########################### Execution Started ############################# JobId:33609.paroo3.barrine.hpcu.uq.edu.au UserName:uqmbrozy GroupName:uq ExecutionHost:b10a13 WorkingDir:/var/spool/torque/mom_priv ############################################################################### The GATK jar files have been added to the classpath They can also be used as follows: java -jar $GATK_JARS/GenomeAnalysisTK.jar --help java -jar $GATK_JARS/Queue.jar --help The GATK data bundles can be found in $GATK_BUNDLE INFO 07:33:02,928 HelpFormatter - -------------------------------------------------------------------------------- INFO 07:33:02,930 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 07:33:02,930 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 07:33:02,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 07:33:02,934 HelpFormatter - Program Args: -T HaplotypeCaller -R all.chrs.fasta -I JPN2-filtered_subreads_mer.fastq.bwa.sorted.clean.groups.del.bam -o JPN2_raw_variants_20.vcf -stand_emit_conf 10 -stand_call_conf 20 -nct 8 -rf BadCigar INFO 07:33:03,069 HelpFormatter - Executing as uqmbrozy@b10a13 on Linux 3.0.80-0.5-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_02-b13. INFO 07:33:03,070 HelpFormatter - Date/Time: 2015/10/14 07:33:02 INFO 07:33:03,070 HelpFormatter - -------------------------------------------------------------------------------- INFO 07:33:03,070 HelpFormatter - -------------------------------------------------------------------------------- INFO 07:33:04,215 GenomeAnalysisEngine - Strictness is SILENT INFO 07:33:04,276 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 07:33:04,282 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 07:33:04,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 07:33:04,304 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 07:33:04,316 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine INFO 07:33:04,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 07:33:04,921 GenomeAnalysisEngine - Done preparing for traversal INFO 07:33:04,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 07:33:04,922 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 07:33:04,922 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 07:33:05,001 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 07:33:05,002 PairHMM - Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option Profiling is enabled only when running in single thread mode INFO 07:33:06,685 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file INFO 07:33:06,690 VectorLoglessPairHMM - Using vectorized implementation of PairHMM INFO 07:33:34,925 ProgressMeter - Chr1:711867 0.0 30.0 s 49.6 w 0.2% 4.4 h 4.4 h INFO 07:34:04,926 ProgressMeter - Chr1:1765135 0.0 60.0 s 99.2 w 0.5% 3.5 h 3.5 h INFO 07:34:34,927 ProgressMeter - Chr1:2660430 0.0 90.0 s 148.8 w 0.7% 3.5 h 3.5 h INFO 07:35:04,933 ProgressMeter - Chr1:3550459 0.0 120.0 s 198.4 w 1.0% 3.5 h 3.5 h INFO 07:35:35,017 ProgressMeter - Chr1:4318611 0.0 2.5 m 248.2 w 1.2% 3.6 h 3.6 h INFO 07:36:05,018 ProgressMeter - Chr1:5203152 0.0 3.0 m 297.8 w 1.4% 3.6 h 3.5 h INFO 07:36:35,019 ProgressMeter - Chr1:6078062 0.0 3.5 m 347.4 w 1.6% 3.6 h 3.5 h INFO 07:37:05,020 ProgressMeter - Chr1:6914794 0.0 4.0 m 397.0 w 1.9% 3.6 h 3.5 h INFO 07:37:35,028 ProgressMeter - Chr1:7700022 0.0 4.5 m 446.6 w 2.1% 3.6 h 3.6 h INFO 07:38:05,029 ProgressMeter - Chr1:8495087 0.0 5.0 m 496.2 w 2.3% 3.7 h 3.6 h INFO 07:38:35,030 ProgressMeter - Chr1:9457447 0.0 5.5 m 545.8 w 2.5% 3.6 h 3.5 h INFO 07:39:05,032 ProgressMeter - Chr1:10599765 0.0 6.0 m 595.4 w 2.8% 3.5 h 3.4 h INFO 07:39:35,033 ProgressMeter - Chr1:11651819 0.0 6.5 m 645.0 w 3.1% 3.5 h 3.4 h INFO 07:40:05,034 ProgressMeter - Chr1:12687644 0.0 7.0 m 694.6 w 3.4% 3.4 h 3.3 h INFO 07:40:35,035 ProgressMeter - Chr1:13978951 0.0 7.5 m 744.2 w 3.7% 3.3 h 3.2 h INFO 07:41:15,036 ProgressMeter - Chr1:15402856 0.0 8.2 m 810.4 w 4.1% 3.3 h 3.2 h INFO 07:41:55,037 ProgressMeter - Chr1:17212164 0.0 8.8 m 876.5 w 4.6% 3.2 h 3.0 h INFO 07:42:35,038 ProgressMeter - Chr1:18834839 0.0 9.5 m 942.7 w 5.0% 3.1 h 3.0 h INFO 07:43:05,042 ProgressMeter - Chr1:20043551 0.0 10.0 m 992.3 w 5.4% 3.1 h 2.9 h INFO 07:43:35,043 ProgressMeter - Chr1:20986006 0.0 10.5 m 1041.9 w 5.6% 3.1 h 2.9 h INFO 07:44:15,044 ProgressMeter - Chr1:22345722 0.0 11.2 m 1108.0 w 6.0% 3.1 h 2.9 h INFO 07:44:55,045 ProgressMeter - Chr1:23488141 0.0 11.8 m 1174.1 w 6.3% 3.1 h 2.9 h INFO 07:45:25,045 ProgressMeter - Chr1:24330102 0.0 12.3 m 1223.8 w 6.5% 3.2 h 2.9 h INFO 07:45:55,046 ProgressMeter - Chr1:25006715 0.0 12.8 m 1273.4 w 6.7% 3.2 h 3.0 h INFO 07:46:25,047 ProgressMeter - Chr1:25794232 0.0 13.3 m 1323.0 w 6.9% 3.2 h 3.0 h INFO 07:46:55,048 ProgressMeter - Chr1:26704956 0.0 13.8 m 1372.6 w 7.2% 3.2 h 3.0 h INFO 07:47:35,049 ProgressMeter - Chr1:27915379 0.0 14.5 m 1438.7 w 7.5% 3.2 h 3.0 h INFO 07:48:05,050 ProgressMeter - Chr1:28690356 0.0 15.0 m 1488.3 w 7.7% 3.3 h 3.0 h INFO 07:48:35,060 ProgressMeter - Chr1:29597206 0.0 15.5 m 1537.9 w 7.9% 3.3 h 3.0 h INFO 07:49:05,061 ProgressMeter - Chr1:30372591 0.0 16.0 m 1587.5 w 8.1% 3.3 h 3.0 h INFO 07:49:35,062 ProgressMeter - Chr1:31154780 0.0 16.5 m 1637.1 w 8.3% 3.3 h 3.0 h INFO 07:50:05,065 ProgressMeter - Chr1:31947707 0.0 17.0 m 1686.7 w 8.6% 3.3 h 3.0 h INFO 07:50:35,065 ProgressMeter - Chr1:32740103 0.0 17.5 m 1736.3 w 8.8% 3.3 h 3.0 h INFO 07:51:05,066 ProgressMeter - Chr1:33519335 0.0 18.0 m 1786.0 w 9.0% 3.3 h 3.0 h INFO 07:51:35,067 ProgressMeter - Chr1:33536491 0.0 18.5 m 1835.6 w 9.0% 3.4 h 3.1 h INFO 07:52:15,068 ProgressMeter - Chr1:33550106 0.0 19.2 m 1901.7 w 9.0% 3.6 h 3.2 h INFO 07:52:45,068 ProgressMeter - Chr1:33584317 0.0 19.7 m 1951.3 w 9.0% 3.6 h 3.3 h INFO 07:53:15,069 ProgressMeter - Chr1:33587961 0.0 20.2 m 2000.9 w 9.0% 3.7 h 3.4 h INFO 07:53:45,070 ProgressMeter - Chr1:34076350 0.0 20.7 m 2050.5 w 9.1% 3.8 h 3.4 h INFO 07:54:25,071 ProgressMeter - Chr1:35032006 0.0 21.3 m 2116.6 w 9.4% 3.8 h 3.4 h INFO 07:54:55,072 ProgressMeter - Chr1:35879033 0.0 21.8 m 2166.3 w 9.6% 3.8 h 3.4 h INFO 07:55:25,072 ProgressMeter - Chr1:36749706 0.0 22.3 m 2215.9 w 9.8% 3.8 h 3.4 h INFO 07:55:55,073 ProgressMeter - Chr1:37697379 0.0 22.8 m 2265.5 w 10.1% 3.8 h 3.4 h INFO 07:56:25,074 ProgressMeter - Chr1:38471089 0.0 23.3 m 2315.1 w 10.3% 3.8 h 3.4 h INFO 07:56:55,075 ProgressMeter - Chr1:39165169 0.0 23.8 m 2364.7 w 10.5% 3.8 h 3.4 h INFO 07:57:35,076 ProgressMeter - Chr1:39998118 0.0 24.5 m 2430.8 w 10.7% 3.8 h 3.4 h INFO 07:58:05,076 ProgressMeter - Chr1:40791682 0.0 25.0 m 2480.4 w 10.9% 3.8 h 3.4 h INFO 07:58:35,077 ProgressMeter - Chr1:41541387 0.0 25.5 m 2530.0 w 11.1% 3.8 h 3.4 h INFO 07:59:05,078 ProgressMeter - Chr1:42316486 0.0 26.0 m 2579.6 w 11.3% 3.8 h 3.4 h INFO 07:59:35,079 ProgressMeter - Chr1:43215071 0.0 26.5 m 2629.2 w 11.6% 3.8 h 3.4 h INFO 08:00:15,080 ProgressMeter - Chr2:581677 4.3270923E7 27.2 m 37.0 s 11.7% 3.9 h 3.4 h INFO 08:00:45,081 ProgressMeter - Chr2:1414610 4.3270923E7 27.7 m 38.0 s 12.0% 3.9 h 3.4 h INFO 08:01:25,082 ProgressMeter - Chr2:2478973 4.3270923E7 28.3 m 39.0 s 12.3% 3.9 h 3.4 h INFO 08:02:05,083 ProgressMeter - Chr2:3470710 4.3270923E7 29.0 m 40.0 s 12.5% 3.9 h 3.4 h INFO 08:02:35,084 ProgressMeter - Chr2:4350129 4.3270923E7 29.5 m 40.0 s 12.8% 3.9 h 3.4 h INFO 08:03:05,084 ProgressMeter - Chr2:5163638 4.3270923E7 30.0 m 41.0 s 13.0% 3.9 h 3.4 h INFO 08:03:35,085 ProgressMeter - Chr2:6020745 4.3270923E7 30.5 m 42.0 s 13.2% 3.8 h 3.3 h INFO 08:04:05,097 ProgressMeter - Chr2:7003175 4.3270923E7 31.0 m 42.0 s 13.5% 3.8 h 3.3 h INFO 08:04:35,098 ProgressMeter - Chr2:8015129 4.3270923E7 31.5 m 43.0 s 13.7% 3.8 h 3.3 h INFO 08:05:05,098 ProgressMeter - Chr2:9100409 4.3270923E7 32.0 m 44.0 s 14.0% 3.8 h 3.3 h INFO 08:05:35,099 ProgressMeter - Chr2:10340212 4.3270923E7 32.5 m 45.0 s 14.4% 3.8 h 3.2 h INFO 08:06:05,100 ProgressMeter - Chr2:11312112 4.3270923E7 33.0 m 45.0 s 14.6% 3.8 h 3.2 h INFO 08:06:35,101 ProgressMeter - Chr2:12260564 4.3270923E7 33.5 m 46.0 s 14.9% 3.8 h 3.2 h INFO 08:07:15,102 ProgressMeter - Chr2:13507750 4.3270923E7 34.2 m 47.0 s 15.2% 3.7 h 3.2 h INFO 08:07:55,103 ProgressMeter - Chr2:14285930 4.3270923E7 34.8 m 48.0 s 15.4% 3.8 h 3.2 h INFO 08:08:25,103 ProgressMeter - Chr2:14835361 4.3270923E7 35.3 m 48.0 s 15.6% 3.8 h 3.2 h INFO 08:08:55,104 ProgressMeter - Chr2:15708184 4.3270923E7 35.8 m 49.0 s 15.8% 3.8 h 3.2 h INFO 08:09:25,105 ProgressMeter - Chr2:16532668 4.3270923E7 36.3 m 50.0 s 16.0% 3.8 h 3.2 h INFO 08:09:55,106 ProgressMeter - Chr2:17656583 4.3270923E7 36.8 m 51.0 s 16.3% 3.8 h 3.1 h INFO 08:10:35,112 ProgressMeter - Chr2:18934087 4.3270923E7 37.5 m 52.0 s 16.7% 3.8 h 3.1 h INFO 08:11:15,113 ProgressMeter - Chr2:19919128 4.3270923E7 38.2 m 52.0 s 16.9% 3.8 h 3.1 h INFO 08:11:45,114 ProgressMeter - Chr2:20629001 4.3270923E7 38.7 m 53.0 s 17.1% 3.8 h 3.1 h INFO 08:12:15,114 ProgressMeter - Chr2:21535060 4.3270923E7 39.2 m 54.0 s 17.4% 3.8 h 3.1 h INFO 08:12:45,115 ProgressMeter - Chr2:22585658 4.3270923E7 39.7 m 55.0 s 17.6% 3.7 h 3.1 h INFO 08:13:15,116 ProgressMeter - Chr2:23755621 4.3270923E7 40.2 m 55.0 s 18.0% 3.7 h 3.1 h INFO 08:13:45,117 ProgressMeter - Chr2:24742731 4.3270923E7 40.7 m 56.0 s 18.2% 3.7 h 3.0 h INFO 08:14:15,125 ProgressMeter - Chr2:25739670 4.3270923E7 41.2 m 57.0 s 18.5% 3.7 h 3.0 h INFO 08:14:45,125 ProgressMeter - Chr2:26821813 4.3270923E7 41.7 m 57.0 s 18.8% 3.7 h 3.0 h INFO 08:15:15,126 ProgressMeter - Chr2:27599546 4.3270923E7 42.2 m 58.0 s 19.0% 3.7 h 3.0 h INFO 08:15:45,127 ProgressMeter - Chr2:28665536 4.3270923E7 42.7 m 59.0 s 19.3% 3.7 h 3.0 h INFO 08:16:25,128 ProgressMeter - Chr2:28719813 4.3270923E7 43.3 m 60.0 s 19.3% 3.7 h 3.0 h INFO 08:16:55,128 ProgressMeter - Chr2:28721984 4.3270923E7 43.8 m 60.0 s 19.3% 3.8 h 3.1 h INFO 08:17:25,129 ProgressMeter - Chr2:29083372 4.3270923E7 44.3 m 61.0 s 19.4% 3.8 h 3.1 h INFO 08:17:55,130 ProgressMeter - Chr2:29895881 4.3270923E7 44.8 m 62.0 s 19.6% 3.8 h 3.1 h INFO 08:18:35,131 ProgressMeter - Chr2:30879736 4.3270923E7 45.5 m 63.0 s 19.9% 3.8 h 3.1 h INFO 08:19:15,132 ProgressMeter - Chr2:31914591 4.3270923E7 46.2 m 64.0 s 20.1% 3.8 h 3.1 h INFO 08:19:55,133 ProgressMeter - Chr2:33090382 4.3270923E7 46.8 m 64.0 s 20.5% 3.8 h 3.0 h INFO 08:20:35,134 ProgressMeter - Chr2:34301402 4.3270923E7 47.5 m 65.0 s 20.8% 3.8 h 3.0 h INFO 08:21:05,143 ProgressMeter - Chr2:35247008 4.3270923E7 48.0 m 66.0 s 21.0% 3.8 h 3.0 h INFO 08:21:35,144 ProgressMeter - Chr2:35937250 4.3270923E7 48.5 m 67.0 s 21.2% 3.8 h 3.0 h INFO 08:22:05,145 ProgressMeter - Chr3:677673 7.9208173E7 49.0 m 37.0 s 21.4% 3.8 h 3.0 h INFO 08:22:35,156 ProgressMeter - Chr3:1511828 7.9208173E7 49.5 m 37.0 s 21.6% 3.8 h 3.0 h INFO 08:23:05,157 ProgressMeter - Chr3:2287389 7.9208173E7 50.0 m 37.0 s 21.8% 3.8 h 3.0 h INFO 08:23:35,158 ProgressMeter - Chr3:3048247 7.9208173E7 50.5 m 38.0 s 22.0% 3.8 h 3.0 h INFO 08:24:05,159 ProgressMeter - Chr3:3798345 7.9208173E7 51.0 m 38.0 s 22.2% 3.8 h 3.0 h INFO 08:24:45,160 ProgressMeter - Chr3:4374048 7.9208173E7 51.7 m 39.0 s 22.4% 3.8 h 3.0 h INFO 08:25:25,161 ProgressMeter - Chr3:5231945 7.9208173E7 52.3 m 39.0 s 22.6% 3.9 h 3.0 h INFO 08:25:55,161 ProgressMeter - Chr3:5962462 7.9208173E7 52.8 m 40.0 s 22.8% 3.9 h 3.0 h INFO 08:26:25,164 ProgressMeter - Chr3:6756195 7.9208173E7 53.3 m 40.0 s 23.0% 3.9 h 3.0 h INFO 08:27:05,165 ProgressMeter - Chr3:7818105 7.9208173E7 54.0 m 40.0 s 23.3% 3.9 h 3.0 h INFO 08:27:35,165 ProgressMeter - Chr3:8703433 7.9208173E7 54.5 m 41.0 s 23.6% 3.9 h 2.9 h INFO 08:28:05,166 ProgressMeter - Chr3:9548172 7.9208173E7 55.0 m 41.0 s 23.8% 3.9 h 2.9 h INFO 08:28:35,167 ProgressMeter - Chr3:10301028 7.9208173E7 55.5 m 42.0 s 24.0% 3.9 h 2.9 h INFO 08:29:05,168 ProgressMeter - Chr3:11046251 7.9208173E7 56.0 m 42.0 s 24.2% 3.9 h 2.9 h INFO 08:29:45,169 ProgressMeter - Chr3:12101612 7.9208173E7 56.7 m 42.0 s 24.5% 3.9 h 2.9 h INFO 08:30:15,169 ProgressMeter - Chr3:12908642 7.9208173E7 57.2 m 43.0 s 24.7% 3.9 h 2.9 h INFO 08:30:45,170 ProgressMeter - Chr3:13781976 7.9208173E7 57.7 m 43.0 s 24.9% 3.9 h 2.9 h INFO 08:31:15,171 ProgressMeter - Chr3:14587569 7.9208173E7 58.2 m 44.0 s 25.1% 3.9 h 2.9 h INFO 08:31:45,172 ProgressMeter - Chr3:15414647 7.9208173E7 58.7 m 44.0 s 25.4% 3.9 h 2.9 h INFO 08:32:25,173 ProgressMeter - Chr3:16483443 7.9208173E7 59.3 m 44.0 s 25.6% 3.9 h 2.9 h INFO 08:32:55,174 ProgressMeter - Chr3:17427242 7.9208173E7 59.8 m 45.0 s 25.9% 3.9 h 2.9 h INFO 08:33:25,177 ProgressMeter - Chr3:18286418 7.9208173E7 60.3 m 45.0 s 26.1% 3.8 h 2.8 h INFO 08:33:55,178 ProgressMeter - Chr3:19648657 7.9208173E7 60.8 m 46.0 s 26.5% 3.8 h 2.8 h INFO 08:34:25,178 ProgressMeter - Chr3:20566129 7.9208173E7 61.3 m 46.0 s 26.7% 3.8 h 2.8 h INFO 08:34:55,179 ProgressMeter - Chr3:21480572 7.9208173E7 61.8 m 46.0 s 27.0% 3.8 h 2.8 h INFO 08:35:25,180 ProgressMeter - Chr3:22347317 7.9208173E7 62.3 m 47.0 s 27.2% 3.8 h 2.8 h INFO 08:35:55,181 ProgressMeter - Chr3:23335118 7.9208173E7 62.8 m 47.0 s 27.5% 3.8 h 2.8 h INFO 08:36:25,186 ProgressMeter - Chr3:24220774 7.9208173E7 63.3 m 47.0 s 27.7% 3.8 h 2.8 h INFO 08:36:55,188 ProgressMeter - Chr3:25126591 7.9208173E7 63.8 m 48.0 s 28.0% 3.8 h 2.7 h INFO 08:37:25,189 ProgressMeter - Chr3:25984608 7.9208173E7 64.3 m 48.0 s 28.2% 3.8 h 2.7 h INFO 08:37:55,190 ProgressMeter - Chr3:26925161 7.9208173E7 64.8 m 49.0 s 28.4% 3.8 h 2.7 h INFO 08:38:25,196 ProgressMeter - Chr3:27746072 7.9208173E7 65.3 m 49.0 s 28.7% 3.8 h 2.7 h INFO 08:38:55,197 ProgressMeter - Chr3:28549972 7.9208173E7 65.8 m 49.0 s 28.9% 3.8 h 2.7 h INFO 08:39:25,201 ProgressMeter - Chr3:29334165 7.9208173E7 66.3 m 50.0 s 29.1% 3.8 h 2.7 h INFO 08:40:05,202 ProgressMeter - Chr3:30458940 7.9208173E7 67.0 m 50.0 s 29.4% 3.8 h 2.7 h INFO 08:40:45,203 ProgressMeter - Chr3:31565141 7.9208173E7 67.7 m 51.0 s 29.7% 3.8 h 2.7 h INFO 08:41:15,205 ProgressMeter - Chr3:32408837 7.9208173E7 68.2 m 51.0 s 29.9% 3.8 h 2.7 h INFO 08:41:45,212 ProgressMeter - Chr3:33221416 7.9208173E7 68.7 m 52.0 s 30.1% 3.8 h 2.7 h INFO 08:42:25,213 ProgressMeter - Chr3:34311960 7.9208173E7 69.3 m 52.0 s 30.4% 3.8 h 2.6 h INFO 08:43:05,214 ProgressMeter - Chr3:35428710 7.9208173E7 70.0 m 53.0 s 30.7% 3.8 h 2.6 h INFO 08:43:35,223 ProgressMeter - Chr3:36188557 7.9208173E7 70.5 m 53.0 s 30.9% 3.8 h 2.6 h INFO 08:44:05,225 ProgressMeter - Chr4:580381 1.15621992E8 71.0 m 36.0 s 31.1% 3.8 h 2.6 h INFO 08:44:35,231 ProgressMeter - Chr4:1406003 1.15621992E8 71.5 m 37.0 s 31.4% 3.8 h 2.6 h INFO 08:45:05,231 ProgressMeter - Chr4:1505462 1.15621992E8 72.0 m 37.0 s 31.4% 3.8 h 2.6 h INFO 08:45:35,232 ProgressMeter - Chr4:2042487 1.15621992E8 72.5 m 37.0 s 31.5% 3.8 h 2.6 h INFO 08:46:05,233 ProgressMeter - Chr4:3098494 1.15621992E8 73.0 m 37.0 s 31.8% 3.8 h 2.6 h INFO 08:46:35,237 ProgressMeter - Chr4:4251828 1.15621992E8 73.5 m 38.0 s 32.1% 3.8 h 2.6 h INFO 08:47:05,237 ProgressMeter - Chr4:5188414 1.15621992E8 74.0 m 38.0 s 32.4% 3.8 h 2.6 h INFO 08:47:35,238 ProgressMeter - Chr4:6407332 1.15621992E8 74.5 m 38.0 s 32.7% 3.8 h 2.6 h INFO 08:48:05,239 ProgressMeter - Chr4:7590250 1.15621992E8 75.0 m 38.0 s 33.0% 3.8 h 2.5 h INFO 08:48:35,240 ProgressMeter - Chr4:9100094 1.15621992E8 75.5 m 39.0 s 33.4% 3.8 h 2.5 h INFO 08:49:05,241 ProgressMeter - Chr4:9185921 1.15621992E8 76.0 m 39.0 s 33.4% 3.8 h 2.5 h INFO 08:49:45,242 ProgressMeter - Chr4:9678032 1.15621992E8 76.7 m 39.0 s 33.6% 3.8 h 2.5 h INFO 08:50:15,242 ProgressMeter - Chr4:10993349 1.15621992E8 77.2 m 40.0 s 33.9% 3.8 h 2.5 h INFO 08:50:45,243 ProgressMeter - Chr4:12114638 1.15621992E8 77.7 m 40.0 s 34.2% 3.8 h 2.5 h INFO 08:51:15,244 ProgressMeter - Chr4:13208322 1.15621992E8 78.2 m 40.0 s 34.5% 3.8 h 2.5 h INFO 08:51:55,245 ProgressMeter - Chr4:13910432 1.15621992E8 78.8 m 40.0 s 34.7% 3.8 h 2.5 h INFO 08:52:25,245 ProgressMeter - Chr4:15270826 1.15621992E8 79.3 m 41.0 s 35.1% 3.8 h 2.4 h INFO 08:52:55,246 ProgressMeter - Chr4:16404277 1.15621992E8 79.8 m 41.0 s 35.4% 3.8 h 2.4 h INFO 08:53:25,247 ProgressMeter - Chr4:17569232 1.15621992E8 80.3 m 41.0 s 35.7% 3.8 h 2.4 h INFO 08:53:55,248 ProgressMeter - Chr4:18865164 1.15621992E8 80.8 m 41.0 s 36.0% 3.7 h 2.4 h INFO 08:54:25,249 ProgressMeter - Chr4:19885237 1.15621992E8 81.3 m 42.0 s 36.3% 3.7 h 2.4 h INFO 08:54:55,250 ProgressMeter - Chr4:20952902 1.15621992E8 81.8 m 42.0 s 36.6% 3.7 h 2.4 h INFO 08:55:35,251 ProgressMeter - Chr4:21403784 1.15621992E8 82.5 m 42.0 s 36.7% 3.7 h 2.4 h INFO 08:56:05,251 ProgressMeter - Chr4:21856475 1.15621992E8 83.0 m 43.0 s 36.8% 3.8 h 2.4 h INFO 08:56:35,252 ProgressMeter - Chr4:22768677 1.15621992E8 83.5 m 43.0 s 37.1% 3.8 h 2.4 h INFO 08:57:05,253 ProgressMeter - Chr4:23187415 1.15621992E8 84.0 m 43.0 s 37.2% 3.8 h 2.4 h INFO 08:57:45,254 ProgressMeter - Chr4:24414459 1.15621992E8 84.7 m 43.0 s 37.5% 3.8 h 2.3 h INFO 08:58:25,255 ProgressMeter - Chr4:25730755 1.15621992E8 85.3 m 44.0 s 37.9% 3.8 h 2.3 h INFO 08:58:55,262 ProgressMeter - Chr4:26776546 1.15621992E8 85.8 m 44.0 s 38.2% 3.7 h 2.3 h INFO 08:59:35,263 ProgressMeter - Chr4:28115658 1.15621992E8 86.5 m 44.0 s 38.5% 3.7 h 2.3 h INFO 09:00:05,263 ProgressMeter - Chr4:29117082 1.15621992E8 87.0 m 45.0 s 38.8% 3.7 h 2.3 h INFO 09:00:35,264 ProgressMeter - Chr4:29926272 1.15621992E8 87.5 m 45.0 s 39.0% 3.7 h 2.3 h INFO 09:01:05,265 ProgressMeter - Chr4:30854802 1.15621992E8 88.0 m 45.0 s 39.2% 3.7 h 2.3 h INFO 09:01:35,266 ProgressMeter - Chr4:31749049 1.15621992E8 88.5 m 45.0 s 39.5% 3.7 h 2.3 h INFO 09:02:05,268 ProgressMeter - Chr4:32708680 1.15621992E8 89.0 m 46.0 s 39.7% 3.7 h 2.2 h INFO 09:02:35,269 ProgressMeter - Chr4:32887137 1.15621992E8 89.5 m 46.0 s 39.8% 3.7 h 2.3 h INFO 09:03:15,270 ProgressMeter - Chr4:32890205 1.15621992E8 90.2 m 46.0 s 39.8% 3.8 h 2.3 h INFO 09:03:45,270 ProgressMeter - Chr4:32934575 1.15621992E8 90.7 m 47.0 s 39.8% 3.8 h 2.3 h INFO 09:04:15,271 ProgressMeter - Chr4:33531416 1.15621992E8 91.2 m 47.0 s 40.0% 3.8 h 2.3 h INFO 09:04:55,272 ProgressMeter - Chr4:34491660 1.15621992E8 91.8 m 47.0 s 40.2% 3.8 h 2.3 h INFO 09:05:25,273 ProgressMeter - Chr4:35382717 1.15621992E8 92.3 m 47.0 s 40.5% 3.8 h 2.3 h INFO 09:05:55,274 ProgressMeter - Chr5:462876 1.51124686E8 92.8 m 36.0 s 40.6% 3.8 h 2.3 h INFO 09:06:35,275 ProgressMeter - Chr5:1554968 1.51124686E8 93.5 m 37.0 s 40.9% 3.8 h 2.3 h INFO 09:07:05,275 ProgressMeter - Chr5:2509993 1.51124686E8 94.0 m 37.0 s 41.2% 3.8 h 2.2 h INFO 09:07:35,276 ProgressMeter - Chr5:3326335 1.51124686E8 94.5 m 37.0 s 41.4% 3.8 h 2.2 h INFO 09:08:05,277 ProgressMeter - Chr5:4225562 1.51124686E8 95.0 m 37.0 s 41.6% 3.8 h 2.2 h INFO 09:08:35,278 ProgressMeter - Chr5:5288106 1.51124686E8 95.5 m 37.0 s 41.9% 3.8 h 2.2 h INFO 09:09:15,279 ProgressMeter - Chr5:6602507 1.51124686E8 96.2 m 38.0 s 42.3% 3.8 h 2.2 h INFO 09:09:45,279 ProgressMeter - Chr5:7459781 1.51124686E8 96.7 m 38.0 s 42.5% 3.8 h 2.2 h INFO 09:10:15,280 ProgressMeter - Chr5:8521193 1.51124686E8 97.2 m 38.0 s 42.8% 3.8 h 2.2 h INFO 09:10:45,281 ProgressMeter - Chr5:9655382 1.51124686E8 97.7 m 38.0 s 43.1% 3.8 h 2.2 h INFO 09:11:15,282 ProgressMeter - Chr5:11419154 1.51124686E8 98.2 m 38.0 s 43.5% 3.8 h 2.1 h INFO 09:11:55,283 ProgressMeter - Chr5:13429036 1.51124686E8 98.8 m 39.0 s 44.1% 3.7 h 2.1 h INFO 09:12:25,283 ProgressMeter - Chr5:14608066 1.51124686E8 99.3 m 39.0 s 44.4% 3.7 h 2.1 h INFO 09:12:55,284 ProgressMeter - Chr5:15901640 1.51124686E8 99.8 m 39.0 s 44.7% 3.7 h 2.1 h INFO 09:13:25,285 ProgressMeter - Chr5:16888140 1.51124686E8 100.3 m 39.0 s 45.0% 3.7 h 2.0 h INFO 09:14:05,286 ProgressMeter - Chr5:18397220 1.51124686E8 101.0 m 40.0 s 45.4% 3.7 h 2.0 h INFO 09:14:45,287 ProgressMeter - Chr5:19504053 1.51124686E8 101.7 m 40.0 s 45.7% 3.7 h 2.0 h INFO 09:15:15,288 ProgressMeter - Chr5:20317228 1.51124686E8 102.2 m 40.0 s 45.9% 3.7 h 2.0 h INFO 09:15:45,288 ProgressMeter - Chr5:21374216 1.51124686E8 102.7 m 40.0 s 46.2% 3.7 h 119.5 m INFO 09:16:15,290 ProgressMeter - Chr5:22452199 1.51124686E8 103.2 m 40.0 s 46.5% 3.7 h 118.7 m INFO 09:16:45,291 ProgressMeter - Chr5:23507563 1.51124686E8 103.7 m 41.0 s 46.8% 3.7 h 117.9 m INFO 09:17:15,292 ProgressMeter - Chr5:24481058 1.51124686E8 104.2 m 41.0 s 47.0% 3.7 h 117.2 m INFO 09:17:45,293 ProgressMeter - Chr5:25670484 1.51124686E8 104.7 m 41.0 s 47.4% 3.7 h 116.3 m INFO 09:18:25,294 ProgressMeter - Chr5:26972747 1.51124686E8 105.3 m 41.0 s 47.7% 3.7 h 115.4 m INFO 09:18:55,294 ProgressMeter - Chr5:27868798 1.51124686E8 105.8 m 42.0 s 48.0% 3.7 h 114.9 m INFO 09:19:25,295 ProgressMeter - Chr5:28745780 1.51124686E8 106.3 m 42.0 s 48.2% 3.7 h 114.3 m INFO 09:19:55,296 ProgressMeter - Chr5:29633080 1.51124686E8 106.8 m 42.0 s 48.4% 3.7 h 113.8 m INFO 09:20:25,400 ProgressMeter - Chr5:29854460 1.51124686E8 107.3 m 42.0 s 48.5% 3.7 h 114.0 m INFO 09:20:55,401 ProgressMeter - Chr5:29958434 1.51124686E8 107.8 m 42.0 s 48.5% 3.7 h 114.4 m INFO 09:21:25,402 ProgressMeter - Chr6:148390 1.8108312E8 108.3 m 35.0 s 48.6% 3.7 h 114.8 m INFO 09:22:05,403 ProgressMeter - Chr6:1406968 1.8108312E8 109.0 m 36.0 s 48.9% 3.7 h 113.9 m INFO 09:22:45,404 ProgressMeter - Chr6:2547928 1.8108312E8 109.7 m 36.0 s 49.2% 3.7 h 113.2 m INFO 09:23:15,405 ProgressMeter - Chr6:3362945 1.8108312E8 110.2 m 36.0 s 49.4% 3.7 h 112.8 m INFO 09:23:45,405 ProgressMeter - Chr6:4324102 1.8108312E8 110.7 m 36.0 s 49.7% 3.7 h 112.1 m INFO 09:24:15,406 ProgressMeter - Chr6:5318150 1.8108312E8 111.2 m 36.0 s 49.9% 3.7 h 111.4 m INFO 09:24:45,407 ProgressMeter - Chr6:6206357 1.8108312E8 111.7 m 37.0 s 50.2% 3.7 h 110.9 m INFO 09:25:15,408 ProgressMeter - Chr6:7055875 1.8108312E8 112.2 m 37.0 s 50.4% 3.7 h 110.4 m INFO 09:25:45,409 ProgressMeter - Chr6:8007145 1.8108312E8 112.7 m 37.0 s 50.7% 3.7 h 109.7 m INFO 09:26:15,410 ProgressMeter - Chr6:8993257 1.8108312E8 113.2 m 37.0 s 50.9% 3.7 h 109.1 m INFO 09:26:45,411 ProgressMeter - Chr6:10163969 1.8108312E8 113.7 m 37.0 s 51.2% 3.7 h 108.2 m INFO 09:27:15,412 ProgressMeter - Chr6:11460830 1.8108312E8 114.2 m 37.0 s 51.6% 3.7 h 107.1 m INFO 09:27:45,413 ProgressMeter - Chr6:12540053 1.8108312E8 114.7 m 37.0 s 51.9% 3.7 h 106.4 m INFO 09:28:25,414 ProgressMeter - Chr6:13736681 1.8108312E8 115.3 m 38.0 s 52.2% 3.7 h 105.6 m INFO 09:28:55,414 ProgressMeter - Chr6:14550726 1.8108312E8 115.8 m 38.0 s 52.4% 3.7 h 105.2 m INFO 09:29:25,415 ProgressMeter - Chr6:15740955 1.8108312E8 116.3 m 38.0 s 52.7% 3.7 h 104.3 m INFO 09:29:55,416 ProgressMeter - Chr6:16549994 1.8108312E8 116.8 m 38.0 s 52.9% 3.7 h 103.8 m INFO 09:30:35,417 ProgressMeter - Chr6:17746583 1.8108312E8 117.5 m 38.0 s 53.3% 3.7 h 103.1 m INFO 09:31:15,418 ProgressMeter - Chr6:19435473 1.8108312E8 118.2 m 39.0 s 53.7% 3.7 h 101.8 m INFO 09:31:45,418 ProgressMeter - Chr6:20443692 1.8108312E8 118.7 m 39.0 s 54.0% 3.7 h 101.1 m INFO 09:32:15,420 ProgressMeter - Chr6:21660178 1.8108312E8 119.2 m 39.0 s 54.3% 3.7 h 100.2 m INFO 09:32:45,421 ProgressMeter - Chr6:22166561 1.8108312E8 119.7 m 39.0 s 54.5% 3.7 h 100.1 m INFO 09:33:25,422 ProgressMeter - Chr6:22169188 1.8108312E8 2.0 h 39.0 s 54.5% 3.7 h 100.6 m INFO 09:33:55,422 ProgressMeter - Chr6:22169188 1.8108312E8 2.0 h 40.0 s 54.5% 3.7 h 101.1 m INFO 09:34:25,423 ProgressMeter - Chr6:22170664 1.8108312E8 2.0 h 40.0 s 54.5% 3.7 h 101.5 m INFO 09:35:05,424 ProgressMeter - Chr6:22183439 1.8108312E8 2.0 h 40.0 s 54.5% 3.7 h 102.0 m INFO 09:35:35,424 ProgressMeter - Chr6:23138627 1.8108312E8 2.0 h 40.0 s 54.7% 3.7 h 101.4 m INFO 09:36:05,425 ProgressMeter - Chr6:23575056 1.8108312E8 2.1 h 40.0 s 54.8% 3.7 h 101.3 m INFO 09:36:35,426 ProgressMeter - Chr6:23829412 1.8108312E8 2.1 h 40.0 s 54.9% 3.7 h 101.5 m INFO 09:37:15,427 ProgressMeter - Chr6:25169732 1.8108312E8 2.1 h 41.0 s 55.3% 3.7 h 100.5 m INFO 09:37:45,430 ProgressMeter - Chr6:26317621 1.8108312E8 2.1 h 41.0 s 55.6% 3.7 h 99.7 m INFO 09:38:15,431 ProgressMeter - Chr6:27257069 1.8108312E8 2.1 h 41.0 s 55.8% 3.7 h 99.1 m INFO 09:38:45,432 ProgressMeter - Chr6:28161779 1.8108312E8 2.1 h 41.0 s 56.1% 3.7 h 98.5 m INFO 09:39:25,433 ProgressMeter - Chr6:29621525 1.8108312E8 2.1 h 41.0 s 56.5% 3.7 h 97.5 m INFO 09:39:55,434 ProgressMeter - Chr6:30797047 1.8108312E8 2.1 h 42.0 s 56.8% 3.7 h 96.6 m INFO 09:40:25,434 ProgressMeter - Chr7:513442 2.12331907E8 2.1 h 35.0 s 57.0% 3.7 h 96.0 m INFO 09:40:55,435 ProgressMeter - Chr7:1606332 2.12331907E8 2.1 h 36.0 s 57.3% 3.7 h 95.2 m INFO 09:41:25,436 ProgressMeter - Chr7:2466970 2.12331907E8 2.1 h 36.0 s 57.5% 3.7 h 94.7 m INFO 09:41:55,437 ProgressMeter - Chr7:3227046 2.12331907E8 2.1 h 36.0 s 57.8% 3.7 h 94.2 m INFO 09:42:35,438 ProgressMeter - Chr7:4502387 2.12331907E8 2.2 h 36.0 s 58.1% 3.7 h 93.4 m INFO 09:43:05,439 ProgressMeter - Chr7:5679511 2.12331907E8 2.2 h 36.0 s 58.4% 3.7 h 92.6 m INFO 09:43:45,440 ProgressMeter - Chr7:7357518 2.12331907E8 2.2 h 36.0 s 58.9% 3.7 h 91.3 m INFO 09:44:15,440 ProgressMeter - Chr7:8300189 2.12331907E8 2.2 h 37.0 s 59.1% 3.7 h 90.7 m INFO 09:44:45,441 ProgressMeter - Chr7:9684470 2.12331907E8 2.2 h 37.0 s 59.5% 3.7 h 89.7 m INFO 09:45:15,442 ProgressMeter - Chr7:11307705 2.12331907E8 2.2 h 37.0 s 59.9% 3.7 h 88.4 m INFO 09:45:55,443 ProgressMeter - Chr7:13026606 2.12331907E8 2.2 h 37.0 s 60.4% 3.7 h 87.2 m INFO 09:46:35,444 ProgressMeter - Chr7:14831746 2.12331907E8 2.2 h 37.0 s 60.9% 3.7 h 85.8 m INFO 09:47:05,447 ProgressMeter - Chr7:16142620 2.12331907E8 2.2 h 37.0 s 61.2% 3.6 h 84.9 m INFO 09:47:35,447 ProgressMeter - Chr7:17067220 2.12331907E8 2.2 h 38.0 s 61.5% 3.6 h 84.3 m INFO 09:48:05,448 ProgressMeter - Chr7:18207126 2.12331907E8 2.3 h 38.0 s 61.8% 3.6 h 83.6 m INFO 09:48:35,452 ProgressMeter - Chr7:19263724 2.12331907E8 2.3 h 38.0 s 62.0% 3.6 h 82.9 m INFO 09:49:05,453 ProgressMeter - Chr7:20369023 2.12331907E8 2.3 h 38.0 s 62.3% 3.6 h 82.1 m INFO 09:49:35,454 ProgressMeter - Chr7:21449821 2.12331907E8 2.3 h 38.0 s 62.6% 3.6 h 81.4 m INFO 09:50:15,455 ProgressMeter - Chr7:22838597 2.12331907E8 2.3 h 38.0 s 63.0% 3.6 h 80.5 m INFO 09:50:55,456 ProgressMeter - Chr7:24213899 2.12331907E8 2.3 h 38.0 s 63.4% 3.6 h 79.7 m INFO 09:51:35,457 ProgressMeter - Chr7:25402577 2.12331907E8 2.3 h 39.0 s 63.7% 3.6 h 78.9 m INFO 09:52:15,457 ProgressMeter - Chr7:26780275 2.12331907E8 2.3 h 39.0 s 64.1% 3.6 h 78.1 m INFO 09:52:45,458 ProgressMeter - Chr7:27378216 2.12331907E8 2.3 h 39.0 s 64.2% 3.6 h 77.8 m INFO 09:53:15,459 ProgressMeter - Chr7:27446553 2.12331907E8 2.3 h 39.0 s 64.2% 3.6 h 78.0 m INFO 09:53:55,460 ProgressMeter - Chr7:27872641 2.12331907E8 2.3 h 39.0 s 64.4% 3.6 h 78.0 m INFO 09:54:35,461 ProgressMeter - Chr7:28929209 2.12331907E8 2.4 h 39.0 s 64.6% 3.6 h 77.4 m INFO 09:55:05,461 ProgressMeter - Chr8:89683 2.42029528E8 2.4 h 35.0 s 64.9% 3.6 h 76.9 m INFO 09:55:35,462 ProgressMeter - Chr8:973406 2.42029528E8 2.4 h 35.0 s 65.1% 3.6 h 76.4 m INFO 09:56:05,463 ProgressMeter - Chr8:1843298 2.42029528E8 2.4 h 35.0 s 65.3% 3.6 h 75.9 m INFO 09:56:35,464 ProgressMeter - Chr8:2954399 2.42029528E8 2.4 h 35.0 s 65.6% 3.6 h 75.1 m INFO 09:57:15,465 ProgressMeter - Chr8:4366866 2.42029528E8 2.4 h 35.0 s 66.0% 3.6 h 74.2 m INFO 09:57:55,468 ProgressMeter - Chr8:5669887 2.42029528E8 2.4 h 35.0 s 66.4% 3.6 h 73.4 m INFO 09:58:25,469 ProgressMeter - Chr8:6579492 2.42029528E8 2.4 h 36.0 s 66.6% 3.6 h 72.9 m INFO 09:58:55,469 ProgressMeter - Chr8:6811182 2.42029528E8 2.4 h 36.0 s 66.7% 3.6 h 72.9 m INFO 09:59:25,470 ProgressMeter - Chr8:7620040 2.42029528E8 2.4 h 36.0 s 66.9% 3.6 h 72.4 m INFO 09:59:55,472 ProgressMeter - Chr8:8896852 2.42029528E8 2.4 h 36.0 s 67.2% 3.6 h 71.6 m INFO 10:00:25,473 ProgressMeter - Chr8:10180551 2.42029528E8 2.5 h 36.0 s 67.6% 3.6 h 70.7 m INFO 10:00:55,474 ProgressMeter - Chr8:11586083 2.42029528E8 2.5 h 36.0 s 67.9% 3.6 h 69.7 m INFO 10:01:25,475 ProgressMeter - Chr8:12848128 2.42029528E8 2.5 h 36.0 s 68.3% 3.6 h 68.9 m INFO 10:02:05,476 ProgressMeter - Chr8:14653378 2.42029528E8 2.5 h 36.0 s 68.8% 3.6 h 67.7 m INFO 10:02:35,477 ProgressMeter - Chr8:15753252 2.42029528E8 2.5 h 37.0 s 69.1% 3.6 h 67.0 m INFO 10:03:05,478 ProgressMeter - Chr8:16936012 2.42029528E8 2.5 h 37.0 s 69.4% 3.6 h 66.2 m INFO 10:03:35,479 ProgressMeter - Chr8:18094020 2.42029528E8 2.5 h 37.0 s 69.7% 3.6 h 65.4 m INFO 10:04:05,480 ProgressMeter - Chr8:19098176 2.42029528E8 2.5 h 37.0 s 70.0% 3.6 h 64.8 m INFO 10:04:35,481 ProgressMeter - Chr8:19978035 2.42029528E8 2.5 h 37.0 s 70.2% 3.6 h 64.3 m INFO 10:05:15,482 ProgressMeter - Chr8:20212779 2.42029528E8 2.5 h 37.0 s 70.3% 3.6 h 64.4 m INFO 10:05:45,482 ProgressMeter - Chr8:21209271 2.42029528E8 2.5 h 37.0 s 70.5% 3.6 h 63.8 m INFO 10:06:15,483 ProgressMeter - Chr8:22369737 2.42029528E8 2.6 h 37.0 s 70.8% 3.6 h 63.1 m INFO 10:06:45,484 ProgressMeter - Chr8:23513798 2.42029528E8 2.6 h 38.0 s 71.1% 3.6 h 62.3 m INFO 10:07:15,485 ProgressMeter - Chr8:24528434 2.42029528E8 2.6 h 38.0 s 71.4% 3.6 h 61.7 m INFO 10:07:45,486 ProgressMeter - Chr8:25495146 2.42029528E8 2.6 h 38.0 s 71.7% 3.6 h 61.1 m INFO 10:08:15,491 ProgressMeter - Chr8:26576164 2.42029528E8 2.6 h 38.0 s 72.0% 3.6 h 60.4 m INFO 10:08:45,491 ProgressMeter - Chr8:27507999 2.42029528E8 2.6 h 38.0 s 72.2% 3.6 h 59.9 m INFO 10:09:15,492 ProgressMeter - Chr8:28428719 2.42029528E8 2.6 h 38.0 s 72.5% 3.6 h 59.4 m INFO 10:09:45,493 ProgressMeter - Chr9:968899 2.7047255E8 2.6 h 34.0 s 72.7% 3.6 h 58.8 m INFO 10:10:15,497 ProgressMeter - Chr9:2228646 2.7047255E8 2.6 h 34.0 s 73.1% 3.6 h 57.9 m INFO 10:10:45,498 ProgressMeter - Chr9:3461085 2.7047255E8 2.6 h 34.0 s 73.4% 3.6 h 57.2 m INFO 10:11:15,504 ProgressMeter - Chr9:4676559 2.7047255E8 2.6 h 35.0 s 73.7% 3.6 h 56.4 m INFO 10:11:45,504 ProgressMeter - Chr9:4694846 2.7047255E8 2.6 h 35.0 s 73.7% 3.6 h 56.6 m INFO 10:12:15,505 ProgressMeter - Chr9:4705376 2.7047255E8 2.7 h 35.0 s 73.7% 3.6 h 56.7 m INFO 10:12:55,506 ProgressMeter - Chr9:4724670 2.7047255E8 2.7 h 35.0 s 73.7% 3.6 h 56.9 m INFO 10:13:25,506 ProgressMeter - Chr9:4727523 2.7047255E8 2.7 h 35.0 s 73.7% 3.6 h 57.1 m INFO 10:13:55,507 ProgressMeter - Chr9:4728682 2.7047255E8 2.7 h 35.0 s 73.7% 3.6 h 57.3 m INFO 10:14:35,508 ProgressMeter - Chr9:4729965 2.7047255E8 2.7 h 35.0 s 73.7% 3.7 h 57.5 m INFO 10:15:05,560 ProgressMeter - Chr9:4731242 2.7047255E8 2.7 h 35.0 s 73.7% 3.7 h 57.7 m INFO 10:15:45,560 ProgressMeter - Chr9:5783040 2.7047255E8 2.7 h 36.0 s 74.0% 3.7 h 57.1 m INFO 10:16:15,561 ProgressMeter - Chr9:6907828 2.7047255E8 2.7 h 36.0 s 74.3% 3.7 h 56.4 m INFO 10:16:45,562 ProgressMeter - Chr9:8164713 2.7047255E8 2.7 h 36.0 s 74.7% 3.7 h 55.6 m INFO 10:17:15,563 ProgressMeter - Chr9:9546290 2.7047255E8 2.7 h 36.0 s 75.0% 3.6 h 54.7 m INFO 10:17:55,564 ProgressMeter - Chr9:10980170 2.7047255E8 2.7 h 36.0 s 75.4% 3.6 h 53.8 m INFO 10:18:25,564 ProgressMeter - Chr9:11933004 2.7047255E8 2.8 h 36.0 s 75.7% 3.6 h 53.2 m INFO 10:18:55,565 ProgressMeter - Chr9:13182051 2.7047255E8 2.8 h 36.0 s 76.0% 3.6 h 52.4 m INFO 10:19:25,566 ProgressMeter - Chr9:14124868 2.7047255E8 2.8 h 36.0 s 76.2% 3.6 h 51.8 m INFO 10:19:55,567 ProgressMeter - Chr9:15220229 2.7047255E8 2.8 h 37.0 s 76.5% 3.6 h 51.1 m INFO 10:20:35,569 ProgressMeter - Chr9:16636909 2.7047255E8 2.8 h 37.0 s 76.9% 3.6 h 50.3 m INFO 10:21:05,570 ProgressMeter - Chr9:17544202 2.7047255E8 2.8 h 37.0 s 77.2% 3.6 h 49.7 m INFO 10:21:35,571 ProgressMeter - Chr9:18615273 2.7047255E8 2.8 h 37.0 s 77.5% 3.6 h 49.1 m INFO 10:22:05,572 ProgressMeter - Chr9:19599109 2.7047255E8 2.8 h 37.0 s 77.7% 3.6 h 48.5 m INFO 10:22:35,592 ProgressMeter - Chr9:20543611 2.7047255E8 2.8 h 37.0 s 78.0% 3.6 h 47.9 m INFO 10:23:05,593 ProgressMeter - Chr9:21419877 2.7047255E8 2.8 h 37.0 s 78.2% 3.6 h 47.4 m INFO 10:23:35,594 ProgressMeter - Chr9:22238427 2.7047255E8 2.8 h 37.0 s 78.4% 3.6 h 46.9 m INFO 10:24:05,595 ProgressMeter - Chr10:136357 2.9348527E8 2.9 h 34.0 s 78.7% 3.6 h 46.4 m INFO 10:24:45,596 ProgressMeter - Chr10:1186061 2.9348527E8 2.9 h 35.0 s 78.9% 3.6 h 45.8 m INFO 10:25:15,596 ProgressMeter - Chr10:2200491 2.9348527E8 2.9 h 35.0 s 79.2% 3.6 h 45.2 m INFO 10:25:45,597 ProgressMeter - Chr10:3137430 2.9348527E8 2.9 h 35.0 s 79.5% 3.6 h 44.6 m INFO 10:26:15,598 ProgressMeter - Chr10:4021783 2.9348527E8 2.9 h 35.0 s 79.7% 3.6 h 44.1 m INFO 10:26:45,599 ProgressMeter - Chr10:5144263 2.9348527E8 2.9 h 35.0 s 80.0% 3.6 h 43.4 m INFO 10:27:15,616 ProgressMeter - Chr10:6116280 2.9348527E8 2.9 h 35.0 s 80.3% 3.6 h 42.8 m INFO 10:27:45,617 ProgressMeter - Chr10:7467832 2.9348527E8 2.9 h 35.0 s 80.6% 3.6 h 42.0 m INFO 10:28:15,618 ProgressMeter - Chr10:8814630 2.9348527E8 2.9 h 35.0 s 81.0% 3.6 h 41.1 m INFO 10:28:55,619 ProgressMeter - Chr10:9311162 2.9348527E8 2.9 h 35.0 s 81.1% 3.6 h 40.9 m INFO 10:29:25,620 ProgressMeter - Chr10:10553711 2.9348527E8 2.9 h 36.0 s 81.5% 3.6 h 40.1 m INFO 10:29:55,621 ProgressMeter - Chr10:10810340 2.9348527E8 2.9 h 36.0 s 81.5% 3.6 h 40.1 m INFO 10:30:35,622 ProgressMeter - Chr10:10814438 2.9348527E8 3.0 h 36.0 s 81.5% 3.6 h 40.2 m INFO 10:31:05,622 ProgressMeter - Chr10:10814961 2.9348527E8 3.0 h 36.0 s 81.5% 3.6 h 40.3 m INFO 10:31:35,623 ProgressMeter - Chr10:10827614 2.9348527E8 3.0 h 36.0 s 81.5% 3.6 h 40.4 m INFO 10:32:05,624 ProgressMeter - Chr10:10837083 2.9348527E8 3.0 h 36.0 s 81.5% 3.7 h 40.5 m INFO 10:32:45,625 ProgressMeter - Chr10:10838619 2.9348527E8 3.0 h 36.0 s 81.5% 3.7 h 40.7 m INFO 10:33:15,625 ProgressMeter - Chr10:10841924 2.9348527E8 3.0 h 36.0 s 81.5% 3.7 h 40.8 m INFO 10:33:45,626 ProgressMeter - Chr10:10853024 2.9348527E8 3.0 h 36.0 s 81.5% 3.7 h 40.9 m INFO 10:34:25,627 ProgressMeter - Chr10:10862369 2.9348527E8 3.0 h 37.0 s 81.5% 3.7 h 41.1 m INFO 10:34:55,627 ProgressMeter - Chr10:10866235 2.9348527E8 3.0 h 37.0 s 81.5% 3.7 h 41.2 m INFO 10:35:25,628 ProgressMeter - Chr10:10909224 2.9348527E8 3.0 h 37.0 s 81.6% 3.7 h 41.2 m INFO 10:35:55,664 ProgressMeter - Chr10:10913209 2.9348527E8 3.0 h 37.0 s 81.6% 3.7 h 41.4 m INFO 10:36:25,665 ProgressMeter - Chr10:10918293 2.9348527E8 3.1 h 37.0 s 81.6% 3.7 h 41.5 m INFO 10:36:55,666 ProgressMeter - Chr10:11387833 2.9348527E8 3.1 h 37.0 s 81.7% 3.8 h 41.2 m INFO 10:37:25,673 ProgressMeter - Chr10:12490443 2.9348527E8 3.1 h 37.0 s 82.0% 3.7 h 40.5 m INFO 10:37:55,673 ProgressMeter - Chr10:13591196 2.9348527E8 3.1 h 37.0 s 82.3% 3.7 h 39.8 m INFO 10:38:25,674 ProgressMeter - Chr10:14642274 2.9348527E8 3.1 h 37.0 s 82.6% 3.7 h 39.2 m INFO 10:38:55,675 ProgressMeter - Chr10:15578491 2.9348527E8 3.1 h 37.0 s 82.8% 3.7 h 38.6 m INFO 10:39:35,676 ProgressMeter - Chr10:16577489 2.9348527E8 3.1 h 38.0 s 83.1% 3.7 h 38.0 m INFO 10:40:15,677 ProgressMeter - Chr10:17957137 2.9348527E8 3.1 h 38.0 s 83.4% 3.7 h 37.1 m INFO 10:40:45,679 ProgressMeter - Chr10:18931056 2.9348527E8 3.1 h 38.0 s 83.7% 3.7 h 36.5 m INFO 10:41:15,680 ProgressMeter - Chr10:19919605 2.9348527E8 3.1 h 38.0 s 84.0% 3.7 h 35.9 m INFO 10:41:55,681 ProgressMeter - Chr10:20471668 2.9348527E8 3.1 h 38.0 s 84.1% 3.7 h 35.7 m INFO 10:42:25,681 ProgressMeter - Chr10:20484646 2.9348527E8 3.2 h 38.0 s 84.1% 3.8 h 35.7 m INFO 10:42:55,682 ProgressMeter - Chr10:20799519 2.9348527E8 3.2 h 38.0 s 84.2% 3.8 h 35.6 m INFO 10:43:25,683 ProgressMeter - Chr10:21591112 2.9348527E8 3.2 h 38.0 s 84.4% 3.8 h 35.1 m INFO 10:43:55,684 ProgressMeter - Chr10:22495114 2.9348527E8 3.2 h 39.0 s 84.7% 3.8 h 34.6 m INFO 10:44:35,685 ProgressMeter - Chr10:23207287 2.9348527E8 3.2 h 39.0 s 84.8% 3.8 h 34.2 m INFO 10:45:05,686 ProgressMeter - Chr10:23207287 2.9348527E8 3.2 h 39.0 s 84.8% 3.8 h 34.3 m INFO 10:45:35,686 ProgressMeter - Chr11:1293440 3.16692557E8 3.2 h 36.0 s 85.2% 3.8 h 33.5 m INFO 10:46:05,687 ProgressMeter - Chr11:2456558 3.16692557E8 3.2 h 36.0 s 85.5% 3.8 h 32.7 m INFO 10:46:35,688 ProgressMeter - Chr11:3501547 3.16692557E8 3.2 h 36.0 s 85.8% 3.8 h 32.1 m INFO 10:47:05,689 ProgressMeter - Chr11:4611057 3.16692557E8 3.2 h 36.0 s 86.1% 3.8 h 31.4 m INFO 10:47:35,690 ProgressMeter - Chr11:5850566 3.16692557E8 3.2 h 36.0 s 86.4% 3.8 h 30.6 m INFO 10:48:05,691 ProgressMeter - Chr11:7011373 3.16692557E8 3.3 h 36.0 s 86.7% 3.7 h 29.8 m INFO 10:48:45,692 ProgressMeter - Chr11:8478208 3.16692557E8 3.3 h 37.0 s 87.1% 3.7 h 28.9 m INFO 10:49:15,692 ProgressMeter - Chr11:9589068 3.16692557E8 3.3 h 37.0 s 87.4% 3.7 h 28.2 m INFO 10:49:45,693 ProgressMeter - Chr11:11017551 3.16692557E8 3.3 h 37.0 s 87.8% 3.7 h 27.3 m INFO 10:50:15,694 ProgressMeter - Chr11:12078657 3.16692557E8 3.3 h 37.0 s 88.1% 3.7 h 26.7 m INFO 10:50:45,695 ProgressMeter - Chr11:13466204 3.16692557E8 3.3 h 37.0 s 88.5% 3.7 h 25.8 m INFO 10:51:15,696 ProgressMeter - Chr11:13912246 3.16692557E8 3.3 h 37.0 s 88.6% 3.7 h 25.6 m INFO 10:51:55,697 ProgressMeter - Chr11:15598881 3.16692557E8 3.3 h 37.0 s 89.0% 3.7 h 24.5 m INFO 10:52:25,697 ProgressMeter - Chr11:16884551 3.16692557E8 3.3 h 37.0 s 89.4% 3.7 h 23.7 m INFO 10:52:55,705 ProgressMeter - Chr11:17973483 3.16692557E8 3.3 h 37.0 s 89.7% 3.7 h 23.0 m INFO 10:53:25,706 ProgressMeter - Chr11:18998002 3.16692557E8 3.3 h 37.0 s 89.9% 3.7 h 22.4 m INFO 10:54:05,707 ProgressMeter - Chr11:20546065 3.16692557E8 3.4 h 38.0 s 90.4% 3.7 h 21.5 m INFO 10:54:35,707 ProgressMeter - Chr11:21601895 3.16692557E8 3.4 h 38.0 s 90.6% 3.7 h 20.8 m INFO 10:55:05,708 ProgressMeter - Chr11:22925779 3.16692557E8 3.4 h 38.0 s 91.0% 3.7 h 20.0 m INFO 10:55:35,709 ProgressMeter - Chr11:23989943 3.16692557E8 3.4 h 38.0 s 91.3% 3.7 h 19.4 m INFO 10:56:05,710 ProgressMeter - Chr11:25210448 3.16692557E8 3.4 h 38.0 s 91.6% 3.7 h 18.6 m INFO 10:56:35,711 ProgressMeter - Chr11:26044531 3.16692557E8 3.4 h 38.0 s 91.8% 3.7 h 18.1 m INFO 10:57:15,712 ProgressMeter - Chr11:27588965 3.16692557E8 3.4 h 38.0 s 92.2% 3.7 h 17.2 m INFO 10:57:55,713 ProgressMeter - Chr11:29021106 3.16692557E8 3.4 h 38.0 s 92.6% 3.7 h 16.3 m INFO 10:58:35,714 ProgressMeter - Chr12:939019 3.45713663E8 3.4 h 35.0 s 92.9% 3.7 h 15.8 m INFO 10:59:05,714 ProgressMeter - Chr12:1910801 3.45713663E8 3.4 h 35.0 s 93.1% 3.7 h 15.2 m INFO 10:59:35,715 ProgressMeter - Chr12:2857211 3.45713663E8 3.4 h 35.0 s 93.4% 3.7 h 14.6 m INFO 11:00:05,716 ProgressMeter - Chr12:3721243 3.45713663E8 3.5 h 35.0 s 93.6% 3.7 h 14.1 m INFO 11:00:35,717 ProgressMeter - Chr12:4737424 3.45713663E8 3.5 h 36.0 s 93.9% 3.7 h 13.5 m INFO 11:01:15,718 ProgressMeter - Chr12:4978851 3.45713663E8 3.5 h 36.0 s 94.0% 3.7 h 13.4 m INFO 11:01:45,718 ProgressMeter - Chr12:5508485 3.45713663E8 3.5 h 36.0 s 94.1% 3.7 h 13.1 m INFO 11:02:15,719 ProgressMeter - Chr12:5655629 3.45713663E8 3.5 h 36.0 s 94.1% 3.7 h 13.0 m INFO 11:02:55,720 ProgressMeter - Chr12:6288145 3.45713663E8 3.5 h 36.0 s 94.3% 3.7 h 12.7 m INFO 11:03:25,720 ProgressMeter - Chr12:7389262 3.45713663E8 3.5 h 36.0 s 94.6% 3.7 h 12.0 m INFO 11:03:55,724 ProgressMeter - Chr12:8374638 3.45713663E8 3.5 h 36.0 s 94.9% 3.7 h 11.4 m INFO 11:04:25,725 ProgressMeter - Chr12:8533787 3.45713663E8 3.5 h 36.0 s 94.9% 3.7 h 11.3 m INFO 11:05:05,725 ProgressMeter - Chr12:8544680 3.45713663E8 3.5 h 36.0 s 94.9% 3.7 h 11.4 m INFO 11:05:35,726 ProgressMeter - Chr12:9099499 3.45713663E8 3.5 h 36.0 s 95.1% 3.7 h 11.0 m INFO 11:06:05,727 ProgressMeter - Chr12:10342017 3.45713663E8 3.6 h 36.0 s 95.4% 3.7 h 10.3 m INFO 11:06:35,728 ProgressMeter - Chr12:11367388 3.45713663E8 3.6 h 37.0 s 95.7% 3.7 h 9.7 m INFO 11:07:15,729 ProgressMeter - Chr12:12786445 3.45713663E8 3.6 h 37.0 s 96.0% 3.7 h 8.8 m INFO 11:07:45,729 ProgressMeter - Chr12:13408450 3.45713663E8 3.6 h 37.0 s 96.2% 3.7 h 8.4 m INFO 11:08:15,730 ProgressMeter - Chr12:14267056 3.45713663E8 3.6 h 37.0 s 96.4% 3.7 h 7.9 m INFO 11:08:45,731 ProgressMeter - Chr12:16111373 3.45713663E8 3.6 h 37.0 s 96.9% 3.7 h 6.8 m INFO 11:09:25,732 ProgressMeter - Chr12:18163395 3.45713663E8 3.6 h 37.0 s 97.5% 3.7 h 5.6 m INFO 11:09:55,733 ProgressMeter - Chr12:19580895 3.45713663E8 3.6 h 37.0 s 97.9% 3.7 h 4.7 m INFO 11:10:25,733 ProgressMeter - Chr12:20499647 3.45713663E8 3.6 h 37.0 s 98.1% 3.7 h 4.2 m INFO 11:10:55,748 ProgressMeter - Chr12:20503315 3.45713663E8 3.6 h 37.0 s 98.1% 3.7 h 4.2 m INFO 11:11:35,748 ProgressMeter - Chr12:20506354 3.45713663E8 3.6 h 37.0 s 98.1% 3.7 h 4.2 m INFO 11:12:05,749 ProgressMeter - Chr12:20509757 3.45713663E8 3.7 h 38.0 s 98.1% 3.7 h 4.2 m INFO 11:12:35,750 ProgressMeter - Chr12:20512813 3.45713663E8 3.7 h 38.0 s 98.1% 3.7 h 4.2 m INFO 11:13:05,792 ProgressMeter - Chr12:20516542 3.45713663E8 3.7 h 38.0 s 98.1% 3.7 h 4.2 m INFO 11:13:35,792 ProgressMeter - Chr12:20518854 3.45713663E8 3.7 h 38.0 s 98.1% 3.7 h 4.2 m INFO 11:14:05,793 ProgressMeter - Chr12:20526878 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.2 m INFO 11:14:35,794 ProgressMeter - Chr12:20530349 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.2 m INFO 11:15:15,794 ProgressMeter - Chr12:20535179 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.2 m INFO 11:15:45,795 ProgressMeter - Chr12:20536339 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.3 m INFO 11:16:25,796 ProgressMeter - Chr12:20539392 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.3 m INFO 11:17:05,796 ProgressMeter - Chr12:20542451 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.3 m INFO 11:17:35,797 ProgressMeter - Chr12:20544333 3.45713663E8 3.7 h 38.0 s 98.1% 3.8 h 4.3 m INFO 11:18:15,798 ProgressMeter - Chr12:20607026 3.45713663E8 3.8 h 39.0 s 98.1% 3.8 h 4.3 m INFO 11:18:55,798 ProgressMeter - Chr12:20623691 3.45713663E8 3.8 h 39.0 s 98.1% 3.8 h 4.3 m INFO 11:19:25,799 ProgressMeter - Chr12:20633536 3.45713663E8 3.8 h 39.0 s 98.2% 3.8 h 4.3 m INFO 11:19:55,800 ProgressMeter - Chr12:20641722 3.45713663E8 3.8 h 39.0 s 98.2% 3.9 h 4.3 m INFO 11:20:35,801 ProgressMeter - Chr12:20646179 3.45713663E8 3.8 h 39.0 s 98.2% 3.9 h 4.3 m INFO 11:21:05,801 ProgressMeter - Chr12:20657414 3.45713663E8 3.8 h 39.0 s 98.2% 3.9 h 4.3 m INFO 11:21:35,802 ProgressMeter - Chr12:20660022 3.45713663E8 3.8 h 39.0 s 98.2% 3.9 h 4.3 m INFO 11:22:15,803 ProgressMeter - Chr12:20856200 3.45713663E8 3.8 h 39.0 s 98.2% 3.9 h 4.2 m INFO 11:22:45,803 ProgressMeter - Chr12:21748508 3.45713663E8 3.8 h 39.0 s 98.5% 3.9 h 3.6 m INFO 11:23:15,806 ProgressMeter - Chr12:22936080 3.45713663E8 3.8 h 39.0 s 98.8% 3.9 h 2.9 m INFO 11:23:45,807 ProgressMeter - Chr12:23826294 3.45713663E8 3.8 h 40.0 s 99.0% 3.9 h 2.3 m INFO 11:24:15,808 ProgressMeter - Chr12:24910011 3.45713663E8 3.9 h 40.0 s 99.3% 3.9 h 98.0 s INFO 11:24:45,809 ProgressMeter - Chr12:26001382 3.45713663E8 3.9 h 40.0 s 99.6% 3.9 h 57.0 s INFO 11:25:25,810 ProgressMeter - Chr12:27365162 3.45713663E8 3.9 h 40.0 s 100.0% 3.9 h 6.0 s INFO 11:25:32,430 HaplotypeCaller - Ran local assembly on 0 active regions INFO 11:25:32,438 ProgressMeter - done 3.73245519E8 3.9 h 37.0 s 100.0% 3.9 h 0.0 s INFO 11:25:32,438 ProgressMeter - Total runtime 13947.52 secs, 232.46 min, 3.87 hours INFO 11:25:32,438 MicroScheduler - 7126920 reads were filtered out during the traversal out of approximately 13502457 total reads (52.78%) INFO 11:25:32,438 MicroScheduler - -> 49556 reads (0.37% of total) failing BadCigarFilter INFO 11:25:32,438 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter INFO 11:25:32,439 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 11:25:32,439 MicroScheduler - -> 7077364 reads (52.42% of total) failing HCMappingQualityFilter INFO 11:25:32,439 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 11:25:32,439 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 11:25:32,439 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 11:25:32,439 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter INFO 11:25:34,779 GATKRunReport - Uploaded run statistics report to AWS S3 ########################### Job Execution History ############################# JobId:33609.paroo3.barrine.hpcu.uq.edu.au UserName:uqmbrozy GroupName:uq JobName:gatk2 SessionId:11577 ResourcesRequested:mem=71680mb,ncpus=1,neednodes=1:ppn=8,nodes=1:ppn=8,vmem=71680mb,walltime=336:00:00 ResourcesUsed:cput=24:47:16,energy_used=0,mem=1771056kb,vmem=2546224kb,walltime=03:52:44 QueueUsed:MemoryL AccountString:uq-QAAFI ExitStatus:0 ###############################################################################