressMeter - FBgn0246861:10095 4.27e+07 95.7 m 2.2 m 73.5% 2.2 h 34.4 m INFO 17:07:26,844 ProgressMeter - FBgn0080866:11842 4.30e+07 96.2 m 2.2 m 74.1% 2.2 h 33.6 m INFO 17:07:56,845 ProgressMeter - FBgn0080080:3809 4.33e+07 96.7 m 2.2 m 74.6% 2.2 h 32.9 m INFO 17:08:26,846 ProgressMeter - FBgn0080155:33570 4.37e+07 97.2 m 2.2 m 75.2% 2.2 h 32.0 m INFO 17:08:56,847 ProgressMeter - FBgn0076025:4674 4.40e+07 97.7 m 2.2 m 75.7% 2.2 h 31.4 m INFO 17:09:36,848 ProgressMeter - FBgn0247161:264 4.42e+07 98.3 m 2.2 m 76.1% 2.2 h 30.9 m INFO 17:10:16,849 ProgressMeter - FBgn0246807:6493 4.45e+07 99.0 m 2.2 m 76.6% 2.2 h 30.2 m INFO 17:10:56,850 ProgressMeter - FBgn0070173:11482 4.49e+07 99.7 m 2.2 m 77.3% 2.1 h 29.2 m INFO 17:11:36,851 ProgressMeter - FBgn0246712:1845 4.52e+07 100.3 m 2.2 m 77.8% 2.1 h 28.6 m INFO 17:12:16,852 ProgressMeter - FBgn0264773:74944 4.55e+07 101.0 m 2.2 m 78.4% 2.1 h 27.9 m INFO 17:12:46,853 ProgressMeter - FBgn0244634:23310 4.57e+07 101.5 m 2.2 m 78.7% 2.1 h 27.4 m INFO 17:13:16,853 ProgressMeter - FBgn0247126:5798 4.60e+07 102.0 m 2.2 m 79.2% 2.1 h 26.8 m INFO 17:13:46,854 ProgressMeter - FBgn0244305:8136 4.63e+07 102.5 m 2.2 m 79.7% 2.1 h 26.1 m INFO 17:14:16,855 ProgressMeter - FBgn0244305:35354 4.63e+07 103.0 m 2.2 m 79.7% 2.2 h 26.2 m INFO 17:14:56,856 ProgressMeter - FBgn0078421:1910 4.64e+07 103.7 m 2.2 m 79.9% 2.2 h 26.0 m INFO 17:15:36,857 ProgressMeter - FBgn0249130:420 4.66e+07 104.3 m 2.2 m 80.3% 2.2 h 25.6 m INFO 17:16:16,858 ProgressMeter - FBgn0249676:3530 4.71e+07 105.0 m 2.2 m 81.1% 2.2 h 24.5 m INFO 17:16:56,859 ProgressMeter - FBgn0071666:19100 4.74e+07 105.7 m 2.2 m 81.7% 2.2 h 23.7 m INFO 17:17:36,860 ProgressMeter - FBgn0249118:10158 4.76e+07 106.3 m 2.2 m 82.0% 2.2 h 23.4 m INFO 17:18:16,861 ProgressMeter - FBgn0244749:17118 4.79e+07 107.0 m 2.2 m 82.5% 2.2 h 22.7 m INFO 17:18:46,862 ProgressMeter - FBgn0081521:2125 4.82e+07 107.5 m 2.2 m 82.9% 2.2 h 22.2 m INFO 17:19:26,863 ProgressMeter - FBgn0078167:1664 4.84e+07 108.2 m 2.2 m 83.2% 2.2 h 21.8 m INFO 17:20:06,864 ProgressMeter - FBgn0245545:918 4.86e+07 108.8 m 2.2 m 83.7% 2.2 h 21.2 m INFO 17:20:36,865 ProgressMeter - FBgn0081140:18605 4.90e+07 109.3 m 2.2 m 84.3% 2.2 h 20.3 m INFO 17:21:06,865 ProgressMeter - FBgn0246545:5005 4.91e+07 109.8 m 2.2 m 84.5% 2.2 h 20.2 m INFO 17:21:36,866 ProgressMeter - FBgn0246548:3975 4.93e+07 110.3 m 2.2 m 84.8% 2.2 h 19.8 m INFO 17:22:06,867 ProgressMeter - FBgn0064435:12296 4.94e+07 110.8 m 2.2 m 85.0% 2.2 h 19.5 m INFO 17:22:36,868 ProgressMeter - FBgn0244710:585 4.95e+07 111.3 m 2.2 m 85.2% 2.2 h 19.3 m INFO 17:23:06,872 ProgressMeter - FBgn0245772:19105 4.98e+07 111.8 m 2.2 m 85.7% 2.2 h 18.6 m INFO 17:23:36,873 ProgressMeter - FBgn0081231:18553 5.00e+07 112.3 m 2.2 m 86.1% 2.2 h 18.1 m INFO 17:24:06,874 ProgressMeter - FBgn0244687:5614 5.00e+07 112.8 m 2.3 m 86.1% 2.2 h 18.2 m INFO 17:24:36,875 ProgressMeter - FBgn0250532:2469 5.02e+07 113.3 m 2.3 m 86.3% 2.2 h 17.9 m INFO 17:25:06,876 ProgressMeter - FBgn0243913:12852 5.03e+07 113.8 m 2.3 m 86.5% 2.2 h 17.7 m INFO 17:25:36,877 ProgressMeter - FBgn0247286:20164 5.04e+07 114.3 m 2.3 m 86.8% 2.2 h 17.3 m INFO 17:26:06,878 ProgressMeter - FBgn0074556:5465 5.07e+07 114.8 m 2.3 m 87.3% 2.2 h 16.7 m INFO 17:26:46,879 ProgressMeter - FBgn0076414:15073 5.11e+07 115.5 m 2.3 m 88.0% 2.2 h 15.8 m INFO 17:27:16,880 ProgressMeter - FBgn0244731:1206 5.12e+07 116.0 m 2.3 m 88.1% 2.2 h 15.6 m INFO 17:27:46,881 ProgressMeter - FBgn0247193:1546 5.13e+07 116.5 m 2.3 m 88.3% 2.2 h 15.5 m INFO 17:28:16,881 ProgressMeter - FBgn0081876:1692 5.15e+07 117.0 m 2.3 m 88.6% 2.2 h 15.1 m INFO 17:28:46,882 ProgressMeter - FBgn0075615:25048 5.17e+07 117.5 m 2.3 m 89.0% 2.2 h 14.5 m INFO 17:29:16,883 ProgressMeter - FBgn0243747:8282 5.20e+07 118.0 m 2.3 m 89.4% 2.2 h 13.9 m INFO 17:29:46,884 ProgressMeter - FBgn0250615:1027 5.23e+07 118.5 m 2.3 m 89.9% 2.2 h 13.2 m INFO 17:30:16,885 ProgressMeter - FBgn0075537:2044 5.26e+07 119.0 m 2.3 m 90.5% 2.2 h 12.5 m INFO 17:30:46,886 ProgressMeter - FBgn0245500:39545 5.28e+07 119.5 m 2.3 m 91.0% 2.2 h 11.8 m INFO 17:31:26,887 ProgressMeter - FBgn0075871:3918 5.32e+07 2.0 h 2.3 m 91.5% 2.2 h 11.2 m INFO 17:32:06,888 ProgressMeter - FBgn0070498:9616 5.35e+07 2.0 h 2.3 m 92.0% 2.2 h 10.5 m INFO 17:32:36,889 ProgressMeter - FBgn0261902:10233 5.37e+07 2.0 h 2.3 m 92.5% 2.2 h 9.8 m INFO 17:33:16,890 ProgressMeter - FBgn0074944:31644 5.41e+07 2.0 h 2.3 m 93.1% 2.2 h 9.0 m INFO 17:33:56,891 ProgressMeter - FBgn0250642:10448 5.45e+07 2.0 h 2.3 m 93.8% 2.2 h 8.1 m INFO 17:34:26,892 ProgressMeter - FBgn0244872:9630 5.47e+07 2.1 h 2.2 m 94.3% 2.2 h 7.5 m INFO 17:34:56,893 ProgressMeter - FBgn0243846:2314 5.49e+07 2.1 h 2.3 m 94.4% 2.2 h 7.3 m INFO 17:35:26,894 ProgressMeter - FBgn0243628:2174 5.50e+07 2.1 h 2.3 m 94.8% 2.2 h 6.9 m INFO 17:35:56,894 ProgressMeter - FBgn0249922:20514 5.54e+07 2.1 h 2.3 m 95.4% 2.2 h 6.1 m INFO 17:36:26,895 ProgressMeter - FBgn0078092:2059 5.54e+07 2.1 h 2.3 m 95.4% 2.2 h 6.0 m INFO 17:36:56,896 ProgressMeter - FBgn0250076:1938 5.57e+07 2.1 h 2.3 m 95.9% 2.2 h 5.4 m INFO 17:37:26,897 ProgressMeter - FBgn0248096:3395 5.59e+07 2.1 h 2.3 m 96.3% 2.2 h 4.9 m INFO 17:37:56,916 ProgressMeter - FBgn0012735:4840 5.62e+07 2.1 h 2.3 m 96.7% 2.2 h 4.3 m INFO 17:38:26,917 ProgressMeter - FBgn0244199:9477 5.65e+07 2.1 h 2.3 m 97.2% 2.2 h 3.7 m INFO 17:38:56,918 ProgressMeter - FBgn0075385:1147 5.66e+07 2.1 h 2.3 m 97.4% 2.2 h 3.4 m INFO 17:39:26,919 ProgressMeter - FBgn0246151:3812 5.69e+07 2.1 h 2.3 m 97.9% 2.2 h 2.8 m INFO 17:39:56,920 ProgressMeter - FBgn0245228:6159 5.70e+07 2.1 h 2.3 m 98.1% 2.2 h 2.4 m INFO 17:40:26,921 ProgressMeter - FBgn0074990:5524 5.72e+07 2.2 h 2.3 m 98.4% 2.2 h 2.0 m INFO 17:40:56,922 ProgressMeter - FBgn0247608:1281 5.75e+07 2.2 h 2.3 m 98.9% 2.2 h 85.0 s INFO 17:41:26,923 ProgressMeter - FBgn0081994:1096 5.77e+07 2.2 h 2.3 m 99.3% 2.2 h 58.0 s INFO 17:41:56,924 ProgressMeter - FBgn0247218:2515 5.80e+07 2.2 h 2.3 m 99.8% 2.2 h 19.0 s INFO 17:42:20,615 HaplotypeCaller - Ran local assembly on 187998 active regions INFO 17:42:27,128 ProgressMeter - done 5.81e+07 2.2 h 2.3 m 100.0% 2.2 h 0.0 s INFO 17:42:27,128 ProgressMeter - Total runtime 7870.48 secs, 131.17 min, 2.19 hours INFO 17:42:27,129 MicroScheduler - 359727 reads were filtered out during the traversal out of approximately 5300430 total reads (6.79%) INFO 17:42:27,129 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter INFO 17:42:27,129 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 17:42:27,129 MicroScheduler - -> 359727 reads (6.79% of total) failing HCMappingQualityFilter INFO 17:42:27,129 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 17:42:27,129 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 17:42:27,130 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 17:42:27,130 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter