GATK working, but -ERC command not found
Answered
I am attempting to use HaplotypeCaller for the first time -yay! For every sample (blah_case_blah) passed to the below script, I get two output files (e.g., GBM9_R2.DNA.g.vcf.gz.tbi and GBM9_R2.DNA.g.vcf.gz). However, I inspected my log, and at the very end, I get the following error: /var/spool/slurred/job42730395/slurm_script: line 16: -ERC: command not found.
Does this mean that HaplotypeCaller is not being run in gVCF mode? If so, how do I correct this error? Thank you in advance for your help!
GATK version used: 4.2.5.0
Exact command used:
#!/bin/bash
lee=/pine/scr/a/n/anndo1/Lee_NatureGenetics_2017_Germline
align_dir=$lee/bulk_align
HaplotypeCaller_dir=$lee/HaplotypeCaller
tm=blah_case_blah
module load gatk
gatk --java-options "-Xmx4g" HaplotypeCaller \
-R /proj/yuchaojlab/lib/ucsc.hg19.fasta \
-I $align_dir/*$tm.sorted.rg.dedup.realigned.recal.bam \
-O $HaplotypeCaller_dir/$tm.g.vcf.gz \
-ERC GVCF
Entire program log:
Using GATK jar /nas/longleaf/apps/gatk/4.2.5.0/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /nas/longleaf/apps/gatk/4.2.5.0/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar HaplotypeCaller -R /proj/yuchaojlab/lib/ucsc.hg19.fasta -I /pine/scr/a/n/anndo1/Lee_NatureGenetics_2017_Germline/bulk_align/_EGAR00001456470_GBM9_R2.DNA.sorted.rg.dedup.realigned.recal.bam -O /pine/scr/a/n/anndo1/Lee_NatureGenetics_2017_Germline/HaplotypeCaller/GBM9_R2.DNA.g.vcf.gz
16:42:39.908 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nas/longleaf/apps/gatk/4.2.5.0/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 11, 2022 4:42:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:42:40.232 INFO HaplotypeCaller - ------------------------------------------------------------
16:42:40.232 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.5.0
16:42:40.232 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
16:42:40.232 INFO HaplotypeCaller - Executing as anndo1@c0401.ll.unc.edu on Linux v3.10.0-1160.2.2.el7.x86_64 amd64
16:42:40.232 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-b10
16:42:40.232 INFO HaplotypeCaller - Start Date/Time: April 11, 2022 4:42:39 PM EDT
16:42:40.232 INFO HaplotypeCaller - ------------------------------------------------------------
16:42:40.232 INFO HaplotypeCaller - ------------------------------------------------------------
16:42:40.233 INFO HaplotypeCaller - HTSJDK Version: 2.24.1
16:42:40.233 INFO HaplotypeCaller - Picard Version: 2.25.4
16:42:40.233 INFO HaplotypeCaller - Built for Spark Version: 2.4.5
16:42:40.233 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:42:40.233 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:42:40.233 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:42:40.233 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:42:40.233 INFO HaplotypeCaller - Deflater: IntelDeflater
16:42:40.233 INFO HaplotypeCaller - Inflater: IntelInflater
16:42:40.233 INFO HaplotypeCaller - GCS max retries/reopens: 20
16:42:40.233 INFO HaplotypeCaller - Requester pays: disabled
16:42:40.233 INFO HaplotypeCaller - Initializing engine
16:42:40.694 INFO HaplotypeCaller - Done initializing engine
16:42:40.733 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
16:42:40.759 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nas/longleaf/apps/gatk/4.2.5.0/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
16:42:40.760 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/nas/longleaf/apps/gatk/4.2.5.0/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
16:42:40.799 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
16:42:40.799 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
16:42:40.800 INFO IntelPairHmm - Available threads: 1
16:42:40.800 INFO IntelPairHmm - Requested threads: 4
16:42:40.800 WARN IntelPairHmm - Using 1 available threads, but 4 were requested
16:42:40.800 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
16:42:40.843 INFO ProgressMeter - Starting traversal
16:42:40.844 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
16:42:42.159 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chrM:195 and possibly subsequent; at least 10 samples must have called genotypes
16:42:50.847 INFO ProgressMeter - chr1:840550 0.2 3140 18834.3
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16:47:55.264 INFO ProgressMeter - chr1:43395246 5.2 185110 35324.1
16:48:05.337 INFO ProgressMeter - chr1:45213880 5.4 192780 35645.8
16:48:15.358 INFO ProgressMeter - chr1:47099309 5.6 200760 36009.3
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16:49:45.469 INFO ProgressMeter - chr1:76098517 7.1 315660 44603.1
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16:50:05.553 INFO ProgressMeter - chr1:85041792 7.4 349940 47213.8
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16:57:38.909 INFO ProgressMeter - chr1:204485925 15.0 810630 54158.4
16:57:48.940 INFO ProgressMeter - chr1:206566655 15.1 819210 54127.1
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16:58:38.955 INFO ProgressMeter - chr1:220681096 16.0 875610 54833.5
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16:59:49.416 INFO ProgressMeter - chr1:236705843 17.1 941900 54944.1
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17:00:09.438 INFO ProgressMeter - chr1:241667207 17.5 962020 55046.3
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17:00:39.641 INFO ProgressMeter - chr1:248113386 18.0 988870 54998.5
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17:00:59.906 INFO ProgressMeter - chr2:1228583 18.3 998470 54508.5
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17:03:30.199 INFO ProgressMeter - chr2:41235378 20.8 1160360 55726.0
17:03:40.226 INFO ProgressMeter - chr2:44022764 21.0 1171840 55829.3
17:03:50.227 INFO ProgressMeter - chr2:46734438 21.2 1183020 55917.9
17:04:00.231 INFO ProgressMeter - chr2:49166043 21.3 1193070 55952.0
17:04:10.238 INFO ProgressMeter - chr2:54127500 21.5 1211960 56396.7
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17:04:30.243 INFO ProgressMeter - chr2:61372422 21.8 1240320 56834.6
17:04:40.245 INFO ProgressMeter - chr2:64692513 22.0 1253400 56998.6
17:04:50.245 INFO ProgressMeter - chr2:68571257 22.2 1268580 57255.0
17:05:00.296 INFO ProgressMeter - chr2:70917185 22.3 1278230 57257.6
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17:05:40.307 INFO ProgressMeter - chr2:85109627 23.0 1332830 57971.7
17:05:50.315 INFO ProgressMeter - chr2:86972477 23.2 1340620 57890.5
17:06:00.316 INFO ProgressMeter - chr2:89614205 23.3 1350990 57921.5
17:06:10.345 INFO ProgressMeter - chr2:91766227 23.5 1358820 57842.6
17:06:22.914 INFO ProgressMeter - chr2:91801177 23.7 1359120 57344.0
17:06:33.315 INFO ProgressMeter - chr2:92068711 23.9 1360430 56982.5
17:06:43.320 INFO ProgressMeter - chr2:95729976 24.0 1373060 57112.6
17:06:53.557 INFO ProgressMeter - chr2:96611941 24.2 1376340 56845.7
17:07:03.566 INFO ProgressMeter - chr2:97674426 24.4 1380600 56631.4
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17:17:15.777 INFO ProgressMeter - chr3:24286715 34.6 2053070 59367.8
17:17:25.781 INFO ProgressMeter - chr3:28777509 34.7 2070310 59579.1
17:17:35.783 INFO ProgressMeter - chr3:32563992 34.9 2085240 59722.2
17:17:45.786 INFO ProgressMeter - chr3:36057461 35.1 2098900 59827.8
17:17:55.793 INFO ProgressMeter - chr3:38688751 35.2 2109070 59833.2
17:18:05.795 INFO ProgressMeter - chr3:41651586 35.4 2120790 59882.5
17:18:15.798 INFO ProgressMeter - chr3:44281232 35.6 2131390 59899.8
17:18:25.805 INFO ProgressMeter - chr3:46293409 35.7 2139770 59854.8
17:18:35.808 INFO ProgressMeter - chr3:48072420 35.9 2147120 59781.6
17:18:45.808 INFO ProgressMeter - chr3:49674981 36.1 2153810 59690.9
17:18:55.860 INFO ProgressMeter - chr3:51430938 36.3 2160980 59612.8
17:19:05.911 INFO ProgressMeter - chr3:53214608 36.4 2168080 59533.6
17:19:15.911 INFO ProgressMeter - chr3:55804965 36.6 2178630 59550.7
17:19:25.914 INFO ProgressMeter - chr3:58117284 36.8 2188130 59539.1
17:19:35.922 INFO ProgressMeter - chr3:61363050 36.9 2201120 59621.9
17:19:45.943 INFO ProgressMeter - chr3:64526906 37.1 2213730 59693.5
17:19:55.953 INFO ProgressMeter - chr3:67871047 37.3 2227080 59784.5
17:20:05.956 INFO ProgressMeter - chr3:71268988 37.4 2240360 59873.0
17:20:15.957 INFO ProgressMeter - chr3:74399016 37.6 2253050 59945.1
17:20:25.961 INFO ProgressMeter - chr3:76923328 37.8 2262770 59937.9
17:20:35.961 INFO ProgressMeter - chr3:82333854 37.9 2283070 60209.7
17:20:45.970 INFO ProgressMeter - chr3:88116377 38.1 2304780 60516.1
17:20:55.971 INFO ProgressMeter - chr3:96369025 38.3 2334390 61026.4
17:21:05.976 INFO ProgressMeter - chr3:99538175 38.4 2346470 61076.0
17:21:15.979 INFO ProgressMeter - chr3:102956693 38.6 2359510 61150.0
17:21:25.993 INFO ProgressMeter - chr3:107839378 38.8 2378240 61370.0
17:21:36.003 INFO ProgressMeter - chr3:111168122 38.9 2391220 61440.5
17:21:46.005 INFO ProgressMeter - chr3:113354839 39.1 2400090 61405.3
17:21:56.009 INFO ProgressMeter - chr3:118172567 39.3 2418460 61612.5
17:22:06.079 INFO ProgressMeter - chr3:121210109 39.4 2430280 61650.0
17:22:16.104 INFO ProgressMeter - chr3:122821629 39.6 2436920 61557.6
17:22:26.131 INFO ProgressMeter - chr3:124734604 39.8 2444920 61500.0
17:22:36.133 INFO ProgressMeter - chr3:126374227 39.9 2452040 61421.6
17:22:46.137 INFO ProgressMeter - chr3:128752001 40.1 2461820 61410.1
17:22:56.138 INFO ProgressMeter - chr3:130612590 40.3 2469570 61348.3
17:23:06.146 INFO ProgressMeter - chr3:133583708 40.4 2481260 61384.4
17:23:16.146 INFO ProgressMeter - chr3:136747560 40.6 2493920 61444.2
17:23:26.165 INFO ProgressMeter - chr3:139436031 40.8 2504820 61459.9
17:23:36.172 INFO ProgressMeter - chr3:142464272 40.9 2516850 61503.4
17:23:46.174 INFO ProgressMeter - chr3:147397044 41.1 2535540 61708.7
17:23:56.885 INFO ProgressMeter - chr3:150422357 41.3 2547190 61724.1
17:24:06.885 INFO ProgressMeter - chr3:153739012 41.4 2560160 61788.8
17:24:16.890 INFO ProgressMeter - chr3:157084130 41.6 2573120 61852.7
17:24:26.891 INFO ProgressMeter - chr3:161070160 41.8 2588450 61972.9
17:24:36.891 INFO ProgressMeter - chr3:167142901 41.9 2610970 62263.6
17:24:46.908 INFO ProgressMeter - chr3:170930728 42.1 2625430 62360.2
17:24:56.914 INFO ProgressMeter - chr3:175068008 42.3 2641330 62490.3
17:25:06.914 INFO ProgressMeter - chr3:179407231 42.4 2658100 62640.1
17:25:16.987 INFO ProgressMeter - chr3:183370050 42.6 2673430 62753.1
17:25:27.036 INFO ProgressMeter - chr3:184429756 42.8 2678310 62621.4
17:25:37.036 INFO ProgressMeter - chr3:186685810 42.9 2687540 62593.3
17:25:47.037 INFO ProgressMeter - chr3:190008290 43.1 2700820 62659.4
17:25:57.038 INFO ProgressMeter - chr3:193106278 43.3 2712930 62697.9
17:26:07.102 INFO ProgressMeter - chr3:194843249 43.4 2720560 62631.4
17:26:17.120 INFO ProgressMeter - chr3:196042747 43.6 2726070 62517.9
17:26:27.130 INFO ProgressMeter - chr4:40546 43.8 2734400 62470.0
17:26:37.144 INFO ProgressMeter - chr4:879249 43.9 2737980 62314.2
17:26:47.150 INFO ProgressMeter - chr4:2189675 44.1 2743740 62209.1
17:26:57.168 INFO ProgressMeter - chr4:3516652 44.3 2749500 62104.6
17:27:07.174 INFO ProgressMeter - chr4:3802821 44.4 2751020 61905.8
17:27:17.175 INFO ProgressMeter - chr4:5751503 44.6 2759350 61861.2
17:27:27.177 INFO ProgressMeter - chr4:7058595 44.8 2765420 61766.5
17:27:37.231 INFO ProgressMeter - chr4:8305495 44.9 2771480 61671.0
17:27:47.231 INFO ProgressMeter - chr4:10327023 45.1 2780130 61634.9
17:27:57.233 INFO ProgressMeter - chr4:14411586 45.3 2796080 61760.2
17:28:07.237 INFO ProgressMeter - chr4:17337368 45.4 2807790 61791.3
17:28:17.242 INFO ProgressMeter - chr4:21306148 45.6 2823190 61903.1
17:28:27.249 INFO ProgressMeter - chr4:25310988 45.8 2838860 62019.8
17:28:37.253 INFO ProgressMeter - chr4:28625261 45.9 2852130 62083.6
17:28:47.263 INFO ProgressMeter - chr4:35119536 46.1 2876340 62384.0
17:28:57.264 INFO ProgressMeter - chr4:38398278 46.3 2889440 62442.4
17:29:07.271 INFO ProgressMeter - chr4:40347039 46.4 2897670 62395.4
17:29:17.273 INFO ProgressMeter - chr4:43834512 46.6 2911410 62467.0
17:29:27.276 INFO ProgressMeter - chr4:48097443 46.8 2927620 62590.9
17:29:37.585 INFO ProgressMeter - chr4:49221236 46.9 2932280 62461.1
17:29:47.585 INFO ProgressMeter - chr4:53011688 47.1 2945580 62522.5
17:29:57.592 INFO ProgressMeter - chr4:56368293 47.3 2958800 62581.5
17:30:07.597 INFO ProgressMeter - chr4:59982136 47.4 2972990 62660.7
17:30:17.597 INFO ProgressMeter - chr4:65413351 47.6 2993730 62876.9
17:30:27.613 INFO ProgressMeter - chr4:68915667 47.8 3007260 62940.4
17:30:37.654 INFO ProgressMeter - chr4:71705600 47.9 3017940 62943.5
17:30:47.660 INFO ProgressMeter - chr4:75010839 48.1 3030870 62994.0
17:30:57.983 INFO ProgressMeter - chr4:77066290 48.3 3039150 62941.1
17:31:07.990 INFO ProgressMeter - chr4:79488498 48.5 3048920 62926.0
17:31:17.998 INFO ProgressMeter - chr4:83416593 48.6 3063930 63018.9
17:31:27.999 INFO ProgressMeter - chr4:86183365 48.8 3074940 63029.3
17:31:38.008 INFO ProgressMeter - chr4:88986525 49.0 3085900 63038.4
17:31:48.013 INFO ProgressMeter - chr4:92866763 49.1 3100800 63127.7
17:31:58.013 INFO ProgressMeter - chr4:98646740 49.3 3122280 63350.0
17:32:08.019 INFO ProgressMeter - chr4:102711066 49.5 3137610 63446.4
17:32:18.035 INFO ProgressMeter - chr4:107260240 49.6 3154570 63574.8
17:32:28.062 INFO ProgressMeter - chr4:110687809 49.8 3167930 63629.7
17:32:38.092 INFO ProgressMeter - chr4:114067449 50.0 3181260 63683.6
17:32:48.111 INFO ProgressMeter - chr4:119221351 50.1 3200590 63857.1
17:32:58.110 INFO ProgressMeter - chr4:122082377 50.3 3211860 63869.6
17:33:08.111 INFO ProgressMeter - chr4:125659060 50.5 3225680 63932.5
17:33:18.118 INFO ProgressMeter - chr4:129965064 50.6 3242220 64048.6
17:33:28.119 INFO ProgressMeter - chr4:135449205 50.8 3262960 64246.8
17:33:38.119 INFO ProgressMeter - chr4:140613440 51.0 3282750 64425.0
17:33:48.126 INFO ProgressMeter - chr4:144185241 51.1 3296690 64487.5
17:33:58.140 INFO ProgressMeter - chr4:147438047 51.3 3309190 64521.4
17:34:08.145 INFO ProgressMeter - chr4:151658551 51.5 3325460 64628.5
17:34:18.148 INFO ProgressMeter - chr4:154859411 51.6 3337980 64662.3
17:34:28.149 INFO ProgressMeter - chr4:158438625 51.8 3351810 64721.2
17:34:38.150 INFO ProgressMeter - chr4:162882006 52.0 3369020 64844.8
17:34:48.157 INFO ProgressMeter - chr4:166748701 52.1 3384100 64926.7
17:34:58.178 INFO ProgressMeter - chr4:170322660 52.3 3398060 64986.3
17:35:08.179 INFO ProgressMeter - chr4:174629278 52.5 3414670 65096.4
17:35:18.214 INFO ProgressMeter - chr4:178356022 52.6 3429380 65169.1
17:35:28.278 INFO ProgressMeter - chr4:183250757 52.8 3448450 65323.2
17:35:38.280 INFO ProgressMeter - chr4:185654337 53.0 3458620 65309.6
17:35:48.507 INFO ProgressMeter - chr4:187519021 53.1 3466590 65250.1
17:35:58.522 INFO ProgressMeter - chr4:190198919 53.3 3477730 65254.8
17:36:08.979 INFO ProgressMeter - chr4:190598794 53.5 3479540 65075.9
17:36:20.537 INFO ProgressMeter - chr4:190876100 53.7 3480940 64868.4
17:36:30.576 INFO ProgressMeter - chr5:457790 53.8 3483960 64722.9
17:36:40.580 INFO ProgressMeter - chr5:1543373 54.0 3488870 64614.0
17:36:50.596 INFO ProgressMeter - chr5:3671563 54.2 3498180 64586.7
17:37:00.607 INFO ProgressMeter - chr5:6605309 54.3 3510050 64606.9
17:37:10.616 INFO ProgressMeter - chr5:9950250 54.5 3523360 64653.3
17:37:20.639 INFO ProgressMeter - chr5:13829762 54.7 3538500 64732.7
17:37:30.642 INFO ProgressMeter - chr5:16830465 54.8 3550400 64752.9
17:37:40.647 INFO ProgressMeter - chr5:21463222 55.0 3568500 64885.7
17:37:50.650 INFO ProgressMeter - chr5:26892962 55.2 3588830 65058.2
17:38:00.649 INFO ProgressMeter - chr5:31846855 55.3 3607750 65204.1
17:38:10.659 INFO ProgressMeter - chr5:34421942 55.5 3618180 65196.1
17:38:20.661 INFO ProgressMeter - chr5:37006367 55.7 3628500 65186.2
17:38:30.667 INFO ProgressMeter - chr5:40132478 55.8 3640890 65213.4
17:38:40.667 INFO ProgressMeter - chr5:43740677 56.0 3654570 65263.6
17:38:50.723 INFO ProgressMeter - chr5:52371333 56.2 3685230 65614.8
17:39:00.725 INFO ProgressMeter - chr5:55112606 56.3 3696350 65618.0
17:39:10.728 INFO ProgressMeter - chr5:58427934 56.5 3709360 65654.6
17:39:20.737 INFO ProgressMeter - chr5:63371247 56.7 3727960 65789.6
17:39:30.744 INFO ProgressMeter - chr5:67294135 56.8 3742910 65859.6
17:39:40.751 INFO ProgressMeter - chr5:71326386 57.0 3758110 65933.5
17:39:50.822 INFO ProgressMeter - chr5:74401038 57.2 3770210 65951.6
17:40:00.825 INFO ProgressMeter - chr5:77219583 57.3 3781380 65954.7
17:40:10.826 INFO ProgressMeter - chr5:79906735 57.5 3792220 65952.0
17:40:20.826 INFO ProgressMeter - chr5:84254958 57.7 3808770 66048.4
17:40:30.838 INFO ProgressMeter - chr5:89988842 57.8 3829990 66224.7
17:40:40.838 INFO ProgressMeter - chr5:94918062 58.0 3848360 66351.1
17:40:50.838 INFO ProgressMeter - chr5:98029386 58.2 3860320 66366.6
17:41:00.849 INFO ProgressMeter - chr5:102926350 58.3 3878680 66491.6
17:41:10.868 INFO ProgressMeter - chr5:109154923 58.5 3901770 66696.5
17:41:20.874 INFO ProgressMeter - chr5:111943898 58.7 3912400 66688.1
17:41:30.880 INFO ProgressMeter - chr5:114850884 58.8 3924050 66697.1
17:41:40.887 INFO ProgressMeter - chr5:119811867 59.0 3942640 66823.6
17:41:50.899 INFO ProgressMeter - chr5:123973403 59.2 3958620 66905.2
17:42:00.903 INFO ProgressMeter - chr5:127678978 59.3 3973140 66961.9
17:42:10.928 INFO ProgressMeter - chr5:131796461 59.5 3988640 67034.4
17:42:20.937 INFO ProgressMeter - chr5:134216064 59.7 3998430 67011.1
17:42:30.942 INFO ProgressMeter - chr5:137029151 59.8 4009700 67012.7
17:42:40.950 INFO ProgressMeter - chr5:139567255 60.0 4019840 66995.4
17:42:50.972 INFO ProgressMeter - chr5:140789051 60.2 4024640 66889.2
17:43:00.972 INFO ProgressMeter - chr5:143042955 60.3 4033870 66857.4
17:43:10.972 INFO ProgressMeter - chr5:147385005 60.5 4050240 66943.8
17:43:20.982 INFO ProgressMeter - chr5:149425004 60.7 4058510 66896.0
17:43:31.062 INFO ProgressMeter - chr5:150930983 60.8 4064820 66815.0
17:43:41.070 INFO ProgressMeter - chr5:154318595 61.0 4078190 66851.5
17:43:51.070 INFO ProgressMeter - chr5:157463863 61.2 4090390 66868.7
17:44:01.080 INFO ProgressMeter - chr5:161317733 61.3 4105300 66929.9
17:44:11.083 INFO ProgressMeter - chr5:166809452 61.5 4126230 67088.8
17:44:21.134 INFO ProgressMeter - chr5:169568444 61.7 4137370 67087.2
17:44:31.135 INFO ProgressMeter - chr5:171974317 61.8 4147440 67069.2
17:44:41.138 INFO ProgressMeter - chr5:174670354 62.0 4158590 67068.7
17:44:51.222 INFO ProgressMeter - chr5:176637187 62.2 4166860 67020.4
17:45:01.223 INFO ProgressMeter - chr5:178174758 62.3 4173510 66947.9
17:45:11.277 INFO ProgressMeter - chr5:179291183 62.5 4178760 66852.4
17:45:21.278 INFO ProgressMeter - chr6:256073 62.7 4186570 66799.3
17:45:31.278 INFO ProgressMeter - chr6:3196155 62.8 4198470 66811.5
17:45:41.284 INFO ProgressMeter - chr6:6311526 63.0 4210960 66832.9
17:45:51.394 INFO ProgressMeter - chr6:9798044 63.2 4224830 66874.2
17:46:01.395 INFO ProgressMeter - chr6:13407649 63.3 4238940 66920.9
17:46:11.397 INFO ProgressMeter - chr6:17593035 63.5 4255350 67003.7
17:46:21.400 INFO ProgressMeter - chr6:21862784 63.7 4271980 67089.4
17:46:31.410 INFO ProgressMeter - chr6:25510692 63.8 4286170 67136.4
17:46:41.501 INFO ProgressMeter - chr6:28270085 64.0 4296790 67125.9
17:46:51.505 INFO ProgressMeter - chr6:33938441 64.2 4316770 67262.8
17:47:01.515 INFO ProgressMeter - chr6:35738879 64.3 4324730 67212.1
17:47:11.523 INFO ProgressMeter - chr6:37260789 64.5 4331360 67141.1
17:47:21.529 INFO ProgressMeter - chr6:39586794 64.7 4341020 67117.3
17:47:31.530 INFO ProgressMeter - chr6:41946895 64.8 4350810 67095.8
17:47:41.531 INFO ProgressMeter - chr6:43371132 65.0 4356990 67018.8
17:47:51.541 INFO ProgressMeter - chr6:45391247 65.2 4365330 66975.2
17:48:01.541 INFO ProgressMeter - chr6:48557999 65.3 4377650 66992.9
17:48:11.564 INFO ProgressMeter - chr6:52358931 65.5 4392220 67044.5
17:48:21.578 INFO ProgressMeter - chr6:55268850 65.7 4403890 67051.8
17:48:32.351 INFO ProgressMeter - chr6:57255070 65.9 4411670 66987.2
17:48:43.184 INFO ProgressMeter - chr6:57397958 66.0 4412490 66816.4
17:48:53.864 INFO ProgressMeter - chr6:57467595 66.2 4412930 66643.5
17:49:03.966 INFO ProgressMeter - chr6:57518874 66.4 4413250 66479.3
17:49:17.110 INFO ProgressMeter - chr6:58778624 66.6 4418090 66333.3
17:49:27.111 INFO ProgressMeter - chr6:65714961 66.8 4442940 66539.8
17:49:37.121 INFO ProgressMeter - chr6:70706864 66.9 4461980 66658.5
17:49:47.163 INFO ProgressMeter - chr6:74123401 67.1 4475180 66688.9
17:49:57.165 INFO ProgressMeter - chr6:77378028 67.3 4487800 66711.3
17:50:07.164 INFO ProgressMeter - chr6:82923259 67.4 4508640 66855.4
17:50:17.168 INFO ProgressMeter - chr6:88066509 67.6 4527830 66974.4
17:50:27.168 INFO ProgressMeter - chr6:91765211 67.8 4542060 67019.6
17:50:37.198 INFO ProgressMeter - chr6:99323592 67.9 4569740 67262.2
17:50:47.211 INFO ProgressMeter - chr6:105595502 68.1 4592850 67436.7
17:50:57.214 INFO ProgressMeter - chr6:108368738 68.3 4604080 67436.5
17:51:07.217 INFO ProgressMeter - chr6:111492456 68.4 4616350 67451.5
17:51:17.230 INFO ProgressMeter - chr6:116786432 68.6 4636200 67576.8
17:51:27.232 INFO ProgressMeter - chr6:121933887 68.8 4655390 67692.0
17:51:37.232 INFO ProgressMeter - chr6:127602655 68.9 4676440 67833.7
17:51:47.237 INFO ProgressMeter - chr6:132131545 69.1 4693330 67914.4
17:51:57.248 INFO ProgressMeter - chr6:136632301 69.3 4710160 67993.8
17:52:07.252 INFO ProgressMeter - chr6:141958898 69.4 4730120 68118.0
17:52:17.269 INFO ProgressMeter - chr6:147051137 69.6 4749030 68226.2
17:52:27.296 INFO ProgressMeter - chr6:150387952 69.8 4762070 68249.7
17:52:37.338 INFO ProgressMeter - chr6:152675175 69.9 4771450 68220.5
17:52:47.341 INFO ProgressMeter - chr6:155669790 70.1 4783430 68229.2
17:52:57.342 INFO ProgressMeter - chr6:158876663 70.3 4796260 68249.9
17:53:07.352 INFO ProgressMeter - chr6:160580465 70.4 4803410 68189.8
17:53:17.363 INFO ProgressMeter - chr6:163463364 70.6 4815140 68194.8
17:53:27.378 INFO ProgressMeter - chr6:166862469 70.8 4828850 68227.7
17:53:37.407 INFO ProgressMeter - chr6:168623654 70.9 4836450 68174.0
17:53:47.423 INFO ProgressMeter - chr6:170627281 71.1 4845310 68138.6
17:53:57.438 INFO ProgressMeter - chr7:888411 71.3 4851550 68066.6
17:54:07.440 INFO ProgressMeter - chr7:1879526 71.4 4856380 67975.3
17:54:17.441 INFO ProgressMeter - chr7:2885928 71.6 4861250 67885.1
17:54:27.482 INFO ProgressMeter - chr7:4947743 71.8 4870130 67850.6
17:54:37.536 INFO ProgressMeter - chr7:6064764 71.9 4875580 67768.3
17:54:47.540 INFO ProgressMeter - chr7:7448781 72.1 4881900 67699.2
17:54:57.540 INFO ProgressMeter - chr7:10663117 72.3 4894750 67720.9
17:55:07.544 INFO ProgressMeter - chr7:13666068 72.4 4906750 67730.7
17:55:17.546 INFO ProgressMeter - chr7:16755770 72.6 4919080 67745.0
17:55:27.552 INFO ProgressMeter - chr7:20144273 72.8 4932400 67772.8
17:55:37.598 INFO ProgressMeter - chr7:22203271 72.9 4940970 67734.7
17:55:47.600 INFO ProgressMeter - chr7:24538024 73.1 4950790 67714.6
17:55:57.600 INFO ProgressMeter - chr7:27305487 73.3 4962000 67713.6
17:56:07.657 INFO ProgressMeter - chr7:29552426 73.4 4971420 67687.3
17:56:17.663 INFO ProgressMeter - chr7:31976318 73.6 4981250 67667.5
17:56:27.669 INFO ProgressMeter - chr7:34171614 73.8 4990580 67641.0
17:56:37.762 INFO ProgressMeter - chr7:36731822 73.9 5001090 67629.2
17:56:47.773 INFO ProgressMeter - chr7:38694379 74.1 5009180 67586.1
17:56:57.775 INFO ProgressMeter - chr7:41955885 74.3 5022300 67611.1
17:57:07.776 INFO ProgressMeter - chr7:44250203 74.4 5031710 67586.1
17:57:17.784 INFO ProgressMeter - chr7:46230330 74.6 5040130 67547.9
17:57:27.820 INFO ProgressMeter - chr7:48413868 74.8 5049210 67518.2
17:57:37.822 INFO ProgressMeter - chr7:50739775 74.9 5058780 67495.7
17:57:47.825 INFO ProgressMeter - chr7:54053523 75.1 5072230 67525.0
17:57:57.837 INFO ProgressMeter - chr7:56067054 75.3 5080830 67489.5
17:58:07.869 INFO ProgressMeter - chr7:56700214 75.5 5083780 67379.1
17:58:18.384 INFO ProgressMeter - chr7:57701272 75.6 5088310 67282.8
17:58:28.408 INFO ProgressMeter - chr7:61819608 75.8 5102670 67324.0
17:58:44.035 INFO ProgressMeter - chr7:61969490 76.1 5103300 67101.7
17:58:54.076 INFO ProgressMeter - chr7:63563653 76.2 5109790 67039.5
17:59:04.292 INFO ProgressMeter - chr7:64555552 76.4 5114390 66950.3
17:59:14.293 INFO ProgressMeter - chr7:66084012 76.6 5121060 66891.7
17:59:24.303 INFO ProgressMeter - chr7:68042068 76.7 5129810 66860.3
17:59:34.305 INFO ProgressMeter - chr7:70814764 76.9 5141580 66868.4
17:59:44.338 INFO ProgressMeter - chr7:73009721 77.1 5150990 66845.4
17:59:54.338 INFO ProgressMeter - chr7:75226406 77.2 5160130 66819.5
18:00:04.354 INFO ProgressMeter - chr7:76889392 77.4 5167540 66771.1
18:00:14.363 INFO ProgressMeter - chr7:79705258 77.6 5178980 66775.0
18:00:24.378 INFO ProgressMeter - chr7:83022312 77.7 5191940 66798.4
18:00:34.389 INFO ProgressMeter - chr7:87105387 77.9 5207450 66854.4
18:00:44.390 INFO ProgressMeter - chr7:90319593 78.1 5220040 66872.9
18:00:54.392 INFO ProgressMeter - chr7:93317435 78.2 5231680 66879.2
18:01:04.396 INFO ProgressMeter - chr7:96319512 78.4 5243370 66886.1
18:01:14.403 INFO ProgressMeter - chr7:98476301 78.6 5252680 66862.6
18:01:24.418 INFO ProgressMeter - chr7:99811167 78.7 5258170 66790.6
18:01:47.607 INFO ProgressMeter - chr7:100550103 79.1 5261410 66505.2
18:02:13.269 INFO ProgressMeter - chr7:100551977 79.5 5261420 66147.8
18:02:23.641 INFO ProgressMeter - chr7:100609929 79.7 5261640 66007.1
18:02:33.781 INFO ProgressMeter - chr7:100937963 79.9 5263190 65886.8
18:02:43.805 INFO ProgressMeter - chr7:102669715 80.0 5270730 65843.5
18:02:53.812 INFO ProgressMeter - chr7:104893903 80.2 5279640 65817.7
18:03:03.812 INFO ProgressMeter - chr7:107278939 80.4 5289530 65804.3
18:03:13.814 INFO ProgressMeter - chr7:110680000 80.5 5302780 65832.6
18:03:23.816 INFO ProgressMeter - chr7:115307716 80.7 5320160 65911.9
18:03:33.819 INFO ProgressMeter - chr7:119130420 80.9 5334570 65954.2
18:03:43.820 INFO ProgressMeter - chr7:122996461 81.0 5349190 65999.0
18:03:53.826 INFO ProgressMeter - chr7:126949112 81.2 5364460 66051.5
18:04:03.830 INFO ProgressMeter - chr7:128556936 81.4 5371410 66001.6
18:04:13.831 INFO ProgressMeter - chr7:130282627 81.5 5378670 65955.7
18:04:23.831 INFO ProgressMeter - chr7:132473752 81.7 5388040 65935.8
18:04:33.838 INFO ProgressMeter - chr7:134896099 81.9 5398030 65923.5
18:04:43.843 INFO ProgressMeter - chr7:137789393 82.0 5409670 65931.4
18:04:53.843 INFO ProgressMeter - chr7:139570629 82.2 5417270 65890.2
18:05:03.851 INFO ProgressMeter - chr7:141629665 82.4 5425700 65859.1
18:05:14.281 INFO ProgressMeter - chr7:142101688 82.6 5427710 65744.8
18:05:24.649 INFO ProgressMeter - chr7:142149561 82.7 5427950 65610.4
18:05:35.244 INFO ProgressMeter - chr7:142199264 82.9 5428220 65473.9
18:05:47.584 INFO ProgressMeter - chr7:142461617 83.1 5429380 65325.8
18:05:58.350 INFO ProgressMeter - chr7:142479753 83.3 5429490 65186.4
18:06:08.372 INFO ProgressMeter - chr7:143826089 83.5 5434650 65117.8
18:06:18.372 INFO ProgressMeter - chr7:147989894 83.6 5450590 65178.6
18:06:28.430 INFO ProgressMeter - chr7:149513598 83.8 5457410 65129.6
18:06:38.446 INFO ProgressMeter - chr7:150761188 84.0 5462850 65064.9
18:06:50.230 INFO ProgressMeter - chr7:151945255 84.2 5468130 64975.8
18:07:00.285 INFO ProgressMeter - chr7:152107053 84.3 5468800 64854.6
18:07:10.292 INFO ProgressMeter - chr7:153271172 84.5 5473880 64786.7
18:07:20.305 INFO ProgressMeter - chr7:155191089 84.7 5482230 64757.6
18:07:30.306 INFO ProgressMeter - chr7:156784951 84.8 5489480 64715.8
18:07:40.306 INFO ProgressMeter - chr7:158191557 85.0 5496210 64668.1
18:07:50.351 INFO ProgressMeter - chr8:608242 85.2 5502930 64619.9
18:08:00.354 INFO ProgressMeter - chr8:2223614 85.3 5510220 64579.1
18:08:10.360 INFO ProgressMeter - chr8:4409121 85.5 5519610 64562.9
18:08:20.360 INFO ProgressMeter - chr8:6536814 85.7 5529000 64546.9
18:08:30.367 INFO ProgressMeter - chr8:9336513 85.8 5540390 64554.2
18:08:40.367 INFO ProgressMeter - chr8:11582086 86.0 5549890 64539.6
18:08:50.373 INFO ProgressMeter - chr8:13173601 86.2 5556920 64496.2
18:09:00.375 INFO ProgressMeter - chr8:16486720 86.3 5570430 64528.2
18:09:10.420 INFO ProgressMeter - chr8:17931055 86.5 5576700 64475.8
18:09:20.424 INFO ProgressMeter - chr8:20390833 86.7 5587050 64471.2
18:09:31.146 INFO ProgressMeter - chr8:22493081 86.8 5595680 64437.9
18:09:41.147 INFO ProgressMeter - chr8:24386366 87.0 5603600 64405.5
18:09:51.155 INFO ProgressMeter - chr8:26906272 87.2 5613840 64399.7
18:10:01.225 INFO ProgressMeter - chr8:29024101 87.3 5622560 64375.8
18:10:11.229 INFO ProgressMeter - chr8:31552388 87.5 5632980 64372.2
18:10:21.229 INFO ProgressMeter - chr8:36049197 87.7 5650330 64447.7
18:10:31.240 INFO ProgressMeter - chr8:38828703 87.8 5661360 64450.9
18:10:41.244 INFO ProgressMeter - chr8:41591229 88.0 5672530 64455.7
18:10:51.247 INFO ProgressMeter - chr8:47402703 88.2 5693640 64573.2
18:11:01.254 INFO ProgressMeter - chr8:52264672 88.3 5712090 64660.2
18:11:11.256 INFO ProgressMeter - chr8:55273394 88.5 5724110 64674.2
18:11:21.276 INFO ProgressMeter - chr8:58129225 88.7 5735460 64680.4
18:11:31.278 INFO ProgressMeter - chr8:62118832 88.8 5750980 64733.7
18:11:41.278 INFO ProgressMeter - chr8:66398764 89.0 5767440 64797.4
18:11:51.278 INFO ProgressMeter - chr8:70377958 89.2 5782520 64845.4
18:12:01.280 INFO ProgressMeter - chr8:74378631 89.3 5797840 64895.9
18:12:11.282 INFO ProgressMeter - chr8:79253403 89.5 5816240 64980.6
18:12:21.285 INFO ProgressMeter - chr8:83982565 89.7 5834230 65060.4
18:12:31.286 INFO ProgressMeter - chr8:88817340 89.8 5852340 65141.3
18:12:41.289 INFO ProgressMeter - chr8:94226310 90.0 5872590 65245.6
18:12:51.293 INFO ProgressMeter - chr8:97051491 90.2 5883960 65251.1
18:13:01.293 INFO ProgressMeter - chr8:101067953 90.3 5899340 65300.9
18:13:11.294 INFO ProgressMeter - chr8:103257440 90.5 5908070 65277.1
18:13:21.299 INFO ProgressMeter - chr8:107009019 90.7 5922330 65314.4
18:13:31.299 INFO ProgressMeter - chr8:110590423 90.8 5936170 65346.9
18:13:41.304 INFO ProgressMeter - chr8:116950329 91.0 5959620 65484.8
18:13:51.332 INFO ProgressMeter - chr8:121211188 91.2 5975920 65543.5
18:14:01.513 INFO ProgressMeter - chr8:124442525 91.3 5988610 65560.7
18:14:11.517 INFO ProgressMeter - chr8:127345389 91.5 6000190 65567.8
18:14:21.531 INFO ProgressMeter - chr8:131495863 91.7 6016410 65625.4
18:14:31.537 INFO ProgressMeter - chr8:134389856 91.8 6028010 65632.5
18:14:41.549 INFO ProgressMeter - chr8:138634986 92.0 6044690 65694.8
18:14:51.555 INFO ProgressMeter - chr8:141697154 92.2 6057110 65710.6
18:15:01.564 INFO ProgressMeter - chr8:143435265 92.3 6064950 65676.8
18:15:11.664 INFO ProgressMeter - chr8:144393155 92.5 6069580 65607.4
18:15:21.668 INFO ProgressMeter - chr8:145171164 92.7 6073210 65528.5
18:15:31.729 INFO ProgressMeter - chr9:453236 92.8 6079990 65483.2
18:15:41.732 INFO ProgressMeter - chr9:4439840 93.0 6095500 65532.6
18:15:51.742 INFO ProgressMeter - chr9:6876879 93.2 6105500 65522.6
18:16:01.850 INFO ProgressMeter - chr9:11012472 93.4 6121670 65577.5
18:16:11.851 INFO ProgressMeter - chr9:15412181 93.5 6138520 65640.8
18:16:21.857 INFO ProgressMeter - chr9:19394757 93.7 6153920 65688.4
18:16:31.863 INFO ProgressMeter - chr9:24910158 93.9 6174500 65790.9
18:16:41.867 INFO ProgressMeter - chr9:28956635 94.0 6190250 65841.8
18:16:51.873 INFO ProgressMeter - chr9:32969067 94.2 6205880 65891.2
18:17:02.164 INFO ProgressMeter - chr9:33795524 94.4 6209480 65809.5
18:17:12.176 INFO ProgressMeter - chr9:34561017 94.5 6212760 65728.1
18:17:22.179 INFO ProgressMeter - chr9:36156051 94.7 6219330 65681.7
18:17:32.206 INFO ProgressMeter - chr9:38412662 94.9 6228650 65664.2
18:17:42.336 INFO ProgressMeter - chr9:45362557 95.0 6253600 65810.1
18:17:54.076 INFO ProgressMeter - chr9:66456107 95.2 6324410 66418.6
18:18:04.349 INFO ProgressMeter - chr9:66463981 95.4 6324460 66299.9
18:18:14.351 INFO ProgressMeter - chr9:66519223 95.6 6324780 66187.6
18:18:24.600 INFO ProgressMeter - chr9:68381610 95.7 6331660 66141.3
18:18:35.889 INFO ProgressMeter - chr9:68414060 95.9 6331840 66013.5
18:18:47.018 INFO ProgressMeter - chr9:68422616 96.1 6331890 65886.6
18:19:01.406 INFO ProgressMeter - chr9:68431343 96.3 6331950 65723.2
18:19:11.414 INFO ProgressMeter - chr9:68479331 96.5 6332190 65612.1
18:19:21.429 INFO ProgressMeter - chr9:69824616 96.7 6337230 65550.9
18:19:31.432 INFO ProgressMeter - chr9:73032523 96.8 6349740 65567.3
18:19:41.434 INFO ProgressMeter - chr9:76635970 97.0 6363870 65600.3
18:19:51.473 INFO ProgressMeter - chr9:79326808 97.2 6374490 65596.6
18:20:01.473 INFO ProgressMeter - chr9:83293892 97.3 6390050 65644.1
18:20:11.476 INFO ProgressMeter - chr9:86818130 97.5 6403820 65673.1
18:20:21.480 INFO ProgressMeter - chr9:90047394 97.7 6416630 65692.2
18:20:31.486 INFO ProgressMeter - chr9:92207453 97.8 6425610 65672.0
18:20:41.522 INFO ProgressMeter - chr9:95236978 98.0 6437800 65684.3
18:20:51.552 INFO ProgressMeter - chr9:97219294 98.2 6446270 65658.7
18:21:01.556 INFO ProgressMeter - chr9:99872023 98.3 6457030 65656.8
18:21:11.562 INFO ProgressMeter - chr9:101902848 98.5 6465480 65631.4
18:21:21.566 INFO ProgressMeter - chr9:106242023 98.7 6482000 65687.9
18:21:31.569 INFO ProgressMeter - chr9:109207728 98.8 6493470 65693.2
18:21:41.587 INFO ProgressMeter - chr9:112185469 99.0 6505420 65703.1
18:21:51.592 INFO ProgressMeter - chr9:114523538 99.2 6514910 65688.3
18:22:01.594 INFO ProgressMeter - chr9:116697655 99.3 6524110 65670.7
18:22:11.595 INFO ProgressMeter - chr9:119287518 99.5 6534540 65665.5
18:22:21.595 INFO ProgressMeter - chr9:123377427 99.7 6550550 65716.3
18:22:31.597 INFO ProgressMeter - chr9:125503198 99.8 6559190 65693.1
18:22:41.609 INFO ProgressMeter - chr9:127701316 100.0 6568270 65674.3
18:22:51.612 INFO ProgressMeter - chr9:130166268 100.2 6578530 65667.4
18:23:01.637 INFO ProgressMeter - chr9:131280224 100.3 6583500 65607.6
18:23:11.814 INFO ProgressMeter - chr9:132199045 100.5 6587740 65539.1
18:23:21.828 INFO ProgressMeter - chr9:133441860 100.7 6593570 65488.4
18:23:31.834 INFO ProgressMeter - chr9:135104479 100.8 6600800 65451.8
18:23:41.837 INFO ProgressMeter - chr9:136248708 101.0 6605970 65394.9
18:23:51.875 INFO ProgressMeter - chr9:137630625 101.2 6612290 65349.3
18:24:01.928 INFO ProgressMeter - chr9:138662236 101.4 6617140 65289.1
18:24:11.981 INFO ProgressMeter - chr9:139694484 101.5 6621850 65227.7
18:24:21.985 INFO ProgressMeter - chr9:140138209 101.7 6623960 65141.5
18:24:31.990 INFO ProgressMeter - chr10:688717 101.9 6631370 65107.6
18:24:41.996 INFO ProgressMeter - chr10:3309291 102.0 6642290 65108.2
18:24:52.014 INFO ProgressMeter - chr10:5966534 102.2 6653040 65107.1
18:25:02.014 INFO ProgressMeter - chr10:8942424 102.4 6665150 65119.4
18:25:12.015 INFO ProgressMeter - chr10:12665836 102.5 6679900 65157.3
18:25:22.015 INFO ProgressMeter - chr10:15018180 102.7 6689740 65147.4
18:25:32.017 INFO ProgressMeter - chr10:18727755 102.9 6704090 65181.4
18:25:42.095 INFO ProgressMeter - chr10:23303136 103.0 6721430 65243.4
18:25:52.096 INFO ProgressMeter - chr10:27144516 103.2 6736260 65281.7
18:26:02.117 INFO ProgressMeter - chr10:29835029 103.4 6747220 65282.3
18:26:12.129 INFO ProgressMeter - chr10:33125362 103.5 6760180 65302.2
18:26:22.139 INFO ProgressMeter - chr10:37661084 103.7 6777740 65366.5
18:26:32.252 INFO ProgressMeter - chr10:42381019 103.9 6794760 65424.3
18:26:53.041 INFO ProgressMeter - chr10:42385783 104.2 6794790 65207.1
18:27:09.288 INFO ProgressMeter - chr10:42396682 104.5 6794860 65038.7
18:27:31.131 INFO ProgressMeter - chr10:42597146 104.8 6795620 64820.1
18:27:44.260 INFO ProgressMeter - chr10:42600184 105.1 6795640 64685.3
18:27:54.267 INFO ProgressMeter - chr10:43466667 105.2 6799160 64616.2
18:28:04.453 INFO ProgressMeter - chr10:46993069 105.4 6813060 64644.0
18:28:14.469 INFO ProgressMeter - chr10:49804119 105.6 6823700 64642.6
18:28:24.478 INFO ProgressMeter - chr10:52429705 105.7 6833860 64636.7
18:28:34.489 INFO ProgressMeter - chr10:58120314 105.9 6855220 64736.6
18:28:44.493 INFO ProgressMeter - chr10:63450238 106.1 6875120 64822.4
18:28:54.497 INFO ProgressMeter - chr10:68590625 106.2 6894700 64905.0
18:29:04.499 INFO ProgressMeter - chr10:71360669 106.4 6905720 64906.9
18:29:14.500 INFO ProgressMeter - chr10:73513566 106.6 6914840 64890.9
18:29:24.526 INFO ProgressMeter - chr10:76929087 106.7 6927920 64911.9
18:29:34.527 INFO ProgressMeter - chr10:81117276 106.9 6944210 64963.1
18:29:44.528 INFO ProgressMeter - chr10:84630734 107.1 6957930 64990.1
18:29:54.542 INFO ProgressMeter - chr10:88941934 107.2 6974530 65043.7
18:30:04.544 INFO ProgressMeter - chr10:93617644 107.4 6991970 65105.2
18:30:14.605 INFO ProgressMeter - chr10:96354811 107.6 7002960 65105.9
18:30:24.612 INFO ProgressMeter - chr10:99279589 107.7 7014570 65112.8
18:30:34.617 INFO ProgressMeter - chr10:102456026 107.9 7027020 65127.6
18:30:44.621 INFO ProgressMeter - chr10:104902375 108.1 7036840 65118.0
18:30:54.637 INFO ProgressMeter - chr10:108522504 108.2 7050830 65146.8
18:31:04.658 INFO ProgressMeter - chr10:113922163 108.4 7071200 65234.3
18:31:14.660 INFO ProgressMeter - chr10:117351521 108.6 7084330 65255.1
18:31:24.664 INFO ProgressMeter - chr10:120823335 108.7 7098040 65281.1
18:31:34.677 INFO ProgressMeter - chr10:123243160 108.9 7108280 65275.1
18:31:44.678 INFO ProgressMeter - chr10:125447831 109.1 7117380 65258.8
18:31:54.996 INFO ProgressMeter - chr10:127585206 109.2 7126110 65236.0
18:32:04.998 INFO ProgressMeter - chr10:130298736 109.4 7137260 65238.5
18:32:14.999 INFO ProgressMeter - chr10:133453697 109.6 7150370 65258.9
18:32:25.010 INFO ProgressMeter - chr10:135196015 109.7 7158110 65230.2
18:32:35.056 INFO ProgressMeter - chr11:307659 109.9 7160790 65155.2
18:33:14.977 INFO ProgressMeter - chr11:1018272 110.6 7164160 64793.6
18:33:25.405 INFO ProgressMeter - chr11:1260594 110.7 7165310 64702.3
18:33:35.407 INFO ProgressMeter - chr11:2423219 110.9 7170850 64655.0
18:33:45.437 INFO ProgressMeter - chr11:3848846 111.1 7177290 64615.7
18:33:55.445 INFO ProgressMeter - chr11:5431325 111.2 7183770 64577.1
18:34:05.556 INFO ProgressMeter - chr11:6630375 111.4 7188750 64524.1
18:34:15.722 INFO ProgressMeter - chr11:7950362 111.6 7194210 64475.1
18:34:25.725 INFO ProgressMeter - chr11:9724987 111.7 7201760 64446.4
18:34:35.730 INFO ProgressMeter - chr11:11655354 111.9 7209820 64422.4
18:34:45.737 INFO ProgressMeter - chr11:14286730 112.1 7220640 64423.1
18:34:55.747 INFO ProgressMeter - chr11:17434641 112.2 7233100 64438.3
18:35:05.850 INFO ProgressMeter - chr11:18736520 112.4 7238550 64390.3
18:35:15.860 INFO ProgressMeter - chr11:20666488 112.6 7246720 64367.5
18:35:25.862 INFO ProgressMeter - chr11:24901944 112.8 7263240 64418.8
18:35:35.866 INFO ProgressMeter - chr11:28289507 112.9 7276410 64440.3
18:35:45.868 INFO ProgressMeter - chr11:32986351 113.1 7294250 64503.1
18:35:56.100 INFO ProgressMeter - chr11:34939299 113.3 7302430 64478.2
18:36:06.117 INFO ProgressMeter - chr11:38818450 113.4 7317510 64516.2
18:36:16.121 INFO ProgressMeter - chr11:43559257 113.6 7335960 64584.0
18:36:26.123 INFO ProgressMeter - chr11:45881014 113.8 7345760 64575.5
18:36:36.127 INFO ProgressMeter - chr11:47624012 113.9 7352890 64543.5
18:36:46.180 INFO ProgressMeter - chr11:48365868 114.1 7356120 64477.1
18:37:00.036 INFO ProgressMeter - chr11:48387731 114.3 7356230 64347.8
18:37:10.036 INFO ProgressMeter - chr11:51317775 114.5 7367700 64354.3
18:37:20.049 INFO ProgressMeter - chr11:55890977 114.7 7383710 64400.3
18:37:30.055 INFO ProgressMeter - chr11:56971739 114.8 7387870 64343.0
18:37:40.072 INFO ProgressMeter - chr11:58981508 115.0 7396050 64320.7
18:37:50.075 INFO ProgressMeter - chr11:61038258 115.2 7404280 64299.0
18:38:00.086 INFO ProgressMeter - chr11:62434425 115.3 7410200 64257.3
18:38:10.101 INFO ProgressMeter - chr11:64064297 115.5 7416970 64223.1
18:38:20.115 INFO ProgressMeter - chr11:65293462 115.7 7422270 64176.2
18:38:30.116 INFO ProgressMeter - chr11:66363200 115.8 7427000 64124.7
18:38:40.146 INFO ProgressMeter - chr11:67790581 116.0 7433080 64084.7
18:38:50.146 INFO ProgressMeter - chr11:69515176 116.2 7440680 64058.2
18:39:00.148 INFO ProgressMeter - chr11:71180938 116.3 7448240 64031.4
18:39:10.149 INFO ProgressMeter - chr11:73031601 116.5 7455860 64005.2
18:39:20.163 INFO ProgressMeter - chr11:75431630 116.7 7465500 63996.2
18:39:30.170 INFO ProgressMeter - chr11:77552572 116.8 7474280 63980.0
18:39:40.177 INFO ProgressMeter - chr11:81240889 117.0 7488750 64012.5
18:39:50.181 INFO ProgressMeter - chr11:85861545 117.2 7506140 64069.8
18:40:00.181 INFO ProgressMeter - chr11:89484614 117.3 7520090 64097.7
18:40:10.216 INFO ProgressMeter - chr11:93530593 117.5 7535350 64136.4
18:40:20.219 INFO ProgressMeter - chr11:96885809 117.7 7548540 64157.6
18:40:30.232 INFO ProgressMeter - chr11:101325586 117.8 7565730 64212.6
18:40:41.585 INFO ProgressMeter - chr11:103229069 118.0 7573340 64174.1
18:40:51.586 INFO ProgressMeter - chr11:106972406 118.2 7587720 64205.3
18:41:01.587 INFO ProgressMeter - chr11:109274097 118.3 7597140 64194.5
18:41:11.594 INFO ProgressMeter - chr11:112220533 118.5 7608750 64202.1
18:41:23.355 INFO ProgressMeter - chr11:114422217 118.7 7617790 64172.2
18:41:33.384 INFO ProgressMeter - chr11:117162032 118.9 7628980 64176.1
18:41:43.392 INFO ProgressMeter - chr11:118509716 119.0 7634870 64135.7
18:41:53.422 INFO ProgressMeter - chr11:119501123 119.2 7639480 64084.4
18:42:03.422 INFO ProgressMeter - chr11:121713145 119.4 7648640 64071.7
18:42:14.087 INFO ProgressMeter - chr11:123895257 119.6 7657640 64051.7
18:42:24.096 INFO ProgressMeter - chr11:124875102 119.7 7661630 63995.8
18:42:34.100 INFO ProgressMeter - chr11:126813964 119.9 7669780 63974.8
18:42:44.100 INFO ProgressMeter - chr11:130083870 120.1 7682690 63993.5
18:42:54.100 INFO ProgressMeter - chr11:133480397 120.2 7696190 64017.1
18:43:04.101 INFO ProgressMeter - chr12:474854 120.4 7704540 63997.8
18:43:14.106 INFO ProgressMeter - chr12:2495054 120.6 7713120 63980.4
18:43:24.112 INFO ProgressMeter - chr12:4117014 120.7 7720250 63951.1
18:43:34.115 INFO ProgressMeter - chr12:6266106 120.9 7729100 63936.1
18:43:44.120 INFO ProgressMeter - chr12:7387166 121.1 7733920 63887.9
18:43:54.136 INFO ProgressMeter - chr12:8804035 121.2 7740160 63851.4
18:44:04.137 INFO ProgressMeter - chr12:10101078 121.4 7745640 63808.8
18:44:18.734 INFO ProgressMeter - chr12:11184778 121.6 7750160 63718.4
18:44:34.030 INFO ProgressMeter - chr12:11245570 121.9 7750430 63587.3
18:44:45.431 INFO ProgressMeter - chr12:11287309 122.1 7750620 63489.9
18:44:55.451 INFO ProgressMeter - chr12:13526666 122.2 7759980 63479.7
18:45:05.454 INFO ProgressMeter - chr12:16672885 122.4 7772330 63494.2
18:45:15.467 INFO ProgressMeter - chr12:20783062 122.6 7788150 63536.8
18:45:25.476 INFO ProgressMeter - chr12:22646058 122.7 7795700 63511.9
18:45:35.517 INFO ProgressMeter - chr12:25957570 122.9 7808660 63530.9
18:45:45.524 INFO ProgressMeter - chr12:29167230 123.1 7821300 63547.5
18:45:55.536 INFO ProgressMeter - chr12:31292040 123.2 7830180 63533.5
18:46:05.536 INFO ProgressMeter - chr12:33797369 123.4 7840590 63532.1
18:46:15.546 INFO ProgressMeter - chr12:40803688 123.6 7865850 63650.7
18:46:25.553 INFO ProgressMeter - chr12:43219434 123.7 7875530 63643.1
18:46:35.555 INFO ProgressMeter - chr12:47097312 123.9 7890480 63678.2
18:46:45.570 INFO ProgressMeter - chr12:49022682 124.1 7898280 63655.4
18:46:55.576 INFO ProgressMeter - chr12:50539563 124.2 7904510 63620.1
18:47:05.585 INFO ProgressMeter - chr12:52246774 124.4 7911910 63594.2
18:47:15.596 INFO ProgressMeter - chr12:53128719 124.6 7915960 63541.6
18:47:25.597 INFO ProgressMeter - chr12:54447351 124.7 7921720 63502.9
18:47:35.603 INFO ProgressMeter - chr12:56106315 124.9 7928450 63472.0
18:47:45.647 INFO ProgressMeter - chr12:57492783 125.1 7934210 63433.1
18:47:55.653 INFO ProgressMeter - chr12:58965037 125.2 7940260 63396.9
18:48:05.704 INFO ProgressMeter - chr12:63543616 125.4 7957710 63451.4
18:48:15.756 INFO ProgressMeter - chr12:66704629 125.6 7970030 63464.8
18:48:25.779 INFO ProgressMeter - chr12:69983411 125.7 7983060 63484.1
18:48:35.779 INFO ProgressMeter - chr12:73092248 125.9 7995080 63495.6
18:48:45.788 INFO ProgressMeter - chr12:77443928 126.1 8011780 63544.0
18:48:55.797 INFO ProgressMeter - chr12:81387769 126.2 8026770 63578.8
18:49:05.802 INFO ProgressMeter - chr12:87234928 126.4 8048550 63667.2
18:49:15.807 INFO ProgressMeter - chr12:92838163 126.6 8069310 63747.3
18:49:25.816 INFO ProgressMeter - chr12:95145857 126.7 8078780 63738.1
18:49:35.818 INFO ProgressMeter - chr12:96977515 126.9 8086630 63716.3
18:49:45.824 INFO ProgressMeter - chr12:100614592 127.1 8100770 63743.9
18:49:55.838 INFO ProgressMeter - chr12:102983496 127.2 8110200 63734.4
18:50:05.855 INFO ProgressMeter - chr12:104927859 127.4 8118130 63713.2
18:50:15.860 INFO ProgressMeter - chr12:107399921 127.6 8128100 63708.0
18:50:25.885 INFO ProgressMeter - chr12:109650884 127.8 8137530 63698.5
18:50:35.930 INFO ProgressMeter - chr12:111801316 127.9 8146240 63683.2
18:50:45.936 INFO ProgressMeter - chr12:113618333 128.1 8153900 63660.1
18:50:55.938 INFO ProgressMeter - chr12:116228877 128.3 8164860 63662.8
18:51:05.947 INFO ProgressMeter - chr12:118682001 128.4 8175220 63660.8
18:51:15.968 INFO ProgressMeter - chr12:120962451 128.6 8184680 63651.7
18:51:25.973 INFO ProgressMeter - chr12:122296747 128.8 8190630 63615.5
18:51:35.975 INFO ProgressMeter - chr12:123464617 128.9 8195950 63574.5
18:51:46.090 INFO ProgressMeter - chr12:124839830 129.1 8202060 63538.8
18:51:56.097 INFO ProgressMeter - chr12:126949868 129.3 8211220 63527.7
18:52:06.114 INFO ProgressMeter - chr12:129474333 129.4 8221940 63528.6
18:52:16.115 INFO ProgressMeter - chr12:131575386 129.6 8231200 63518.3
18:52:26.122 INFO ProgressMeter - chr12:133150844 129.8 8238320 63491.5
18:52:36.124 INFO ProgressMeter - chr13:19552628 129.9 8306900 63937.9
18:52:46.135 INFO ProgressMeter - chr13:20383579 130.1 8310720 63885.3
18:52:56.215 INFO ProgressMeter - chr13:22275432 130.3 8318970 63866.2
18:53:06.218 INFO ProgressMeter - chr13:24774183 130.4 8329410 63864.6
18:53:19.909 INFO ProgressMeter - chr13:25671497 130.7 8333350 63783.3
18:53:29.910 INFO ProgressMeter - chr13:28267212 130.8 8344150 63784.5
18:53:39.913 INFO ProgressMeter - chr13:30657088 131.0 8354210 63780.2
18:53:49.914 INFO ProgressMeter - chr13:32970699 131.2 8363720 63771.6
18:53:59.945 INFO ProgressMeter - chr13:36686176 131.3 8378230 63800.9
18:54:09.961 INFO ProgressMeter - chr13:39673063 131.5 8389990 63809.4
18:54:19.964 INFO ProgressMeter - chr13:42734315 131.7 8402130 63820.8
18:54:29.968 INFO ProgressMeter - chr13:45613616 131.8 8413680 63827.7
18:54:39.973 INFO ProgressMeter - chr13:48571421 132.0 8425520 63836.7
18:54:49.978 INFO ProgressMeter - chr13:51686130 132.2 8437710 63848.4
18:54:59.986 INFO ProgressMeter - chr13:55908247 132.3 8453770 63889.3
18:55:09.992 INFO ProgressMeter - chr13:61824944 132.5 8476060 63977.1
18:55:20.010 INFO ProgressMeter - chr13:67193507 132.7 8496040 64047.2
18:55:30.011 INFO ProgressMeter - chr13:73250363 132.8 8518720 64137.6
18:55:40.074 INFO ProgressMeter - chr13:76764838 133.0 8532720 64162.0
18:55:50.084 INFO ProgressMeter - chr13:80733409 133.2 8547990 64196.3
18:56:00.087 INFO ProgressMeter - chr13:87020025 133.3 8571590 64293.0
18:56:10.098 INFO ProgressMeter - chr13:93120918 133.5 8594530 64384.5
18:56:20.120 INFO ProgressMeter - chr13:96638950 133.7 8608440 64408.1
18:56:30.120 INFO ProgressMeter - chr13:99677888 133.8 8620540 64418.3
18:56:40.123 INFO ProgressMeter - chr13:102597974 134.0 8632460 64427.1
18:56:50.126 INFO ProgressMeter - chr13:106329907 134.2 8646730 64453.4
18:57:00.132 INFO ProgressMeter - chr13:110081703 134.3 8661590 64484.0
18:57:10.138 INFO ProgressMeter - chr13:111600064 134.5 8668310 64454.0
18:57:20.152 INFO ProgressMeter - chr13:113815175 134.7 8677720 64444.0
18:57:30.152 INFO ProgressMeter - chr14:13788901 134.8 8729420 64747.8
18:57:40.326 INFO ProgressMeter - chr14:20149436 135.0 8751370 64829.1
18:57:50.367 INFO ProgressMeter - chr14:20873519 135.2 8754410 64771.3
18:58:00.369 INFO ProgressMeter - chr14:22054681 135.3 8759580 64729.7
18:58:10.369 INFO ProgressMeter - chr14:23043965 135.5 8763870 64681.8
18:58:20.721 INFO ProgressMeter - chr14:24430658 135.7 8769790 64643.2
18:58:30.725 INFO ProgressMeter - chr14:25635588 135.8 8774760 64600.4
18:58:40.728 INFO ProgressMeter - chr14:31476482 136.0 8796580 64681.7
18:58:50.732 INFO ProgressMeter - chr14:34469337 136.2 8808470 64689.8
18:59:00.798 INFO ProgressMeter - chr14:37150820 136.3 8819460 64690.8
18:59:10.800 INFO ProgressMeter - chr14:41361615 136.5 8835630 64730.2
18:59:20.809 INFO ProgressMeter - chr14:47479446 136.7 8858330 64817.3
18:59:30.816 INFO ProgressMeter - chr14:50923953 136.8 8871820 64836.9
18:59:40.824 INFO ProgressMeter - chr14:53174211 137.0 8881030 64825.2
18:59:50.825 INFO ProgressMeter - chr14:56288742 137.2 8893450 64837.0
19:00:00.830 INFO ProgressMeter - chr14:59894528 137.3 8907550 64860.9
19:00:10.838 INFO ProgressMeter - chr14:62326292 137.5 8917230 64852.6
19:00:20.844 INFO ProgressMeter - chr14:64882119 137.7 8927170 64846.3
19:00:30.850 INFO ProgressMeter - chr14:67808288 137.8 8938600 64850.7
19:00:40.850 INFO ProgressMeter - chr14:70042319 138.0 8947740 64838.6
19:00:50.851 INFO ProgressMeter - chr14:72695674 138.2 8958300 64836.9
19:01:00.851 INFO ProgressMeter - chr14:74558281 138.3 8966300 64816.6
19:01:10.868 INFO ProgressMeter - chr14:76422160 138.5 8974030 64794.3
19:01:20.930 INFO ProgressMeter - chr14:78037289 138.7 8981300 64768.3
19:01:30.933 INFO ProgressMeter - chr14:81606971 138.8 8995340 64791.7
19:01:40.933 INFO ProgressMeter - chr14:86998086 139.0 9015890 64861.8
19:01:50.941 INFO ProgressMeter - chr14:90227585 139.2 9028620 64875.6
19:02:00.945 INFO ProgressMeter - chr14:92320806 139.3 9037460 64861.4
19:02:10.950 INFO ProgressMeter - chr14:94081514 139.5 9045140 64838.9
19:02:20.976 INFO ProgressMeter - chr14:95842234 139.7 9052710 64815.5
19:02:30.978 INFO ProgressMeter - chr14:98275029 139.8 9062770 64810.2
19:02:40.978 INFO ProgressMeter - chr14:100759615 140.0 9073210 64807.6
19:02:51.061 INFO ProgressMeter - chr14:102552139 140.2 9080850 64784.4
19:03:01.067 INFO ProgressMeter - chr14:104155603 140.3 9087910 64757.7
19:03:11.076 INFO ProgressMeter - chr14:105404722 140.5 9093630 64721.6
19:03:21.465 INFO ProgressMeter - chr14:106235656 140.7 9097320 64668.1
19:03:31.518 INFO ProgressMeter - chr14:106773895 140.8 9099690 64608.0
19:03:44.958 INFO ProgressMeter - chr14:107034992 141.1 9100940 64514.3
19:03:59.793 INFO ProgressMeter - chr14:107114704 141.3 9101350 64404.3
19:04:09.793 INFO ProgressMeter - chr15:15273601 141.5 9153230 64695.1
19:04:20.581 INFO ProgressMeter - chr15:20476905 141.7 9171130 64739.4
19:04:30.594 INFO ProgressMeter - chr15:22462984 141.8 9178910 64718.1
19:04:40.598 INFO ProgressMeter - chr15:24192327 142.0 9186180 64693.3
19:04:50.597 INFO ProgressMeter - chr15:26694712 142.2 9196420 64689.5
19:05:00.621 INFO ProgressMeter - chr15:29401296 142.3 9207390 64690.6
19:05:10.628 INFO ProgressMeter - chr15:32115929 142.5 9218270 64691.2
19:05:20.638 INFO ProgressMeter - chr15:34499414 142.7 9227870 64682.9
19:05:30.657 INFO ProgressMeter - chr15:37386545 142.8 9239160 64686.3
19:05:40.704 INFO ProgressMeter - chr15:40590097 143.0 9251690 64698.2
19:05:50.711 INFO ProgressMeter - chr15:41985173 143.2 9257870 64666.0
19:06:00.716 INFO ProgressMeter - chr15:43092211 143.3 9262520 64623.2
19:06:10.719 INFO ProgressMeter - chr15:44872650 143.5 9269640 64597.7
19:06:20.788 INFO ProgressMeter - chr15:48055082 143.7 9282110 64609.1
19:06:30.790 INFO ProgressMeter - chr15:50697832 143.8 9292430 64605.9
19:06:40.815 INFO ProgressMeter - chr15:52720192 144.0 9300760 64588.8
19:06:50.827 INFO ProgressMeter - chr15:55758535 144.2 9312970 64598.8
19:07:00.857 INFO ProgressMeter - chr15:58001019 144.3 9322350 64588.9
19:07:10.880 INFO ProgressMeter - chr15:59961790 144.5 9330680 64571.9
19:07:20.880 INFO ProgressMeter - chr15:62766915 144.7 9342150 64576.8
19:07:30.883 INFO ProgressMeter - chr15:64883500 144.8 9351070 64564.1
19:07:40.890 INFO ProgressMeter - chr15:66613579 145.0 9358620 64541.9
19:07:50.899 INFO ProgressMeter - chr15:68623715 145.2 9367250 64527.1
19:08:00.900 INFO ProgressMeter - chr15:70934840 145.3 9377200 64521.6
19:08:10.911 INFO ProgressMeter - chr15:73617684 145.5 9387930 64521.4
19:08:20.912 INFO ProgressMeter - chr15:75440718 145.7 9395740 64501.1
19:08:30.938 INFO ProgressMeter - chr15:77915819 145.8 9405570 64494.6
19:08:40.955 INFO ProgressMeter - chr15:79237286 146.0 9411530 64461.7
19:08:50.988 INFO ProgressMeter - chr15:81612454 146.2 9421370 64455.3
19:09:00.989 INFO ProgressMeter - chr15:84969802 146.3 9434270 64470.0
19:09:10.992 INFO ProgressMeter - chr15:87465329 146.5 9444470 64466.3
19:09:20.993 INFO ProgressMeter - chr15:90169647 146.7 9455290 64466.8
19:09:30.997 INFO ProgressMeter - chr15:91484030 146.8 9461170 64433.6
19:09:41.004 INFO ProgressMeter - chr15:93643642 147.0 9470330 64422.8
19:09:51.007 INFO ProgressMeter - chr15:97255139 147.2 9484840 64448.5
19:10:01.910 INFO ProgressMeter - chr15:100270434 147.4 9497130 64452.4
19:10:11.914 INFO ProgressMeter - chr15:101973569 147.5 9504520 64429.6
19:10:22.027 INFO ProgressMeter - chr16:712492 147.7 9509930 64392.7
19:10:32.027 INFO ProgressMeter - chr16:1375226 147.9 9513220 64342.4
19:10:42.028 INFO ProgressMeter - chr16:2198204 148.0 9517000 64295.5
19:10:52.112 INFO ProgressMeter - chr16:3493339 148.2 9522600 64260.4
19:11:02.119 INFO ProgressMeter - chr16:4967781 148.4 9529100 64231.9
19:11:12.123 INFO ProgressMeter - chr16:7022238 148.5 9538350 64222.1
19:11:22.123 INFO ProgressMeter - chr16:8962871 148.7 9546950 64207.9
19:11:32.129 INFO ProgressMeter - chr16:11010188 148.9 9555920 64196.3
19:11:42.140 INFO ProgressMeter - chr16:12536666 149.0 9562990 64171.8
19:11:52.188 INFO ProgressMeter - chr16:15160688 149.2 9573820 64172.4
19:12:02.200 INFO ProgressMeter - chr16:17728401 149.4 9584300 64170.9
19:12:12.202 INFO ProgressMeter - chr16:20411686 149.5 9595120 64171.7
19:12:22.207 INFO ProgressMeter - chr16:22993490 149.7 9605270 64168.0
19:12:32.211 INFO ProgressMeter - chr16:25653348 149.9 9616130 64169.1
19:12:42.220 INFO ProgressMeter - chr16:28354128 150.0 9627410 64172.9
19:12:52.242 INFO ProgressMeter - chr16:30364721 150.2 9635560 64155.8
19:13:02.245 INFO ProgressMeter - chr16:31543660 150.4 9640570 64118.0
19:13:12.271 INFO ProgressMeter - chr16:32891476 150.5 9646180 64084.1
19:13:22.456 INFO ProgressMeter - chr16:33414667 150.7 9648340 64026.2
19:13:33.174 INFO ProgressMeter - chr16:33540375 150.9 9649070 63955.3
19:13:44.364 INFO ProgressMeter - chr16:33944218 151.1 9650840 63888.0
19:13:54.679 INFO ProgressMeter - chr16:33962869 151.2 9650950 63816.1
19:14:04.679 INFO ProgressMeter - chr16:38089586 151.4 9665240 63840.3
19:14:14.948 INFO ProgressMeter - chr16:46407792 151.6 9693100 63952.0
19:14:24.954 INFO ProgressMeter - chr16:49113126 151.7 9703540 63950.5
19:14:34.961 INFO ProgressMeter - chr16:51489176 151.9 9713490 63945.8
19:14:44.974 INFO ProgressMeter - chr16:55152714 152.1 9727970 63970.8
19:14:54.979 INFO ProgressMeter - chr16:56641940 152.2 9734290 63942.3
19:15:05.048 INFO ProgressMeter - chr16:57779037 152.4 9739430 63905.6
19:15:15.052 INFO ProgressMeter - chr16:59863872 152.6 9748300 63893.9
19:15:25.063 INFO ProgressMeter - chr16:65608912 152.7 9770100 63966.8
19:15:35.124 INFO ProgressMeter - chr16:67914391 152.9 9779250 63956.5
19:15:45.127 INFO ProgressMeter - chr16:69929973 153.1 9787630 63941.6
19:15:55.171 INFO ProgressMeter - chr16:71781837 153.2 9795130 63920.7
19:16:05.222 INFO ProgressMeter - chr16:74426108 153.4 9805850 63920.8
19:16:15.235 INFO ProgressMeter - chr16:76168497 153.6 9813550 63901.5
19:16:25.236 INFO ProgressMeter - chr16:78661290 153.7 9823970 63900.0
19:16:35.494 INFO ProgressMeter - chr16:81145593 153.9 9834460 63897.1
19:16:45.514 INFO ProgressMeter - chr16:82183441 154.1 9839260 63859.0
19:16:55.539 INFO ProgressMeter - chr16:84257334 154.2 9848190 63847.7
19:17:05.548 INFO ProgressMeter - chr16:85350177 154.4 9853530 63813.4
19:17:15.551 INFO ProgressMeter - chr16:87020430 154.6 9861380 63795.3
19:17:25.901 INFO ProgressMeter - chr16:88498335 154.8 9868190 63768.2
19:17:35.912 INFO ProgressMeter - chr16:89291996 154.9 9872070 63724.6
19:17:46.003 INFO ProgressMeter - chr16:90161493 155.1 9876330 63682.9
19:17:56.055 INFO ProgressMeter - chr17:1489942 155.3 9883990 63663.5
19:18:06.087 INFO ProgressMeter - chr17:2700573 155.4 9889530 63630.7
19:18:16.197 INFO ProgressMeter - chr17:4013788 155.6 9895360 63599.3
19:18:26.210 INFO ProgressMeter - chr17:5040281 155.8 9900170 63562.0
19:18:36.251 INFO ProgressMeter - chr17:6560898 155.9 9906980 63537.5
19:18:46.264 INFO ProgressMeter - chr17:7480230 156.1 9911140 63496.2
19:18:56.281 INFO ProgressMeter - chr17:8449805 156.3 9915500 63456.2
19:19:06.331 INFO ProgressMeter - chr17:10364045 156.4 9923610 63440.1
19:19:16.345 INFO ProgressMeter - chr17:12638559 156.6 9933040 63432.7
19:19:26.347 INFO ProgressMeter - chr17:15516312 156.8 9944920 63441.1
19:19:36.359 INFO ProgressMeter - chr17:17255547 156.9 9952340 63420.9
19:19:46.360 INFO ProgressMeter - chr17:18613368 157.1 9958090 63390.2
19:19:56.384 INFO ProgressMeter - chr17:20688867 157.3 9966580 63376.8
19:20:07.062 INFO ProgressMeter - chr17:21204500 157.4 9968900 63319.9
19:20:17.221 INFO ProgressMeter - chr17:21240083 157.6 9969170 63253.6
19:20:27.334 INFO ProgressMeter - chr17:21314250 157.8 9969590 63188.7
19:20:38.047 INFO ProgressMeter - chr17:21326384 158.0 9969670 63117.8
19:20:48.733 INFO ProgressMeter - chr17:21549296 158.1 9970730 63053.4
19:20:59.097 INFO ProgressMeter - chr17:21904397 158.3 9972120 62993.4
19:21:09.954 INFO ProgressMeter - chr17:22261744 158.5 9973510 62930.2
19:21:19.961 INFO ProgressMeter - chr17:26711552 158.7 9989550 62965.2
19:21:29.984 INFO ProgressMeter - chr17:28513816 158.8 9996930 62945.4
19:21:39.984 INFO ProgressMeter - chr17:31046868 159.0 10007090 62943.3
19:21:49.996 INFO ProgressMeter - chr17:33496614 159.2 10017270 62941.3
19:22:00.066 INFO ProgressMeter - chr17:35581842 159.3 10025650 62927.6
19:22:10.067 INFO ProgressMeter - chr17:36864642 159.5 10031130 62896.2
19:22:20.084 INFO ProgressMeter - chr17:38559508 159.7 10038190 62874.7
19:22:30.098 INFO ProgressMeter - chr17:39624563 159.8 10042800 62837.8
19:22:40.155 INFO ProgressMeter - chr17:40652065 160.0 10047380 62800.6
19:22:50.157 INFO ProgressMeter - chr17:41446080 160.2 10050870 62757.1
19:23:00.386 INFO ProgressMeter - chr17:42427695 160.3 10055230 62717.5
19:23:11.315 INFO ProgressMeter - chr17:45215874 160.5 10066140 62714.3
19:23:21.316 INFO ProgressMeter - chr17:46860176 160.7 10073190 62693.1
19:23:31.319 INFO ProgressMeter - chr17:48438826 160.8 10080120 62671.2
19:23:41.327 INFO ProgressMeter - chr17:51098305 161.0 10090760 62672.4
19:23:51.334 INFO ProgressMeter - chr17:55165608 161.2 10106400 62704.6
19:24:01.349 INFO ProgressMeter - chr17:57735180 161.3 10116720 62703.7
19:24:11.349 INFO ProgressMeter - chr17:60379420 161.5 10127080 62703.1
19:24:21.350 INFO ProgressMeter - chr17:62360728 161.7 10134960 62687.2
19:24:31.360 INFO ProgressMeter - chr17:64811465 161.8 10145040 62684.9
19:24:41.369 INFO ProgressMeter - chr17:66879916 162.0 10153870 62674.8
19:24:51.374 INFO ProgressMeter - chr17:70561148 162.2 10168270 62699.2
19:25:01.382 INFO ProgressMeter - chr17:72391446 162.3 10176290 62684.2
19:25:11.429 INFO ProgressMeter - chr17:73570532 162.5 10181780 62653.3
19:25:21.441 INFO ProgressMeter - chr17:74392504 162.7 10185630 62612.7
19:25:31.444 INFO ProgressMeter - chr17:75789925 162.8 10192160 62588.7
19:25:41.445 INFO ProgressMeter - chr17:76915458 163.0 10197370 62556.7
19:25:51.457 INFO ProgressMeter - chr17:78305482 163.2 10203750 62531.8
19:26:01.459 INFO ProgressMeter - chr17:79583306 163.3 10209480 62503.1
19:26:11.473 INFO ProgressMeter - chr17:80615823 163.5 10214150 62467.9
19:26:21.478 INFO ProgressMeter - chr18:447406 163.7 10218740 62432.3
19:26:31.556 INFO ProgressMeter - chr18:2891810 163.8 10228800 62429.7
19:26:41.556 INFO ProgressMeter - chr18:5573400 164.0 10239690 62432.6
19:26:51.559 INFO ProgressMeter - chr18:8560383 164.2 10251700 62442.4
19:27:01.562 INFO ProgressMeter - chr18:10739799 164.3 10260940 62435.3
19:27:11.569 INFO ProgressMeter - chr18:12952076 164.5 10270290 62428.8
19:27:21.576 INFO ProgressMeter - chr18:15168930 164.7 10279470 62421.3
19:27:31.585 INFO ProgressMeter - chr18:19439517 164.8 10294450 62449.0
19:27:41.585 INFO ProgressMeter - chr18:22039561 165.0 10305030 62450.1
19:27:51.585 INFO ProgressMeter - chr18:26731362 165.2 10323150 62496.7
19:28:01.605 INFO ProgressMeter - chr18:30350635 165.3 10337060 62517.7
19:28:11.610 INFO ProgressMeter - chr18:34199238 165.5 10351770 62543.6
19:28:21.613 INFO ProgressMeter - chr18:39044693 165.7 10370520 62593.9
19:28:31.622 INFO ProgressMeter - chr18:43512522 165.8 10387680 62634.4
19:28:41.631 INFO ProgressMeter - chr18:46108511 166.0 10398380 62635.9
19:28:51.639 INFO ProgressMeter - chr18:48575426 166.2 10408650 62634.8
19:29:01.678 INFO ProgressMeter - chr18:52923238 166.3 10425570 62673.5
19:29:11.687 INFO ProgressMeter - chr18:56113190 166.5 10438310 62687.3
19:29:21.734 INFO ProgressMeter - chr18:59158103 166.7 10450530 62697.6
19:29:31.755 INFO ProgressMeter - chr18:61468123 166.8 10459970 62691.4
19:29:41.794 INFO ProgressMeter - chr18:66513578 167.0 10479310 62744.4
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20:04:18.686 INFO HaplotypeCaller - 3876943 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
13433 read(s) filtered by: NotSecondaryAlignmentReadFilter
6797272 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
9 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
10687657 total reads filtered
20:04:18.686 INFO ProgressMeter - chrUn_gl000249:36541 201.6 12360696 61303.6
20:04:18.686 INFO ProgressMeter - Traversal complete. Processed 12360696 total regions in 201.6 minutes.
20:04:18.815 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.817758861
20:04:18.815 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 1282.577164556
20:04:18.815 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1958.63 sec
20:04:18.816 INFO HaplotypeCaller - Shutting down engine
[April 11, 2022 8:04:18 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 201.65 minutes.
Runtime.totalMemory()=1267204096
/var/spool/slurmd/job42730395/slurm_script: line 16: -ERC: command not found
-
Hi Ann W,
Thanks for trying out GATK! Thankfully, I think this error can be easily solved. It looks like it's just a small typo in your command line so that the -ERC line is read as a different command than part of the GATK command line.
Look for a small issue in your script, potentially a newline character or something else after the -O $HaplotypeCaller_dir/$tm.g.vcf.gz argument and before the -ERC GVCF argument.
Let me know if you have any other questions.
Best,
Genevieve
-
That was the issue! Thanks so much, Gen! For reference, here is the new bash script that worked.
#!/bin/bash
lee=/pine/scr/a/n/anndo1/Lee_NatureGenetics_2017_Germline
align_dir=$lee/bulk_align
HaplotypeCaller_dir=$lee/HaplotypeCallertm=blah_case_blah
module load gatk
gatk --java-options "-Xmx4g" HaplotypeCaller \
-R /proj/yuchaojlab/lib/ucsc.hg19.fasta \
-I $align_dir/*$tm.sorted.rg.dedup.realigned.recal.bam \
-O $HaplotypeCaller_dir/$tm.g.vcf.gz \
-ERC GVCF -
Thank you for the update, glad it worked!
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