/Users/strigg/Desktop/20200416/20200416_CollectWgsMetrics.sh INFO 2020-04-17 08:29:19 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 08:29:19.880 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 08:29:19 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 08:29:19 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 08:29:28 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 8s. Last read position: 4:2,571,827 INFO 2020-04-17 08:29:36 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:16s. Time for last 10,000,000: 8s. Last read position: 9:2,185,583 INFO 2020-04-17 08:29:43 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 7s. Last read position: 15:1,277,111 INFO 2020-04-17 08:29:51 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:31s. Time for last 10,000,000: 7s. Last read position: 20:430,949 INFO 2020-04-17 08:29:58 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 7s. Last read position: 26:192,822 INFO 2020-04-17 08:30:06 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 8s. Last read position: 31:1,345,614 INFO 2020-04-17 08:30:14 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:54s. Time for last 10,000,000: 7s. Last read position: 37:1,212,527 INFO 2020-04-17 08:30:22 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 7s. Last read position: 44:228,145 INFO 2020-04-17 08:30:29 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:01:09s. Time for last 10,000,000: 6s. Last read position: 50:1,133,273 INFO 2020-04-17 08:30:36 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:01:16s. Time for last 10,000,000: 7s. Last read position: 57:1,126,989 INFO 2020-04-17 08:30:43 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:01:23s. Time for last 10,000,000: 7s. Last read position: 64:1,029,276 INFO 2020-04-17 08:30:51 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:01:31s. Time for last 10,000,000: 7s. Last read position: 72:202,919 INFO 2020-04-17 08:30:58 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:39s. Time for last 10,000,000: 7s. Last read position: 80:1,003,826 INFO 2020-04-17 08:31:06 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:46s. Time for last 10,000,000: 7s. Last read position: 88:693,929 INFO 2020-04-17 08:31:13 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:53s. Time for last 10,000,000: 7s. Last read position: 97:654,820 INFO 2020-04-17 08:31:21 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 7s. Last read position: 106:954,050 INFO 2020-04-17 08:31:28 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 7s. Last read position: 115:314,973 INFO 2020-04-17 08:31:35 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 7s. Last read position: 124:300,378 INFO 2020-04-17 08:31:43 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:02:23s. Time for last 10,000,000: 7s. Last read position: 134:346,484 INFO 2020-04-17 08:31:50 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:30s. Time for last 10,000,000: 7s. Last read position: 143:937,913 INFO 2020-04-17 08:31:56 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:36s. Time for last 10,000,000: 6s. Last read position: 154:196,816 INFO 2020-04-17 08:32:03 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:43s. Time for last 10,000,000: 7s. Last read position: 164:946,097 INFO 2020-04-17 08:32:10 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:50s. Time for last 10,000,000: 7s. Last read position: 176:142,662 INFO 2020-04-17 08:32:18 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:58s. Time for last 10,000,000: 7s. Last read position: 186:787,532 INFO 2020-04-17 08:32:25 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 6s. Last read position: 197:551,543 INFO 2020-04-17 08:32:32 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:03:12s. Time for last 10,000,000: 6s. Last read position: 210:166,366 INFO 2020-04-17 08:32:39 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 6s. Last read position: 221:702,430 INFO 2020-04-17 08:32:46 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 6s. Last read position: 234:821,523 INFO 2020-04-17 08:32:52 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:32s. Time for last 10,000,000: 6s. Last read position: 247:449,458 INFO 2020-04-17 08:32:59 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 6s. Last read position: 259:701,369 INFO 2020-04-17 08:33:06 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:46s. Time for last 10,000,000: 6s. Last read position: 273:137,205 INFO 2020-04-17 08:33:12 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:53s. Time for last 10,000,000: 6s. Last read position: 287:177,113 INFO 2020-04-17 08:33:19 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 6s. Last read position: 300:416,946 INFO 2020-04-17 08:33:26 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:04:06s. Time for last 10,000,000: 6s. Last read position: 314:424,834 INFO 2020-04-17 08:33:32 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:04:12s. Time for last 10,000,000: 6s. Last read position: 330:127 INFO 2020-04-17 08:33:39 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 6s. Last read position: 344:423,663 INFO 2020-04-17 08:33:45 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 6s. Last read position: 359:634,934 INFO 2020-04-17 08:33:52 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:04:32s. Time for last 10,000,000: 6s. Last read position: 377:83,616 INFO 2020-04-17 08:33:58 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:04:38s. Time for last 10,000,000: 6s. Last read position: 392:532,908 INFO 2020-04-17 08:34:05 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:04:45s. Time for last 10,000,000: 6s. Last read position: 409:150,400 INFO 2020-04-17 08:34:12 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:04:52s. Time for last 10,000,000: 7s. Last read position: 426:510,191 INFO 2020-04-17 08:34:18 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:04:58s. Time for last 10,000,000: 6s. Last read position: 444:356,488 INFO 2020-04-17 08:34:25 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:05:05s. Time for last 10,000,000: 7s. Last read position: 462:132,483 INFO 2020-04-17 08:34:32 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:05:12s. Time for last 10,000,000: 6s. Last read position: 480:476,684 INFO 2020-04-17 08:34:38 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:05:18s. Time for last 10,000,000: 6s. Last read position: 499:472,487 INFO 2020-04-17 08:34:45 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:05:25s. Time for last 10,000,000: 6s. Last read position: 520:167,314 INFO 2020-04-17 08:34:52 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:05:32s. Time for last 10,000,000: 6s. Last read position: 541:218,900 INFO 2020-04-17 08:34:58 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:05:38s. Time for last 10,000,000: 6s. Last read position: 561:89,787 INFO 2020-04-17 08:35:04 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:05:44s. Time for last 10,000,000: 5s. Last read position: 581:275,897 INFO 2020-04-17 08:35:10 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:05:50s. Time for last 10,000,000: 5s. Last read position: 605:50,138 INFO 2020-04-17 08:35:16 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:05:56s. Time for last 10,000,000: 6s. Last read position: 626:305,229 INFO 2020-04-17 08:35:23 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:06:03s. Time for last 10,000,000: 6s. Last read position: 648:244,080 INFO 2020-04-17 08:35:29 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:06:09s. Time for last 10,000,000: 6s. Last read position: 671:195,673 INFO 2020-04-17 08:35:35 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:06:15s. Time for last 10,000,000: 6s. Last read position: 695:85,112 INFO 2020-04-17 08:35:41 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:06:21s. Time for last 10,000,000: 5s. Last read position: 720:113,488 INFO 2020-04-17 08:35:47 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:06:27s. Time for last 10,000,000: 6s. Last read position: 748:34,007 INFO 2020-04-17 08:35:53 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:06:34s. Time for last 10,000,000: 6s. Last read position: 774:112,571 INFO 2020-04-17 08:36:00 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:06:40s. Time for last 10,000,000: 6s. Last read position: 801:129,443 INFO 2020-04-17 08:36:05 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:06:46s. Time for last 10,000,000: 5s. Last read position: 830:46,237 INFO 2020-04-17 08:36:11 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:06:51s. Time for last 10,000,000: 5s. Last read position: 858:343,631 INFO 2020-04-17 08:36:17 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:06:57s. Time for last 10,000,000: 5s. Last read position: 888:3,547 INFO 2020-04-17 08:36:23 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:07:03s. Time for last 10,000,000: 5s. Last read position: 918:326,056 INFO 2020-04-17 08:36:28 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:07:08s. Time for last 10,000,000: 5s. Last read position: 951:37,914 INFO 2020-04-17 08:36:33 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:07:13s. Time for last 10,000,000: 5s. Last read position: 984:126,977 INFO 2020-04-17 08:36:39 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:07:19s. Time for last 10,000,000: 5s. Last read position: 1017:167,455 INFO 2020-04-17 08:36:44 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:07:24s. Time for last 10,000,000: 4s. Last read position: 1052:230,503 INFO 2020-04-17 08:36:49 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:07:29s. Time for last 10,000,000: 5s. Last read position: 1090:74,736 INFO 2020-04-17 08:36:55 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:07:35s. Time for last 10,000,000: 5s. Last read position: 1128:19,199 INFO 2020-04-17 08:37:00 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:07:40s. Time for last 10,000,000: 5s. Last read position: 1168:8,743 INFO 2020-04-17 08:37:05 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:07:45s. Time for last 10,000,000: 5s. Last read position: 1210:48,462 INFO 2020-04-17 08:37:11 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:07:51s. Time for last 10,000,000: 5s. Last read position: 1252:73,681 INFO 2020-04-17 08:37:15 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:07:56s. Time for last 10,000,000: 4s. Last read position: 1298:135,654 INFO 2020-04-17 08:37:21 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:08:01s. Time for last 10,000,000: 5s. Last read position: 1347:42,922 INFO 2020-04-17 08:37:26 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:08:06s. Time for last 10,000,000: 5s. Last read position: 1397:45,967 INFO 2020-04-17 08:37:31 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:08:11s. Time for last 10,000,000: 4s. Last read position: 1450:5,557 INFO 2020-04-17 08:37:36 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:08:16s. Time for last 10,000,000: 4s. Last read position: 1505:129,718 INFO 2020-04-17 08:37:40 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:08:21s. Time for last 10,000,000: 4s. Last read position: 1568:3,714 INFO 2020-04-17 08:37:45 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:08:25s. Time for last 10,000,000: 4s. Last read position: 1631:39,335 INFO 2020-04-17 08:37:50 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:08:30s. Time for last 10,000,000: 4s. Last read position: 1698:107,239 INFO 2020-04-17 08:37:55 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:08:35s. Time for last 10,000,000: 4s. Last read position: 1774:115,449 INFO 2020-04-17 08:37:59 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:08:39s. Time for last 10,000,000: 4s. Last read position: 1853:95,173 INFO 2020-04-17 08:38:03 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:08:44s. Time for last 10,000,000: 4s. Last read position: 1942:62,123 INFO 2020-04-17 08:38:08 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:08:48s. Time for last 10,000,000: 4s. Last read position: 2039:16,006 INFO 2020-04-17 08:38:12 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:08:52s. Time for last 10,000,000: 4s. Last read position: 2147:65,939 INFO 2020-04-17 08:38:16 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:08:56s. Time for last 10,000,000: 4s. Last read position: 2269:65,204 INFO 2020-04-17 08:38:21 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:09:01s. Time for last 10,000,000: 4s. Last read position: 2409:16,999 INFO 2020-04-17 08:38:25 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:09:05s. Time for last 10,000,000: 3s. Last read position: 2580:1,672 INFO 2020-04-17 08:38:28 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:09:08s. Time for last 10,000,000: 3s. Last read position: 2825:574 INFO 2020-04-17 08:38:30 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 08:38:30 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 08:38:30 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 08:38:32 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 08:38:34 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 08:38:36 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 08:38:37 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 08:38:39 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 08:38:41 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 08:38:42 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 08:38:44 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 08:38:46 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 08:38:47 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 08:38:48 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 9.48 minutes. Runtime.totalMemory()=805306368 INFO 2020-04-17 08:38:49 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 08:38:49.988 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 08:38:50 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 08:38:50 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 08:38:59 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:09s. Time for last 10,000,000: 8s. Last read position: 4:2,571,827 INFO 2020-04-17 08:39:06 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:16s. Time for last 10,000,000: 7s. Last read position: 9:2,185,583 INFO 2020-04-17 08:39:13 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 7s. Last read position: 15:1,277,111 INFO 2020-04-17 08:39:20 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:30s. Time for last 10,000,000: 7s. Last read position: 20:430,949 INFO 2020-04-17 08:39:28 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 7s. Last read position: 26:192,822 INFO 2020-04-17 08:39:36 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 7s. Last read position: 31:1,345,614 INFO 2020-04-17 08:39:43 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:53s. Time for last 10,000,000: 6s. Last read position: 37:1,212,527 INFO 2020-04-17 08:39:50 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 7s. Last read position: 44:228,145 INFO 2020-04-17 08:39:57 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:01:07s. Time for last 10,000,000: 6s. Last read position: 50:1,133,273 INFO 2020-04-17 08:40:04 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 7s. Last read position: 57:1,126,989 INFO 2020-04-17 08:40:11 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:01:21s. Time for last 10,000,000: 7s. Last read position: 64:1,029,276 INFO 2020-04-17 08:40:18 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:01:28s. Time for last 10,000,000: 7s. Last read position: 72:202,919 INFO 2020-04-17 08:40:26 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:36s. Time for last 10,000,000: 7s. Last read position: 80:1,003,826 INFO 2020-04-17 08:40:33 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:43s. Time for last 10,000,000: 7s. Last read position: 88:693,929 INFO 2020-04-17 08:40:40 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 6s. Last read position: 97:654,820 INFO 2020-04-17 08:40:48 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 7s. Last read position: 106:954,050 INFO 2020-04-17 08:40:55 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 7s. Last read position: 115:314,973 INFO 2020-04-17 08:41:02 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:12s. Time for last 10,000,000: 6s. Last read position: 124:300,378 INFO 2020-04-17 08:41:09 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:02:19s. Time for last 10,000,000: 7s. Last read position: 134:346,484 INFO 2020-04-17 08:41:16 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 7s. Last read position: 143:937,913 INFO 2020-04-17 08:41:22 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:32s. Time for last 10,000,000: 6s. Last read position: 154:196,816 INFO 2020-04-17 08:41:29 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:39s. Time for last 10,000,000: 6s. Last read position: 164:946,097 INFO 2020-04-17 08:41:36 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:46s. Time for last 10,000,000: 6s. Last read position: 176:142,662 INFO 2020-04-17 08:41:43 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:53s. Time for last 10,000,000: 7s. Last read position: 186:787,532 INFO 2020-04-17 08:41:50 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 7s. Last read position: 197:551,543 INFO 2020-04-17 08:41:57 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:03:07s. Time for last 10,000,000: 6s. Last read position: 210:166,366 INFO 2020-04-17 08:42:04 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 6s. Last read position: 221:702,430 INFO 2020-04-17 08:42:10 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 6s. Last read position: 234:821,523 INFO 2020-04-17 08:42:16 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 5s. Last read position: 247:449,458 INFO 2020-04-17 08:42:23 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:33s. Time for last 10,000,000: 6s. Last read position: 259:701,369 INFO 2020-04-17 08:42:29 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 6s. Last read position: 273:137,205 INFO 2020-04-17 08:42:36 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:46s. Time for last 10,000,000: 6s. Last read position: 287:177,113 INFO 2020-04-17 08:42:42 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 6s. Last read position: 300:416,946 INFO 2020-04-17 08:42:49 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 6s. Last read position: 314:424,834 INFO 2020-04-17 08:42:55 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:04:05s. Time for last 10,000,000: 6s. Last read position: 330:127 INFO 2020-04-17 08:43:01 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 6s. Last read position: 344:423,663 INFO 2020-04-17 08:43:08 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:04:18s. Time for last 10,000,000: 6s. Last read position: 359:634,934 INFO 2020-04-17 08:43:14 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 5s. Last read position: 377:83,616 INFO 2020-04-17 08:43:20 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:04:30s. Time for last 10,000,000: 6s. Last read position: 392:532,908 INFO 2020-04-17 08:43:26 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:04:36s. Time for last 10,000,000: 6s. Last read position: 409:150,400 INFO 2020-04-17 08:43:33 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:04:43s. Time for last 10,000,000: 6s. Last read position: 426:510,191 INFO 2020-04-17 08:43:39 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:04:49s. Time for last 10,000,000: 6s. Last read position: 444:356,488 INFO 2020-04-17 08:43:46 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:04:56s. Time for last 10,000,000: 6s. Last read position: 462:132,483 INFO 2020-04-17 08:43:52 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:05:02s. Time for last 10,000,000: 5s. Last read position: 480:476,684 INFO 2020-04-17 08:43:58 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:05:08s. Time for last 10,000,000: 6s. Last read position: 499:472,487 INFO 2020-04-17 08:44:04 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:05:14s. Time for last 10,000,000: 6s. Last read position: 520:167,314 INFO 2020-04-17 08:44:10 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:05:20s. Time for last 10,000,000: 6s. Last read position: 541:218,900 INFO 2020-04-17 08:44:17 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:05:27s. Time for last 10,000,000: 6s. Last read position: 561:89,787 INFO 2020-04-17 08:44:23 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:05:33s. Time for last 10,000,000: 5s. Last read position: 581:275,897 INFO 2020-04-17 08:44:29 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:05:39s. Time for last 10,000,000: 6s. Last read position: 605:50,138 INFO 2020-04-17 08:44:35 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 6s. Last read position: 626:305,229 INFO 2020-04-17 08:44:41 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:05:51s. Time for last 10,000,000: 6s. Last read position: 648:244,080 INFO 2020-04-17 08:44:47 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:05:57s. Time for last 10,000,000: 5s. Last read position: 671:195,673 INFO 2020-04-17 08:44:53 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:06:03s. Time for last 10,000,000: 6s. Last read position: 695:85,112 INFO 2020-04-17 08:44:59 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:06:09s. Time for last 10,000,000: 5s. Last read position: 720:113,488 INFO 2020-04-17 08:45:05 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:06:15s. Time for last 10,000,000: 6s. Last read position: 748:34,007 INFO 2020-04-17 08:45:11 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:06:21s. Time for last 10,000,000: 5s. Last read position: 774:112,571 INFO 2020-04-17 08:45:16 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:06:26s. Time for last 10,000,000: 5s. Last read position: 801:129,443 INFO 2020-04-17 08:45:22 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:06:32s. Time for last 10,000,000: 5s. Last read position: 830:46,237 INFO 2020-04-17 08:45:27 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:06:37s. Time for last 10,000,000: 4s. Last read position: 858:343,631 INFO 2020-04-17 08:45:32 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:06:42s. Time for last 10,000,000: 5s. Last read position: 888:3,547 INFO 2020-04-17 08:45:38 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:06:48s. Time for last 10,000,000: 5s. Last read position: 918:326,056 INFO 2020-04-17 08:45:44 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:06:54s. Time for last 10,000,000: 5s. Last read position: 951:37,914 INFO 2020-04-17 08:45:49 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:06:59s. Time for last 10,000,000: 5s. Last read position: 984:126,977 INFO 2020-04-17 08:45:54 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:07:04s. Time for last 10,000,000: 5s. Last read position: 1017:167,455 INFO 2020-04-17 08:45:59 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:07:09s. Time for last 10,000,000: 4s. Last read position: 1052:230,503 INFO 2020-04-17 08:46:04 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:07:14s. Time for last 10,000,000: 5s. Last read position: 1090:74,736 INFO 2020-04-17 08:46:09 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:07:19s. Time for last 10,000,000: 5s. Last read position: 1128:19,199 INFO 2020-04-17 08:46:15 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:07:25s. Time for last 10,000,000: 5s. Last read position: 1168:8,743 INFO 2020-04-17 08:46:20 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:07:30s. Time for last 10,000,000: 5s. Last read position: 1210:48,462 INFO 2020-04-17 08:46:25 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:07:35s. Time for last 10,000,000: 5s. Last read position: 1252:73,681 INFO 2020-04-17 08:46:30 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:07:40s. Time for last 10,000,000: 4s. Last read position: 1298:135,654 INFO 2020-04-17 08:46:35 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:07:45s. Time for last 10,000,000: 5s. Last read position: 1347:42,922 INFO 2020-04-17 08:46:40 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:07:50s. Time for last 10,000,000: 4s. Last read position: 1397:45,967 INFO 2020-04-17 08:46:45 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:07:55s. Time for last 10,000,000: 4s. Last read position: 1450:5,557 INFO 2020-04-17 08:46:49 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:07:59s. Time for last 10,000,000: 4s. Last read position: 1505:129,718 INFO 2020-04-17 08:46:54 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:08:04s. Time for last 10,000,000: 4s. Last read position: 1568:3,714 INFO 2020-04-17 08:46:58 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:08:08s. Time for last 10,000,000: 4s. Last read position: 1631:39,335 INFO 2020-04-17 08:47:03 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:08:13s. Time for last 10,000,000: 4s. Last read position: 1698:107,239 INFO 2020-04-17 08:47:07 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:08:17s. Time for last 10,000,000: 4s. Last read position: 1774:115,449 INFO 2020-04-17 08:47:11 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:08:21s. Time for last 10,000,000: 4s. Last read position: 1853:95,173 INFO 2020-04-17 08:47:15 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:08:25s. Time for last 10,000,000: 4s. Last read position: 1942:62,123 INFO 2020-04-17 08:47:19 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:08:29s. Time for last 10,000,000: 4s. Last read position: 2039:16,006 INFO 2020-04-17 08:47:24 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:08:34s. Time for last 10,000,000: 4s. Last read position: 2147:65,939 INFO 2020-04-17 08:47:28 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:08:38s. Time for last 10,000,000: 4s. Last read position: 2269:65,204 INFO 2020-04-17 08:47:32 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:08:42s. Time for last 10,000,000: 4s. Last read position: 2409:16,999 INFO 2020-04-17 08:47:35 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:08:45s. Time for last 10,000,000: 3s. Last read position: 2580:1,672 INFO 2020-04-17 08:47:39 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:08:49s. Time for last 10,000,000: 3s. Last read position: 2825:574 INFO 2020-04-17 08:47:41 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 08:47:41 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 08:47:41 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 08:47:43 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 08:47:44 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 08:47:46 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 08:47:48 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 08:47:49 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 08:47:51 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 08:47:53 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 08:47:54 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 08:47:56 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 08:47:58 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 08:47:59 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 9.15 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-17 08:47:59 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 08:48:00.491 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 08:48:00 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 08:48:00 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 08:48:12 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 11s. Last read position: 4:2,571,827 INFO 2020-04-17 08:48:22 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 10s. Last read position: 9:2,185,583 INFO 2020-04-17 08:48:32 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:31s. Time for last 10,000,000: 9s. Last read position: 15:1,277,111 INFO 2020-04-17 08:48:41 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:40s. Time for last 10,000,000: 9s. Last read position: 20:430,949 INFO 2020-04-17 08:48:50 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:50s. Time for last 10,000,000: 9s. Last read position: 26:192,822 INFO 2020-04-17 08:49:01 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 10s. Last read position: 31:1,345,614 INFO 2020-04-17 08:49:10 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:01:10s. Time for last 10,000,000: 9s. Last read position: 37:1,212,527 INFO 2020-04-17 08:49:20 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:20s. Time for last 10,000,000: 9s. Last read position: 44:228,145 INFO 2020-04-17 08:49:29 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 8s. Last read position: 50:1,133,273 INFO 2020-04-17 08:49:39 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 9s. Last read position: 57:1,126,989 INFO 2020-04-17 08:49:48 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:01:48s. Time for last 10,000,000: 9s. Last read position: 64:1,029,276 INFO 2020-04-17 08:49:57 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:01:57s. Time for last 10,000,000: 9s. Last read position: 72:202,919 INFO 2020-04-17 08:50:08 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:02:07s. Time for last 10,000,000: 10s. Last read position: 80:1,003,826 INFO 2020-04-17 08:50:18 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 10s. Last read position: 88:693,929 INFO 2020-04-17 08:50:28 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:02:27s. Time for last 10,000,000: 9s. Last read position: 97:654,820 INFO 2020-04-17 08:50:39 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:02:38s. Time for last 10,000,000: 10s. Last read position: 106:954,050 INFO 2020-04-17 08:50:47 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:47s. Time for last 10,000,000: 8s. Last read position: 115:314,973 INFO 2020-04-17 08:50:57 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 9s. Last read position: 124:300,378 INFO 2020-04-17 08:51:06 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 9s. Last read position: 134:346,484 INFO 2020-04-17 08:51:16 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:03:15s. Time for last 10,000,000: 9s. Last read position: 143:937,913 INFO 2020-04-17 08:51:24 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 7s. Last read position: 154:196,816 INFO 2020-04-17 08:51:32 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:03:32s. Time for last 10,000,000: 8s. Last read position: 164:946,097 INFO 2020-04-17 08:51:41 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:03:41s. Time for last 10,000,000: 8s. Last read position: 176:142,662 INFO 2020-04-17 08:51:51 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:03:50s. Time for last 10,000,000: 9s. Last read position: 186:787,532 INFO 2020-04-17 08:52:00 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 9s. Last read position: 197:551,543 INFO 2020-04-17 08:52:09 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:04:09s. Time for last 10,000,000: 9s. Last read position: 210:166,366 INFO 2020-04-17 08:52:18 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:04:18s. Time for last 10,000,000: 9s. Last read position: 221:702,430 INFO 2020-04-17 08:52:27 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:04:27s. Time for last 10,000,000: 9s. Last read position: 234:821,523 INFO 2020-04-17 08:52:36 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:04:35s. Time for last 10,000,000: 8s. Last read position: 247:449,458 INFO 2020-04-17 08:52:45 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 8s. Last read position: 259:701,369 INFO 2020-04-17 08:52:54 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:04:53s. Time for last 10,000,000: 9s. Last read position: 273:137,205 INFO 2020-04-17 08:53:02 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:05:02s. Time for last 10,000,000: 8s. Last read position: 287:177,113 INFO 2020-04-17 08:53:11 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:05:11s. Time for last 10,000,000: 8s. Last read position: 300:416,946 INFO 2020-04-17 08:53:20 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:05:19s. Time for last 10,000,000: 8s. Last read position: 314:424,834 INFO 2020-04-17 08:53:28 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:05:28s. Time for last 10,000,000: 8s. Last read position: 330:127 INFO 2020-04-17 08:53:37 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:05:36s. Time for last 10,000,000: 8s. Last read position: 344:423,663 INFO 2020-04-17 08:53:45 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 8s. Last read position: 359:634,934 INFO 2020-04-17 08:53:53 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:05:53s. Time for last 10,000,000: 7s. Last read position: 377:83,616 INFO 2020-04-17 08:54:01 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:06:01s. Time for last 10,000,000: 7s. Last read position: 392:532,908 INFO 2020-04-17 08:54:10 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:06:09s. Time for last 10,000,000: 8s. Last read position: 409:150,400 INFO 2020-04-17 08:54:19 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:06:18s. Time for last 10,000,000: 8s. Last read position: 426:510,191 INFO 2020-04-17 08:54:27 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:06:26s. Time for last 10,000,000: 8s. Last read position: 444:356,488 INFO 2020-04-17 08:54:35 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:06:35s. Time for last 10,000,000: 8s. Last read position: 462:132,483 INFO 2020-04-17 08:54:43 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:06:42s. Time for last 10,000,000: 7s. Last read position: 480:476,684 INFO 2020-04-17 08:54:51 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:06:50s. Time for last 10,000,000: 8s. Last read position: 499:472,487 INFO 2020-04-17 08:54:59 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:06:58s. Time for last 10,000,000: 7s. Last read position: 520:167,314 INFO 2020-04-17 08:55:07 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:07:07s. Time for last 10,000,000: 8s. Last read position: 541:218,900 INFO 2020-04-17 08:55:15 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:07:15s. Time for last 10,000,000: 8s. Last read position: 561:89,787 INFO 2020-04-17 08:55:23 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:07:22s. Time for last 10,000,000: 7s. Last read position: 581:275,897 INFO 2020-04-17 08:55:30 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:07:30s. Time for last 10,000,000: 7s. Last read position: 605:50,138 INFO 2020-04-17 08:55:38 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:07:37s. Time for last 10,000,000: 7s. Last read position: 626:305,229 INFO 2020-04-17 08:55:46 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:07:45s. Time for last 10,000,000: 7s. Last read position: 648:244,080 INFO 2020-04-17 08:55:53 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:07:53s. Time for last 10,000,000: 7s. Last read position: 671:195,673 INFO 2020-04-17 08:56:01 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:08:00s. Time for last 10,000,000: 7s. Last read position: 695:85,112 INFO 2020-04-17 08:56:08 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:08:08s. Time for last 10,000,000: 7s. Last read position: 720:113,488 INFO 2020-04-17 08:56:16 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:08:15s. Time for last 10,000,000: 7s. Last read position: 748:34,007 INFO 2020-04-17 08:56:24 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:08:23s. Time for last 10,000,000: 7s. Last read position: 774:112,571 INFO 2020-04-17 08:56:31 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:08:31s. Time for last 10,000,000: 7s. Last read position: 801:129,443 INFO 2020-04-17 08:56:38 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:08:38s. Time for last 10,000,000: 7s. Last read position: 830:46,237 INFO 2020-04-17 08:56:45 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:08:44s. Time for last 10,000,000: 6s. Last read position: 858:343,631 INFO 2020-04-17 08:56:52 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:08:51s. Time for last 10,000,000: 7s. Last read position: 888:3,547 INFO 2020-04-17 08:56:59 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:08:59s. Time for last 10,000,000: 7s. Last read position: 918:326,056 INFO 2020-04-17 08:57:05 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:09:05s. Time for last 10,000,000: 6s. Last read position: 951:37,914 INFO 2020-04-17 08:57:12 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:09:12s. Time for last 10,000,000: 6s. Last read position: 984:126,977 INFO 2020-04-17 08:57:19 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:09:19s. Time for last 10,000,000: 7s. Last read position: 1017:167,455 INFO 2020-04-17 08:57:25 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:09:24s. Time for last 10,000,000: 5s. Last read position: 1052:230,503 INFO 2020-04-17 08:57:32 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:09:31s. Time for last 10,000,000: 6s. Last read position: 1090:74,736 INFO 2020-04-17 08:57:39 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:09:38s. Time for last 10,000,000: 7s. Last read position: 1128:19,199 INFO 2020-04-17 08:57:46 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:09:45s. Time for last 10,000,000: 6s. Last read position: 1168:8,743 INFO 2020-04-17 08:57:52 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:09:51s. Time for last 10,000,000: 6s. Last read position: 1210:48,462 INFO 2020-04-17 08:57:59 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:09:58s. Time for last 10,000,000: 6s. Last read position: 1252:73,681 INFO 2020-04-17 08:58:04 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:10:04s. Time for last 10,000,000: 5s. Last read position: 1298:135,654 INFO 2020-04-17 08:58:11 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:10:10s. Time for last 10,000,000: 6s. Last read position: 1347:42,922 INFO 2020-04-17 08:58:17 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:10:16s. Time for last 10,000,000: 5s. Last read position: 1397:45,967 INFO 2020-04-17 08:58:23 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:10:23s. Time for last 10,000,000: 6s. Last read position: 1450:5,557 INFO 2020-04-17 08:58:29 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:10:28s. Time for last 10,000,000: 5s. Last read position: 1505:129,718 INFO 2020-04-17 08:58:34 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:10:34s. Time for last 10,000,000: 5s. Last read position: 1568:3,714 INFO 2020-04-17 08:58:40 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:10:39s. Time for last 10,000,000: 5s. Last read position: 1631:39,335 INFO 2020-04-17 08:58:45 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:10:45s. Time for last 10,000,000: 5s. Last read position: 1698:107,239 INFO 2020-04-17 08:58:51 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:10:50s. Time for last 10,000,000: 5s. Last read position: 1774:115,449 INFO 2020-04-17 08:58:56 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:10:56s. Time for last 10,000,000: 5s. Last read position: 1853:95,173 INFO 2020-04-17 08:59:01 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:11:01s. Time for last 10,000,000: 4s. Last read position: 1942:62,123 INFO 2020-04-17 08:59:06 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:11:06s. Time for last 10,000,000: 5s. Last read position: 2039:16,006 INFO 2020-04-17 08:59:12 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:11:11s. Time for last 10,000,000: 5s. Last read position: 2147:65,939 INFO 2020-04-17 08:59:17 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:11:16s. Time for last 10,000,000: 5s. Last read position: 2269:65,204 INFO 2020-04-17 08:59:22 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:11:21s. Time for last 10,000,000: 5s. Last read position: 2409:16,999 INFO 2020-04-17 08:59:26 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:11:26s. Time for last 10,000,000: 4s. Last read position: 2580:1,672 INFO 2020-04-17 08:59:30 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:11:30s. Time for last 10,000,000: 4s. Last read position: 2825:574 INFO 2020-04-17 08:59:33 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 08:59:33 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 08:59:33 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 08:59:34 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 08:59:36 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 08:59:38 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 08:59:39 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 08:59:41 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 08:59:43 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 08:59:45 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 08:59:46 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 08:59:48 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 08:59:50 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 08:59:50 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 11.84 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-17 08:59:51 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 08:59:52.212 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 08:59:52 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 08:59:52 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 09:00:22 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 29s. Last read position: 4:2,571,827 INFO 2020-04-17 09:00:54 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 32s. Last read position: 9:2,185,583 INFO 2020-04-17 09:01:22 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:01:30s. Time for last 10,000,000: 28s. Last read position: 15:1,277,111 INFO 2020-04-17 09:01:52 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:02:00s. Time for last 10,000,000: 29s. Last read position: 20:430,949 INFO 2020-04-17 09:02:20 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:02:28s. Time for last 10,000,000: 28s. Last read position: 26:192,822 INFO 2020-04-17 09:02:52 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 31s. Last read position: 31:1,345,614 INFO 2020-04-17 09:03:18 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 26s. Last read position: 37:1,212,527 INFO 2020-04-17 09:03:47 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:03:55s. Time for last 10,000,000: 29s. Last read position: 44:228,145 INFO 2020-04-17 09:04:15 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:04:23s. Time for last 10,000,000: 27s. Last read position: 50:1,133,273 INFO 2020-04-17 09:04:45 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:04:53s. Time for last 10,000,000: 30s. Last read position: 57:1,126,989 INFO 2020-04-17 09:05:16 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:05:24s. Time for last 10,000,000: 30s. Last read position: 64:1,029,276 INFO 2020-04-17 09:05:42 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:05:50s. Time for last 10,000,000: 25s. Last read position: 72:202,919 INFO 2020-04-17 09:06:13 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:06:21s. Time for last 10,000,000: 30s. Last read position: 80:1,003,826 INFO 2020-04-17 09:06:49 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:06:57s. Time for last 10,000,000: 36s. Last read position: 88:693,929 INFO 2020-04-17 09:07:16 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:07:23s. Time for last 10,000,000: 26s. Last read position: 97:654,820 INFO 2020-04-17 09:07:47 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:07:54s. Time for last 10,000,000: 31s. Last read position: 106:954,050 INFO 2020-04-17 09:08:11 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:08:19s. Time for last 10,000,000: 24s. Last read position: 115:314,973 INFO 2020-04-17 09:08:37 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:08:45s. Time for last 10,000,000: 25s. Last read position: 124:300,378 INFO 2020-04-17 09:09:08 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:09:16s. Time for last 10,000,000: 31s. Last read position: 134:346,484 INFO 2020-04-17 09:09:36 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:09:44s. Time for last 10,000,000: 27s. Last read position: 143:937,913 INFO 2020-04-17 09:09:59 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:10:07s. Time for last 10,000,000: 22s. Last read position: 154:196,816 INFO 2020-04-17 09:10:21 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:10:29s. Time for last 10,000,000: 22s. Last read position: 164:946,097 INFO 2020-04-17 09:10:46 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:10:54s. Time for last 10,000,000: 25s. Last read position: 176:142,662 INFO 2020-04-17 09:11:13 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:11:20s. Time for last 10,000,000: 26s. Last read position: 186:787,532 INFO 2020-04-17 09:11:38 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:11:46s. Time for last 10,000,000: 25s. Last read position: 197:551,543 INFO 2020-04-17 09:12:04 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:12:12s. Time for last 10,000,000: 26s. Last read position: 210:166,366 INFO 2020-04-17 09:12:29 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:12:36s. Time for last 10,000,000: 24s. Last read position: 221:702,430 INFO 2020-04-17 09:12:54 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:13:01s. Time for last 10,000,000: 24s. Last read position: 234:821,523 INFO 2020-04-17 09:13:17 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:13:25s. Time for last 10,000,000: 23s. Last read position: 247:449,458 INFO 2020-04-17 09:13:41 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:13:48s. Time for last 10,000,000: 23s. Last read position: 259:701,369 INFO 2020-04-17 09:14:08 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:14:15s. Time for last 10,000,000: 26s. Last read position: 273:137,205 INFO 2020-04-17 09:14:34 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:14:41s. Time for last 10,000,000: 25s. Last read position: 287:177,113 INFO 2020-04-17 09:14:58 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:15:06s. Time for last 10,000,000: 24s. Last read position: 300:416,946 INFO 2020-04-17 09:15:22 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:15:30s. Time for last 10,000,000: 24s. Last read position: 314:424,834 INFO 2020-04-17 09:15:45 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:15:53s. Time for last 10,000,000: 22s. Last read position: 330:127 INFO 2020-04-17 09:16:07 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:16:15s. Time for last 10,000,000: 22s. Last read position: 344:423,663 INFO 2020-04-17 09:16:34 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:16:42s. Time for last 10,000,000: 26s. Last read position: 359:634,934 INFO 2020-04-17 09:16:54 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:17:02s. Time for last 10,000,000: 20s. Last read position: 377:83,616 INFO 2020-04-17 09:17:15 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:17:23s. Time for last 10,000,000: 20s. Last read position: 392:532,908 INFO 2020-04-17 09:17:38 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:17:45s. Time for last 10,000,000: 22s. Last read position: 409:150,400 INFO 2020-04-17 09:18:04 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:18:11s. Time for last 10,000,000: 26s. Last read position: 426:510,191 INFO 2020-04-17 09:18:28 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:18:36s. Time for last 10,000,000: 24s. Last read position: 444:356,488 INFO 2020-04-17 09:18:54 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:19:01s. Time for last 10,000,000: 25s. Last read position: 462:132,483 INFO 2020-04-17 09:19:14 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:19:22s. Time for last 10,000,000: 20s. Last read position: 480:476,684 INFO 2020-04-17 09:19:35 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:19:43s. Time for last 10,000,000: 21s. Last read position: 499:472,487 INFO 2020-04-17 09:19:56 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:20:03s. Time for last 10,000,000: 20s. Last read position: 520:167,314 INFO 2020-04-17 09:20:21 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:20:29s. Time for last 10,000,000: 25s. Last read position: 541:218,900 INFO 2020-04-17 09:20:42 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:20:50s. Time for last 10,000,000: 21s. Last read position: 561:89,787 INFO 2020-04-17 09:21:01 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:21:09s. Time for last 10,000,000: 19s. Last read position: 581:275,897 INFO 2020-04-17 09:21:22 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:21:30s. Time for last 10,000,000: 20s. Last read position: 605:50,138 INFO 2020-04-17 09:21:42 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:21:50s. Time for last 10,000,000: 20s. Last read position: 626:305,229 INFO 2020-04-17 09:22:04 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:22:12s. Time for last 10,000,000: 22s. Last read position: 648:244,080 INFO 2020-04-17 09:22:23 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:22:30s. Time for last 10,000,000: 18s. Last read position: 671:195,673 INFO 2020-04-17 09:22:44 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:22:52s. Time for last 10,000,000: 21s. Last read position: 695:85,112 INFO 2020-04-17 09:23:02 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:23:10s. Time for last 10,000,000: 18s. Last read position: 720:113,488 INFO 2020-04-17 09:23:24 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:23:31s. Time for last 10,000,000: 21s. Last read position: 748:34,007 INFO 2020-04-17 09:23:48 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:23:56s. Time for last 10,000,000: 24s. Last read position: 774:112,571 INFO 2020-04-17 09:24:08 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:24:16s. Time for last 10,000,000: 20s. Last read position: 801:129,443 INFO 2020-04-17 09:24:27 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:24:35s. Time for last 10,000,000: 18s. Last read position: 830:46,237 INFO 2020-04-17 09:24:43 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:24:51s. Time for last 10,000,000: 16s. Last read position: 858:343,631 INFO 2020-04-17 09:25:02 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:25:09s. Time for last 10,000,000: 18s. Last read position: 888:3,547 INFO 2020-04-17 09:25:21 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:25:29s. Time for last 10,000,000: 19s. Last read position: 918:326,056 INFO 2020-04-17 09:25:39 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:25:46s. Time for last 10,000,000: 17s. Last read position: 951:37,914 INFO 2020-04-17 09:25:58 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:26:06s. Time for last 10,000,000: 19s. Last read position: 984:126,977 INFO 2020-04-17 09:26:18 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:26:26s. Time for last 10,000,000: 19s. Last read position: 1017:167,455 INFO 2020-04-17 09:26:33 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:26:41s. Time for last 10,000,000: 14s. Last read position: 1052:230,503 INFO 2020-04-17 09:26:50 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:26:57s. Time for last 10,000,000: 16s. Last read position: 1090:74,736 INFO 2020-04-17 09:27:10 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:27:17s. Time for last 10,000,000: 19s. Last read position: 1128:19,199 INFO 2020-04-17 09:27:28 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:27:35s. Time for last 10,000,000: 18s. Last read position: 1168:8,743 INFO 2020-04-17 09:27:44 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:27:52s. Time for last 10,000,000: 16s. Last read position: 1210:48,462 INFO 2020-04-17 09:28:10 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:28:18s. Time for last 10,000,000: 26s. Last read position: 1252:73,681 INFO 2020-04-17 09:28:25 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:28:32s. Time for last 10,000,000: 14s. Last read position: 1298:135,654 INFO 2020-04-17 09:28:42 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:28:50s. Time for last 10,000,000: 17s. Last read position: 1347:42,922 INFO 2020-04-17 09:28:57 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:29:05s. Time for last 10,000,000: 14s. Last read position: 1397:45,967 INFO 2020-04-17 09:29:14 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:29:22s. Time for last 10,000,000: 17s. Last read position: 1450:5,557 INFO 2020-04-17 09:29:29 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:29:37s. Time for last 10,000,000: 14s. Last read position: 1505:129,718 INFO 2020-04-17 09:29:42 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:29:50s. Time for last 10,000,000: 13s. Last read position: 1568:3,714 INFO 2020-04-17 09:29:56 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:30:03s. Time for last 10,000,000: 13s. Last read position: 1631:39,335 INFO 2020-04-17 09:30:08 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:30:16s. Time for last 10,000,000: 12s. Last read position: 1698:107,239 INFO 2020-04-17 09:30:22 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:30:30s. Time for last 10,000,000: 13s. Last read position: 1774:115,449 INFO 2020-04-17 09:30:34 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:30:42s. Time for last 10,000,000: 12s. Last read position: 1853:95,173 INFO 2020-04-17 09:30:46 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:30:54s. Time for last 10,000,000: 11s. Last read position: 1942:62,123 INFO 2020-04-17 09:31:00 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:31:08s. Time for last 10,000,000: 14s. Last read position: 2039:16,006 INFO 2020-04-17 09:31:11 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:31:19s. Time for last 10,000,000: 10s. Last read position: 2147:65,939 INFO 2020-04-17 09:31:24 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:31:32s. Time for last 10,000,000: 13s. Last read position: 2269:65,204 INFO 2020-04-17 09:31:46 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:31:53s. Time for last 10,000,000: 21s. Last read position: 2409:16,999 INFO 2020-04-17 09:31:55 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:32:03s. Time for last 10,000,000: 9s. Last read position: 2580:1,672 INFO 2020-04-17 09:32:04 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:32:12s. Time for last 10,000,000: 8s. Last read position: 2825:574 INFO 2020-04-17 09:32:08 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 09:32:08 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 09:32:08 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 09:32:10 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 09:32:12 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 09:32:13 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 09:32:15 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 09:32:17 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 09:32:19 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 09:32:20 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 09:32:22 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 09:32:24 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 09:32:25 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 09:32:26 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 32.57 minutes. Runtime.totalMemory()=1361051648 INFO 2020-04-17 09:32:27 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth14_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 09:32:27.966 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 09:32:27 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth14_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 09:32:27 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 09:32:47 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:19s. Time for last 10,000,000: 19s. Last read position: 4:2,571,827 INFO 2020-04-17 09:33:09 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:41s. Time for last 10,000,000: 21s. Last read position: 9:2,185,583 INFO 2020-04-17 09:33:27 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:59s. Time for last 10,000,000: 18s. Last read position: 15:1,277,111 INFO 2020-04-17 09:33:46 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:18s. Time for last 10,000,000: 19s. Last read position: 20:430,949 INFO 2020-04-17 09:34:07 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:39s. Time for last 10,000,000: 20s. Last read position: 26:192,822 INFO 2020-04-17 09:34:28 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:02:00s. Time for last 10,000,000: 21s. Last read position: 31:1,345,614 INFO 2020-04-17 09:34:45 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:02:17s. Time for last 10,000,000: 16s. Last read position: 37:1,212,527 INFO 2020-04-17 09:35:05 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 20s. Last read position: 44:228,145 INFO 2020-04-17 09:35:23 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 18s. Last read position: 50:1,133,273 INFO 2020-04-17 09:35:42 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 19s. Last read position: 57:1,126,989 INFO 2020-04-17 09:36:03 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:03:35s. Time for last 10,000,000: 20s. Last read position: 64:1,029,276 INFO 2020-04-17 09:36:20 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 17s. Last read position: 72:202,919 INFO 2020-04-17 09:36:41 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 20s. Last read position: 80:1,003,826 INFO 2020-04-17 09:37:02 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:04:34s. Time for last 10,000,000: 20s. Last read position: 88:693,929 INFO 2020-04-17 09:37:19 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:04:51s. Time for last 10,000,000: 17s. Last read position: 97:654,820 INFO 2020-04-17 09:37:39 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:05:11s. Time for last 10,000,000: 20s. Last read position: 106:954,050 INFO 2020-04-17 09:37:58 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:05:30s. Time for last 10,000,000: 18s. Last read position: 115:314,973 INFO 2020-04-17 09:38:14 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:05:46s. Time for last 10,000,000: 16s. Last read position: 124:300,378 INFO 2020-04-17 09:38:35 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:06:07s. Time for last 10,000,000: 21s. Last read position: 134:346,484 INFO 2020-04-17 09:38:54 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:06:26s. Time for last 10,000,000: 18s. Last read position: 143:937,913 INFO 2020-04-17 09:39:08 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:06:40s. Time for last 10,000,000: 14s. Last read position: 154:196,816 INFO 2020-04-17 09:39:26 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:06:58s. Time for last 10,000,000: 17s. Last read position: 164:946,097 INFO 2020-04-17 09:39:44 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:07:16s. Time for last 10,000,000: 17s. Last read position: 176:142,662 INFO 2020-04-17 09:40:01 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:07:33s. Time for last 10,000,000: 17s. Last read position: 186:787,532 INFO 2020-04-17 09:40:21 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:07:52s. Time for last 10,000,000: 19s. Last read position: 197:551,543 INFO 2020-04-17 09:40:38 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:08:10s. Time for last 10,000,000: 17s. Last read position: 210:166,366 INFO 2020-04-17 09:40:54 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:08:26s. Time for last 10,000,000: 16s. Last read position: 221:702,430 INFO 2020-04-17 09:41:11 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:08:43s. Time for last 10,000,000: 16s. Last read position: 234:821,523 INFO 2020-04-17 09:41:26 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:08:58s. Time for last 10,000,000: 15s. Last read position: 247:449,458 INFO 2020-04-17 09:41:42 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:09:14s. Time for last 10,000,000: 15s. Last read position: 259:701,369 INFO 2020-04-17 09:41:59 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:09:31s. Time for last 10,000,000: 17s. Last read position: 273:137,205 INFO 2020-04-17 09:42:18 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:09:50s. Time for last 10,000,000: 18s. Last read position: 287:177,113 INFO 2020-04-17 09:42:33 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:10:05s. Time for last 10,000,000: 15s. Last read position: 300:416,946 INFO 2020-04-17 09:42:50 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:10:22s. Time for last 10,000,000: 16s. Last read position: 314:424,834 INFO 2020-04-17 09:43:06 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:10:38s. Time for last 10,000,000: 15s. Last read position: 330:127 INFO 2020-04-17 09:43:20 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:10:52s. Time for last 10,000,000: 13s. Last read position: 344:423,663 INFO 2020-04-17 09:43:35 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:11:07s. Time for last 10,000,000: 15s. Last read position: 359:634,934 INFO 2020-04-17 09:43:48 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:11:20s. Time for last 10,000,000: 12s. Last read position: 377:83,616 INFO 2020-04-17 09:44:02 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:11:34s. Time for last 10,000,000: 13s. Last read position: 392:532,908 INFO 2020-04-17 09:44:17 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:11:49s. Time for last 10,000,000: 15s. Last read position: 409:150,400 INFO 2020-04-17 09:44:34 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:12:06s. Time for last 10,000,000: 17s. Last read position: 426:510,191 INFO 2020-04-17 09:44:50 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:12:22s. Time for last 10,000,000: 15s. Last read position: 444:356,488 INFO 2020-04-17 09:45:08 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:12:40s. Time for last 10,000,000: 17s. Last read position: 462:132,483 INFO 2020-04-17 09:45:22 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:12:54s. Time for last 10,000,000: 14s. Last read position: 480:476,684 INFO 2020-04-17 09:45:36 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:13:08s. Time for last 10,000,000: 13s. Last read position: 499:472,487 INFO 2020-04-17 09:45:50 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:13:22s. Time for last 10,000,000: 14s. Last read position: 520:167,314 INFO 2020-04-17 09:46:06 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:13:38s. Time for last 10,000,000: 16s. Last read position: 541:218,900 INFO 2020-04-17 09:46:21 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:13:53s. Time for last 10,000,000: 14s. Last read position: 561:89,787 INFO 2020-04-17 09:46:33 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:14:05s. Time for last 10,000,000: 12s. Last read position: 581:275,897 INFO 2020-04-17 09:46:48 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:14:20s. Time for last 10,000,000: 14s. Last read position: 605:50,138 INFO 2020-04-17 09:47:02 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:14:34s. Time for last 10,000,000: 14s. Last read position: 626:305,229 INFO 2020-04-17 09:47:18 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:14:50s. Time for last 10,000,000: 15s. Last read position: 648:244,080 INFO 2020-04-17 09:47:30 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:15:02s. Time for last 10,000,000: 12s. Last read position: 671:195,673 INFO 2020-04-17 09:47:46 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:15:18s. Time for last 10,000,000: 16s. Last read position: 695:85,112 INFO 2020-04-17 09:47:59 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:15:31s. Time for last 10,000,000: 12s. Last read position: 720:113,488 INFO 2020-04-17 09:48:13 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:15:45s. Time for last 10,000,000: 14s. Last read position: 748:34,007 INFO 2020-04-17 09:48:28 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:16:00s. Time for last 10,000,000: 15s. Last read position: 774:112,571 INFO 2020-04-17 09:48:42 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:16:14s. Time for last 10,000,000: 13s. Last read position: 801:129,443 INFO 2020-04-17 09:48:54 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:16:26s. Time for last 10,000,000: 12s. Last read position: 830:46,237 INFO 2020-04-17 09:49:05 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:16:37s. Time for last 10,000,000: 10s. Last read position: 858:343,631 INFO 2020-04-17 09:49:18 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:16:50s. Time for last 10,000,000: 12s. Last read position: 888:3,547 INFO 2020-04-17 09:49:31 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:17:03s. Time for last 10,000,000: 13s. Last read position: 918:326,056 INFO 2020-04-17 09:49:44 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:17:16s. Time for last 10,000,000: 12s. Last read position: 951:37,914 INFO 2020-04-17 09:49:55 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:17:27s. Time for last 10,000,000: 11s. Last read position: 984:126,977 INFO 2020-04-17 09:50:08 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:17:40s. Time for last 10,000,000: 12s. Last read position: 1017:167,455 INFO 2020-04-17 09:50:17 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:17:49s. Time for last 10,000,000: 8s. Last read position: 1052:230,503 INFO 2020-04-17 09:50:29 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:18:01s. Time for last 10,000,000: 12s. Last read position: 1090:74,736 INFO 2020-04-17 09:50:41 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:18:13s. Time for last 10,000,000: 12s. Last read position: 1128:19,199 INFO 2020-04-17 09:50:53 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:18:25s. Time for last 10,000,000: 11s. Last read position: 1168:8,743 INFO 2020-04-17 09:51:04 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:18:36s. Time for last 10,000,000: 11s. Last read position: 1210:48,462 INFO 2020-04-17 09:51:23 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:18:55s. Time for last 10,000,000: 18s. Last read position: 1252:73,681 INFO 2020-04-17 09:51:33 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:19:05s. Time for last 10,000,000: 10s. Last read position: 1298:135,654 INFO 2020-04-17 09:51:47 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:19:19s. Time for last 10,000,000: 13s. Last read position: 1347:42,922 INFO 2020-04-17 09:51:57 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:19:29s. Time for last 10,000,000: 10s. Last read position: 1397:45,967 INFO 2020-04-17 09:52:08 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:19:40s. Time for last 10,000,000: 11s. Last read position: 1450:5,557 INFO 2020-04-17 09:52:16 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:19:48s. Time for last 10,000,000: 8s. Last read position: 1505:129,718 INFO 2020-04-17 09:52:26 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:19:58s. Time for last 10,000,000: 9s. Last read position: 1568:3,714 INFO 2020-04-17 09:52:35 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:20:07s. Time for last 10,000,000: 9s. Last read position: 1631:39,335 INFO 2020-04-17 09:52:45 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:20:17s. Time for last 10,000,000: 9s. Last read position: 1698:107,239 INFO 2020-04-17 09:52:55 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:20:27s. Time for last 10,000,000: 9s. Last read position: 1774:115,449 INFO 2020-04-17 09:53:03 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:20:35s. Time for last 10,000,000: 8s. Last read position: 1853:95,173 INFO 2020-04-17 09:53:11 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:20:43s. Time for last 10,000,000: 7s. Last read position: 1942:62,123 INFO 2020-04-17 09:53:20 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:20:52s. Time for last 10,000,000: 9s. Last read position: 2039:16,006 INFO 2020-04-17 09:53:28 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:21:00s. Time for last 10,000,000: 7s. Last read position: 2147:65,939 INFO 2020-04-17 09:53:37 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:21:09s. Time for last 10,000,000: 9s. Last read position: 2269:65,204 INFO 2020-04-17 09:53:49 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:21:21s. Time for last 10,000,000: 12s. Last read position: 2409:16,999 INFO 2020-04-17 09:53:57 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:21:29s. Time for last 10,000,000: 7s. Last read position: 2580:1,672 INFO 2020-04-17 09:54:03 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:21:35s. Time for last 10,000,000: 6s. Last read position: 2825:574 INFO 2020-04-17 09:54:06 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 09:54:06 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 09:54:06 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 09:54:08 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 09:54:10 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 09:54:12 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 09:54:13 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 09:54:15 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 09:54:17 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 09:54:18 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 09:54:20 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 09:54:22 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 09:54:23 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 09:54:24 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 21.95 minutes. Runtime.totalMemory()=3393191936 INFO 2020-04-17 09:54:25 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth15_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 09:54:27.242 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 09:54:27 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth15_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 09:54:27 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 09:54:55 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:28s. Time for last 10,000,000: 28s. Last read position: 4:2,571,827 INFO 2020-04-17 09:55:29 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 33s. Last read position: 9:2,185,583 INFO 2020-04-17 09:55:56 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 27s. Last read position: 15:1,277,111 INFO 2020-04-17 09:56:26 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:59s. Time for last 10,000,000: 29s. Last read position: 20:430,949 INFO 2020-04-17 09:56:55 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:02:28s. Time for last 10,000,000: 29s. Last read position: 26:192,822 INFO 2020-04-17 09:57:27 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 31s. Last read position: 31:1,345,614 INFO 2020-04-17 09:57:53 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 26s. Last read position: 37:1,212,527 INFO 2020-04-17 09:58:23 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:03:56s. Time for last 10,000,000: 30s. Last read position: 44:228,145 INFO 2020-04-17 09:58:51 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:04:23s. Time for last 10,000,000: 27s. Last read position: 50:1,133,273 INFO 2020-04-17 09:59:21 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:04:53s. Time for last 10,000,000: 29s. Last read position: 57:1,126,989 INFO 2020-04-17 09:59:52 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:05:25s. Time for last 10,000,000: 31s. Last read position: 64:1,029,276 INFO 2020-04-17 10:00:19 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:05:52s. Time for last 10,000,000: 27s. Last read position: 72:202,919 INFO 2020-04-17 10:00:50 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:06:23s. Time for last 10,000,000: 30s. Last read position: 80:1,003,826 INFO 2020-04-17 10:01:21 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:06:54s. Time for last 10,000,000: 30s. Last read position: 88:693,929 INFO 2020-04-17 10:01:47 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 26s. Last read position: 97:654,820 INFO 2020-04-17 10:02:17 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:07:49s. Time for last 10,000,000: 29s. Last read position: 106:954,050 INFO 2020-04-17 10:02:42 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:08:15s. Time for last 10,000,000: 25s. Last read position: 115:314,973 INFO 2020-04-17 10:03:07 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:08:40s. Time for last 10,000,000: 25s. Last read position: 124:300,378 INFO 2020-04-17 10:03:38 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:09:11s. Time for last 10,000,000: 30s. Last read position: 134:346,484 INFO 2020-04-17 10:04:06 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:09:38s. Time for last 10,000,000: 27s. Last read position: 143:937,913 INFO 2020-04-17 10:04:27 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:10:00s. Time for last 10,000,000: 21s. Last read position: 154:196,816 INFO 2020-04-17 10:04:51 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:10:24s. Time for last 10,000,000: 24s. Last read position: 164:946,097 INFO 2020-04-17 10:05:17 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:10:50s. Time for last 10,000,000: 25s. Last read position: 176:142,662 INFO 2020-04-17 10:05:46 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:11:19s. Time for last 10,000,000: 28s. Last read position: 186:787,532 INFO 2020-04-17 10:06:11 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:11:44s. Time for last 10,000,000: 25s. Last read position: 197:551,543 INFO 2020-04-17 10:06:37 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:12:09s. Time for last 10,000,000: 25s. Last read position: 210:166,366 INFO 2020-04-17 10:07:01 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:12:33s. Time for last 10,000,000: 23s. Last read position: 221:702,430 INFO 2020-04-17 10:07:26 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:12:59s. Time for last 10,000,000: 25s. Last read position: 234:821,523 INFO 2020-04-17 10:07:50 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:13:23s. Time for last 10,000,000: 24s. Last read position: 247:449,458 INFO 2020-04-17 10:08:14 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:13:47s. Time for last 10,000,000: 23s. Last read position: 259:701,369 INFO 2020-04-17 10:08:40 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:14:12s. Time for last 10,000,000: 25s. Last read position: 273:137,205 INFO 2020-04-17 10:09:05 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:14:38s. Time for last 10,000,000: 25s. Last read position: 287:177,113 INFO 2020-04-17 10:09:28 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:15:01s. Time for last 10,000,000: 23s. Last read position: 300:416,946 INFO 2020-04-17 10:09:53 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:15:25s. Time for last 10,000,000: 24s. Last read position: 314:424,834 INFO 2020-04-17 10:10:15 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:15:48s. Time for last 10,000,000: 22s. Last read position: 330:127 INFO 2020-04-17 10:10:38 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:16:11s. Time for last 10,000,000: 22s. Last read position: 344:423,663 INFO 2020-04-17 10:11:02 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:16:35s. Time for last 10,000,000: 24s. Last read position: 359:634,934 INFO 2020-04-17 10:11:20 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:16:53s. Time for last 10,000,000: 18s. Last read position: 377:83,616 INFO 2020-04-17 10:11:42 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:17:14s. Time for last 10,000,000: 21s. Last read position: 392:532,908 INFO 2020-04-17 10:12:02 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:17:35s. Time for last 10,000,000: 20s. Last read position: 409:150,400 INFO 2020-04-17 10:12:28 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:18:01s. Time for last 10,000,000: 26s. Last read position: 426:510,191 INFO 2020-04-17 10:12:52 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:18:25s. Time for last 10,000,000: 23s. Last read position: 444:356,488 INFO 2020-04-17 10:13:19 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:18:52s. Time for last 10,000,000: 27s. Last read position: 462:132,483 INFO 2020-04-17 10:13:49 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:19:22s. Time for last 10,000,000: 30s. Last read position: 480:476,684 INFO 2020-04-17 10:14:11 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:19:43s. Time for last 10,000,000: 21s. Last read position: 499:472,487 INFO 2020-04-17 10:14:33 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:20:05s. Time for last 10,000,000: 21s. Last read position: 520:167,314 INFO 2020-04-17 10:14:57 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:20:30s. Time for last 10,000,000: 24s. Last read position: 541:218,900 INFO 2020-04-17 10:15:19 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:20:51s. Time for last 10,000,000: 21s. Last read position: 561:89,787 INFO 2020-04-17 10:15:38 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:21:11s. Time for last 10,000,000: 19s. Last read position: 581:275,897 INFO 2020-04-17 10:15:58 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:21:31s. Time for last 10,000,000: 20s. Last read position: 605:50,138 INFO 2020-04-17 10:16:20 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:21:52s. Time for last 10,000,000: 21s. Last read position: 626:305,229 INFO 2020-04-17 10:16:43 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:22:16s. Time for last 10,000,000: 23s. Last read position: 648:244,080 INFO 2020-04-17 10:17:02 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:22:34s. Time for last 10,000,000: 18s. Last read position: 671:195,673 INFO 2020-04-17 10:17:25 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:22:58s. Time for last 10,000,000: 23s. Last read position: 695:85,112 INFO 2020-04-17 10:17:44 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:23:17s. Time for last 10,000,000: 18s. Last read position: 720:113,488 INFO 2020-04-17 10:18:05 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:23:37s. Time for last 10,000,000: 20s. Last read position: 748:34,007 INFO 2020-04-17 10:18:29 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:24:02s. Time for last 10,000,000: 24s. Last read position: 774:112,571 INFO 2020-04-17 10:18:51 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:24:24s. Time for last 10,000,000: 22s. Last read position: 801:129,443 INFO 2020-04-17 10:19:09 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:24:42s. Time for last 10,000,000: 18s. Last read position: 830:46,237 INFO 2020-04-17 10:19:26 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:24:58s. Time for last 10,000,000: 16s. Last read position: 858:343,631 INFO 2020-04-17 10:19:45 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:25:17s. Time for last 10,000,000: 18s. Last read position: 888:3,547 INFO 2020-04-17 10:20:04 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:25:37s. Time for last 10,000,000: 19s. Last read position: 918:326,056 INFO 2020-04-17 10:20:21 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:25:54s. Time for last 10,000,000: 17s. Last read position: 951:37,914 INFO 2020-04-17 10:20:40 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:26:13s. Time for last 10,000,000: 18s. Last read position: 984:126,977 INFO 2020-04-17 10:20:59 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:26:32s. Time for last 10,000,000: 19s. Last read position: 1017:167,455 INFO 2020-04-17 10:21:12 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:26:45s. Time for last 10,000,000: 12s. Last read position: 1052:230,503 INFO 2020-04-17 10:21:29 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:27:01s. Time for last 10,000,000: 16s. Last read position: 1090:74,736 INFO 2020-04-17 10:21:48 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:27:20s. Time for last 10,000,000: 19s. Last read position: 1128:19,199 INFO 2020-04-17 10:22:06 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:27:39s. Time for last 10,000,000: 18s. Last read position: 1168:8,743 INFO 2020-04-17 10:22:22 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:27:54s. Time for last 10,000,000: 15s. Last read position: 1210:48,462 INFO 2020-04-17 10:22:49 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:28:22s. Time for last 10,000,000: 27s. Last read position: 1252:73,681 INFO 2020-04-17 10:23:04 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:28:37s. Time for last 10,000,000: 15s. Last read position: 1298:135,654 INFO 2020-04-17 10:23:22 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:28:55s. Time for last 10,000,000: 18s. Last read position: 1347:42,922 INFO 2020-04-17 10:23:38 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:29:11s. Time for last 10,000,000: 15s. Last read position: 1397:45,967 INFO 2020-04-17 10:23:54 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:29:26s. Time for last 10,000,000: 15s. Last read position: 1450:5,557 INFO 2020-04-17 10:24:07 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:29:40s. Time for last 10,000,000: 13s. Last read position: 1505:129,718 INFO 2020-04-17 10:24:22 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:29:55s. Time for last 10,000,000: 14s. Last read position: 1568:3,714 INFO 2020-04-17 10:24:36 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:30:09s. Time for last 10,000,000: 14s. Last read position: 1631:39,335 INFO 2020-04-17 10:24:50 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:30:23s. Time for last 10,000,000: 13s. Last read position: 1698:107,239 INFO 2020-04-17 10:25:05 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:30:37s. Time for last 10,000,000: 14s. Last read position: 1774:115,449 INFO 2020-04-17 10:25:17 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:30:50s. Time for last 10,000,000: 12s. Last read position: 1853:95,173 INFO 2020-04-17 10:25:30 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:31:03s. Time for last 10,000,000: 12s. Last read position: 1942:62,123 INFO 2020-04-17 10:25:43 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:31:16s. Time for last 10,000,000: 12s. Last read position: 2039:16,006 INFO 2020-04-17 10:25:54 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:31:27s. Time for last 10,000,000: 11s. Last read position: 2147:65,939 INFO 2020-04-17 10:26:08 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:31:41s. Time for last 10,000,000: 14s. Last read position: 2269:65,204 INFO 2020-04-17 10:26:28 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:32:01s. Time for last 10,000,000: 19s. Last read position: 2409:16,999 INFO 2020-04-17 10:26:38 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:32:11s. Time for last 10,000,000: 9s. Last read position: 2580:1,672 INFO 2020-04-17 10:26:47 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:32:20s. Time for last 10,000,000: 9s. Last read position: 2825:574 INFO 2020-04-17 10:26:51 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 10:26:51 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 10:26:51 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 10:26:53 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 10:26:55 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 10:26:56 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 10:26:58 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 10:27:00 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 10:27:02 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 10:27:03 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 10:27:05 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 10:27:07 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 10:27:08 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 10:27:09 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 32.71 minutes. Runtime.totalMemory()=2887778304 INFO 2020-04-17 10:27:10 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 10:27:12.232 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 10:27:12 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 10:27:12 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 10:27:18 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 6s. Last read position: 4:2,571,827 INFO 2020-04-17 10:27:23 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 4s. Last read position: 9:2,185,583 INFO 2020-04-17 10:27:28 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:15s. Time for last 10,000,000: 4s. Last read position: 15:1,277,111 INFO 2020-04-17 10:27:32 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:20s. Time for last 10,000,000: 4s. Last read position: 20:430,949 INFO 2020-04-17 10:27:37 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:24s. Time for last 10,000,000: 4s. Last read position: 26:192,822 INFO 2020-04-17 10:27:41 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 4s. Last read position: 31:1,345,614 INFO 2020-04-17 10:27:46 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:34s. Time for last 10,000,000: 4s. Last read position: 37:1,212,527 INFO 2020-04-17 10:27:51 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 4s. Last read position: 44:228,145 INFO 2020-04-17 10:27:55 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 4s. Last read position: 50:1,133,273 INFO 2020-04-17 10:27:59 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:47s. Time for last 10,000,000: 4s. Last read position: 57:1,126,989 INFO 2020-04-17 10:28:04 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:51s. Time for last 10,000,000: 4s. Last read position: 64:1,029,276 INFO 2020-04-17 10:28:08 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:56s. Time for last 10,000,000: 4s. Last read position: 72:202,919 INFO 2020-04-17 10:28:13 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:01s. Time for last 10,000,000: 4s. Last read position: 80:1,003,826 INFO 2020-04-17 10:28:17 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:05s. Time for last 10,000,000: 4s. Last read position: 88:693,929 INFO 2020-04-17 10:28:22 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:09s. Time for last 10,000,000: 4s. Last read position: 97:654,820 INFO 2020-04-17 10:28:27 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 4s. Last read position: 106:954,050 INFO 2020-04-17 10:28:31 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 4s. Last read position: 115:314,973 INFO 2020-04-17 10:28:35 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:23s. Time for last 10,000,000: 4s. Last read position: 124:300,378 INFO 2020-04-17 10:28:40 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:28s. Time for last 10,000,000: 4s. Last read position: 134:346,484 INFO 2020-04-17 10:28:44 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:32s. Time for last 10,000,000: 4s. Last read position: 143:937,913 INFO 2020-04-17 10:28:48 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:36s. Time for last 10,000,000: 3s. Last read position: 154:196,816 INFO 2020-04-17 10:28:53 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:40s. Time for last 10,000,000: 4s. Last read position: 164:946,097 INFO 2020-04-17 10:28:57 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:45s. Time for last 10,000,000: 4s. Last read position: 176:142,662 INFO 2020-04-17 10:29:01 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:49s. Time for last 10,000,000: 4s. Last read position: 186:787,532 INFO 2020-04-17 10:29:06 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 4s. Last read position: 197:551,543 INFO 2020-04-17 10:29:10 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 4s. Last read position: 210:166,366 INFO 2020-04-17 10:29:14 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:02:02s. Time for last 10,000,000: 4s. Last read position: 221:702,430 INFO 2020-04-17 10:29:19 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:02:06s. Time for last 10,000,000: 4s. Last read position: 234:821,523 INFO 2020-04-17 10:29:23 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:02:10s. Time for last 10,000,000: 3s. Last read position: 247:449,458 INFO 2020-04-17 10:29:27 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:02:14s. Time for last 10,000,000: 4s. Last read position: 259:701,369 INFO 2020-04-17 10:29:31 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:02:19s. Time for last 10,000,000: 4s. Last read position: 273:137,205 INFO 2020-04-17 10:29:35 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:02:23s. Time for last 10,000,000: 4s. Last read position: 287:177,113 INFO 2020-04-17 10:29:39 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:02:27s. Time for last 10,000,000: 4s. Last read position: 300:416,946 INFO 2020-04-17 10:29:44 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 4s. Last read position: 314:424,834 INFO 2020-04-17 10:29:48 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:35s. Time for last 10,000,000: 4s. Last read position: 330:127 INFO 2020-04-17 10:29:52 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:40s. Time for last 10,000,000: 4s. Last read position: 344:423,663 INFO 2020-04-17 10:29:56 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:44s. Time for last 10,000,000: 4s. Last read position: 359:634,934 INFO 2020-04-17 10:30:00 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:47s. Time for last 10,000,000: 3s. Last read position: 377:83,616 INFO 2020-04-17 10:30:04 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 3s. Last read position: 392:532,908 INFO 2020-04-17 10:30:08 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 4s. Last read position: 409:150,400 INFO 2020-04-17 10:30:12 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 4s. Last read position: 426:510,191 INFO 2020-04-17 10:30:16 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:03:04s. Time for last 10,000,000: 4s. Last read position: 444:356,488 INFO 2020-04-17 10:30:20 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:03:08s. Time for last 10,000,000: 4s. Last read position: 462:132,483 INFO 2020-04-17 10:30:24 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:03:12s. Time for last 10,000,000: 3s. Last read position: 480:476,684 INFO 2020-04-17 10:30:28 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 3s. Last read position: 499:472,487 INFO 2020-04-17 10:30:32 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 3s. Last read position: 520:167,314 INFO 2020-04-17 10:30:37 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:03:24s. Time for last 10,000,000: 4s. Last read position: 541:218,900 INFO 2020-04-17 10:30:41 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:03:28s. Time for last 10,000,000: 4s. Last read position: 561:89,787 INFO 2020-04-17 10:30:44 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:03:32s. Time for last 10,000,000: 3s. Last read position: 581:275,897 INFO 2020-04-17 10:30:48 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:03:36s. Time for last 10,000,000: 3s. Last read position: 605:50,138 INFO 2020-04-17 10:30:52 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:03:40s. Time for last 10,000,000: 4s. Last read position: 626:305,229 INFO 2020-04-17 10:30:57 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:03:44s. Time for last 10,000,000: 4s. Last read position: 648:244,080 INFO 2020-04-17 10:31:00 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 3s. Last read position: 671:195,673 INFO 2020-04-17 10:31:04 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 4s. Last read position: 695:85,112 INFO 2020-04-17 10:31:08 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:03:56s. Time for last 10,000,000: 3s. Last read position: 720:113,488 INFO 2020-04-17 10:31:12 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 4s. Last read position: 748:34,007 INFO 2020-04-17 10:31:16 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 3s. Last read position: 774:112,571 INFO 2020-04-17 10:31:20 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 3s. Last read position: 801:129,443 INFO 2020-04-17 10:31:24 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 3s. Last read position: 830:46,237 INFO 2020-04-17 10:31:27 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:04:15s. Time for last 10,000,000: 3s. Last read position: 858:343,631 INFO 2020-04-17 10:31:31 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 3s. Last read position: 888:3,547 INFO 2020-04-17 10:31:35 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:04:22s. Time for last 10,000,000: 3s. Last read position: 918:326,056 INFO 2020-04-17 10:31:38 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:04:26s. Time for last 10,000,000: 3s. Last read position: 951:37,914 INFO 2020-04-17 10:31:42 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:04:30s. Time for last 10,000,000: 3s. Last read position: 984:126,977 INFO 2020-04-17 10:31:46 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:04:33s. Time for last 10,000,000: 3s. Last read position: 1017:167,455 INFO 2020-04-17 10:31:49 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:04:37s. Time for last 10,000,000: 3s. Last read position: 1052:230,503 INFO 2020-04-17 10:31:52 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:04:40s. Time for last 10,000,000: 3s. Last read position: 1090:74,736 INFO 2020-04-17 10:31:56 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 3s. Last read position: 1128:19,199 INFO 2020-04-17 10:32:00 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:04:47s. Time for last 10,000,000: 3s. Last read position: 1168:8,743 INFO 2020-04-17 10:32:03 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:04:51s. Time for last 10,000,000: 3s. Last read position: 1210:48,462 INFO 2020-04-17 10:32:07 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:04:55s. Time for last 10,000,000: 3s. Last read position: 1252:73,681 INFO 2020-04-17 10:32:10 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:04:58s. Time for last 10,000,000: 3s. Last read position: 1298:135,654 INFO 2020-04-17 10:32:14 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:05:01s. Time for last 10,000,000: 3s. Last read position: 1347:42,922 INFO 2020-04-17 10:32:17 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:05:05s. Time for last 10,000,000: 3s. Last read position: 1397:45,967 INFO 2020-04-17 10:32:21 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:05:08s. Time for last 10,000,000: 3s. Last read position: 1450:5,557 INFO 2020-04-17 10:32:24 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:05:12s. Time for last 10,000,000: 3s. Last read position: 1505:129,718 INFO 2020-04-17 10:32:27 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:05:15s. Time for last 10,000,000: 3s. Last read position: 1568:3,714 INFO 2020-04-17 10:32:30 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:05:18s. Time for last 10,000,000: 3s. Last read position: 1631:39,335 INFO 2020-04-17 10:32:34 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:05:21s. Time for last 10,000,000: 3s. Last read position: 1698:107,239 INFO 2020-04-17 10:32:37 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:05:25s. Time for last 10,000,000: 3s. Last read position: 1774:115,449 INFO 2020-04-17 10:32:40 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:05:28s. Time for last 10,000,000: 3s. Last read position: 1853:95,173 INFO 2020-04-17 10:32:43 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:05:31s. Time for last 10,000,000: 3s. Last read position: 1942:62,123 INFO 2020-04-17 10:32:46 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:05:34s. Time for last 10,000,000: 3s. Last read position: 2039:16,006 INFO 2020-04-17 10:32:49 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:05:37s. Time for last 10,000,000: 3s. Last read position: 2147:65,939 INFO 2020-04-17 10:32:52 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:05:40s. Time for last 10,000,000: 3s. Last read position: 2269:65,204 INFO 2020-04-17 10:32:56 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:05:43s. Time for last 10,000,000: 3s. Last read position: 2409:16,999 INFO 2020-04-17 10:32:59 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:05:46s. Time for last 10,000,000: 2s. Last read position: 2580:1,672 INFO 2020-04-17 10:33:01 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:05:49s. Time for last 10,000,000: 2s. Last read position: 2825:574 INFO 2020-04-17 10:33:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 10:33:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 10:33:03 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 10:33:05 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 10:33:06 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 10:33:08 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 10:33:10 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 10:33:12 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 10:33:13 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 10:33:15 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 10:33:17 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 10:33:18 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 10:33:20 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 10:33:21 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 6.15 minutes. Runtime.totalMemory()=805306368 INFO 2020-04-17 10:33:21 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 10:33:22.530 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 10:33:22 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 10:33:22 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 10:33:27 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:05s. Time for last 10,000,000: 4s. Last read position: 4:2,571,827 INFO 2020-04-17 10:33:31 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 3s. Last read position: 9:2,185,583 INFO 2020-04-17 10:33:35 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:12s. Time for last 10,000,000: 3s. Last read position: 15:1,277,111 INFO 2020-04-17 10:33:38 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:16s. Time for last 10,000,000: 3s. Last read position: 20:430,949 INFO 2020-04-17 10:33:42 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:20s. Time for last 10,000,000: 3s. Last read position: 26:192,822 INFO 2020-04-17 10:33:46 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 3s. Last read position: 31:1,345,614 INFO 2020-04-17 10:33:50 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:27s. Time for last 10,000,000: 3s. Last read position: 37:1,212,527 INFO 2020-04-17 10:33:54 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:31s. Time for last 10,000,000: 3s. Last read position: 44:228,145 INFO 2020-04-17 10:33:57 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:35s. Time for last 10,000,000: 3s. Last read position: 50:1,133,273 INFO 2020-04-17 10:34:01 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 3s. Last read position: 57:1,126,989 INFO 2020-04-17 10:34:05 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:42s. Time for last 10,000,000: 3s. Last read position: 64:1,029,276 INFO 2020-04-17 10:34:08 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 3s. Last read position: 72:202,919 INFO 2020-04-17 10:34:12 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:49s. Time for last 10,000,000: 3s. Last read position: 80:1,003,826 INFO 2020-04-17 10:34:16 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:53s. Time for last 10,000,000: 3s. Last read position: 88:693,929 INFO 2020-04-17 10:34:19 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:57s. Time for last 10,000,000: 3s. Last read position: 97:654,820 INFO 2020-04-17 10:34:23 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:01s. Time for last 10,000,000: 3s. Last read position: 106:954,050 INFO 2020-04-17 10:34:27 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:04s. Time for last 10,000,000: 3s. Last read position: 115:314,973 INFO 2020-04-17 10:34:30 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:08s. Time for last 10,000,000: 3s. Last read position: 124:300,378 INFO 2020-04-17 10:34:34 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 3s. Last read position: 134:346,484 INFO 2020-04-17 10:34:38 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:15s. Time for last 10,000,000: 3s. Last read position: 143:937,913 INFO 2020-04-17 10:34:41 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 3s. Last read position: 154:196,816 INFO 2020-04-17 10:34:45 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:22s. Time for last 10,000,000: 3s. Last read position: 164:946,097 INFO 2020-04-17 10:34:48 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:26s. Time for last 10,000,000: 3s. Last read position: 176:142,662 INFO 2020-04-17 10:34:52 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:30s. Time for last 10,000,000: 3s. Last read position: 186:787,532 INFO 2020-04-17 10:34:56 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:33s. Time for last 10,000,000: 3s. Last read position: 197:551,543 INFO 2020-04-17 10:34:59 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:37s. Time for last 10,000,000: 3s. Last read position: 210:166,366 INFO 2020-04-17 10:35:03 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:40s. Time for last 10,000,000: 3s. Last read position: 221:702,430 INFO 2020-04-17 10:35:06 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:44s. Time for last 10,000,000: 3s. Last read position: 234:821,523 INFO 2020-04-17 10:35:10 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 3s. Last read position: 247:449,458 INFO 2020-04-17 10:35:13 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:51s. Time for last 10,000,000: 3s. Last read position: 259:701,369 INFO 2020-04-17 10:35:17 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 3s. Last read position: 273:137,205 INFO 2020-04-17 10:35:20 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 3s. Last read position: 287:177,113 INFO 2020-04-17 10:35:24 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 3s. Last read position: 300:416,946 INFO 2020-04-17 10:35:27 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 3s. Last read position: 314:424,834 INFO 2020-04-17 10:35:31 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 3s. Last read position: 330:127 INFO 2020-04-17 10:35:34 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:12s. Time for last 10,000,000: 3s. Last read position: 344:423,663 INFO 2020-04-17 10:35:38 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 3s. Last read position: 359:634,934 INFO 2020-04-17 10:35:41 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 3s. Last read position: 377:83,616 INFO 2020-04-17 10:35:44 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 3s. Last read position: 392:532,908 INFO 2020-04-17 10:35:48 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:25s. Time for last 10,000,000: 3s. Last read position: 409:150,400 INFO 2020-04-17 10:35:51 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:02:29s. Time for last 10,000,000: 3s. Last read position: 426:510,191 INFO 2020-04-17 10:35:55 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:32s. Time for last 10,000,000: 3s. Last read position: 444:356,488 INFO 2020-04-17 10:35:58 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:36s. Time for last 10,000,000: 3s. Last read position: 462:132,483 INFO 2020-04-17 10:36:02 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:39s. Time for last 10,000,000: 3s. Last read position: 480:476,684 INFO 2020-04-17 10:36:05 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:43s. Time for last 10,000,000: 3s. Last read position: 499:472,487 INFO 2020-04-17 10:36:09 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:46s. Time for last 10,000,000: 3s. Last read position: 520:167,314 INFO 2020-04-17 10:36:12 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:50s. Time for last 10,000,000: 3s. Last read position: 541:218,900 INFO 2020-04-17 10:36:16 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:53s. Time for last 10,000,000: 3s. Last read position: 561:89,787 INFO 2020-04-17 10:36:19 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 3s. Last read position: 581:275,897 INFO 2020-04-17 10:36:22 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 3s. Last read position: 605:50,138 INFO 2020-04-17 10:36:25 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 3s. Last read position: 626:305,229 INFO 2020-04-17 10:36:29 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 3s. Last read position: 648:244,080 INFO 2020-04-17 10:36:32 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 3s. Last read position: 671:195,673 INFO 2020-04-17 10:36:36 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 3s. Last read position: 695:85,112 INFO 2020-04-17 10:36:39 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 3s. Last read position: 720:113,488 INFO 2020-04-17 10:36:42 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 3s. Last read position: 748:34,007 INFO 2020-04-17 10:36:45 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 3s. Last read position: 774:112,571 INFO 2020-04-17 10:36:49 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 3s. Last read position: 801:129,443 INFO 2020-04-17 10:36:52 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:03:29s. Time for last 10,000,000: 3s. Last read position: 830:46,237 INFO 2020-04-17 10:36:55 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:03:32s. Time for last 10,000,000: 3s. Last read position: 858:343,631 INFO 2020-04-17 10:36:58 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:03:36s. Time for last 10,000,000: 3s. Last read position: 888:3,547 INFO 2020-04-17 10:37:02 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 3s. Last read position: 918:326,056 INFO 2020-04-17 10:37:05 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:42s. Time for last 10,000,000: 3s. Last read position: 951:37,914 INFO 2020-04-17 10:37:08 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 3s. Last read position: 984:126,977 INFO 2020-04-17 10:37:11 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 3s. Last read position: 1017:167,455 INFO 2020-04-17 10:37:14 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:51s. Time for last 10,000,000: 2s. Last read position: 1052:230,503 INFO 2020-04-17 10:37:17 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:54s. Time for last 10,000,000: 3s. Last read position: 1090:74,736 INFO 2020-04-17 10:37:20 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:57s. Time for last 10,000,000: 3s. Last read position: 1128:19,199 INFO 2020-04-17 10:37:23 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:04:01s. Time for last 10,000,000: 3s. Last read position: 1168:8,743 INFO 2020-04-17 10:37:26 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 2s. Last read position: 1210:48,462 INFO 2020-04-17 10:37:29 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 3s. Last read position: 1252:73,681 INFO 2020-04-17 10:37:32 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:04:10s. Time for last 10,000,000: 2s. Last read position: 1298:135,654 INFO 2020-04-17 10:37:35 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 3s. Last read position: 1347:42,922 INFO 2020-04-17 10:37:38 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 2s. Last read position: 1397:45,967 INFO 2020-04-17 10:37:41 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 2s. Last read position: 1450:5,557 INFO 2020-04-17 10:37:44 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:04:22s. Time for last 10,000,000: 2s. Last read position: 1505:129,718 INFO 2020-04-17 10:37:47 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 2s. Last read position: 1568:3,714 INFO 2020-04-17 10:37:50 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:04:27s. Time for last 10,000,000: 2s. Last read position: 1631:39,335 INFO 2020-04-17 10:37:53 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:04:30s. Time for last 10,000,000: 2s. Last read position: 1698:107,239 INFO 2020-04-17 10:37:56 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:04:33s. Time for last 10,000,000: 2s. Last read position: 1774:115,449 INFO 2020-04-17 10:37:58 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:04:36s. Time for last 10,000,000: 2s. Last read position: 1853:95,173 INFO 2020-04-17 10:38:01 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:04:39s. Time for last 10,000,000: 2s. Last read position: 1942:62,123 INFO 2020-04-17 10:38:04 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:41s. Time for last 10,000,000: 2s. Last read position: 2039:16,006 INFO 2020-04-17 10:38:07 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 2s. Last read position: 2147:65,939 INFO 2020-04-17 10:38:09 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:47s. Time for last 10,000,000: 2s. Last read position: 2269:65,204 INFO 2020-04-17 10:38:12 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:50s. Time for last 10,000,000: 2s. Last read position: 2409:16,999 INFO 2020-04-17 10:38:15 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:52s. Time for last 10,000,000: 2s. Last read position: 2580:1,672 INFO 2020-04-17 10:38:18 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:55s. Time for last 10,000,000: 2s. Last read position: 2825:574 INFO 2020-04-17 10:38:19 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 10:38:19 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 10:38:19 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 10:38:21 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 10:38:23 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 10:38:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 10:38:26 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 10:38:28 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 10:38:29 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 10:38:31 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 10:38:33 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 10:38:34 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 10:38:36 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 10:38:37 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 5.25 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-17 10:38:38 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Mcap/Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Mcap/Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa ********** 10:38:39.570 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 10:38:39 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Mcap/Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Mcap/Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Mcap_Genome/Mcap.genome_assembly.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 10:38:39 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 10:38:44 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:05s. Time for last 10,000,000: 4s. Last read position: 4:2,571,827 INFO 2020-04-17 10:38:48 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 3s. Last read position: 9:2,185,583 INFO 2020-04-17 10:38:51 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:12s. Time for last 10,000,000: 3s. Last read position: 15:1,277,111 INFO 2020-04-17 10:38:55 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:15s. Time for last 10,000,000: 3s. Last read position: 20:430,949 INFO 2020-04-17 10:38:58 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 3s. Last read position: 26:192,822 INFO 2020-04-17 10:39:02 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 3s. Last read position: 31:1,345,614 INFO 2020-04-17 10:39:05 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:26s. Time for last 10,000,000: 3s. Last read position: 37:1,212,527 INFO 2020-04-17 10:39:09 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 3s. Last read position: 44:228,145 INFO 2020-04-17 10:39:12 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:32s. Time for last 10,000,000: 3s. Last read position: 50:1,133,273 INFO 2020-04-17 10:39:16 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:36s. Time for last 10,000,000: 3s. Last read position: 57:1,126,989 INFO 2020-04-17 10:39:19 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:39s. Time for last 10,000,000: 3s. Last read position: 64:1,029,276 INFO 2020-04-17 10:39:22 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 3s. Last read position: 72:202,919 INFO 2020-04-17 10:39:26 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 3s. Last read position: 80:1,003,826 INFO 2020-04-17 10:39:29 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:50s. Time for last 10,000,000: 3s. Last read position: 88:693,929 INFO 2020-04-17 10:39:33 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:53s. Time for last 10,000,000: 3s. Last read position: 97:654,820 INFO 2020-04-17 10:39:36 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:57s. Time for last 10,000,000: 3s. Last read position: 106:954,050 INFO 2020-04-17 10:39:40 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 3s. Last read position: 115:314,973 INFO 2020-04-17 10:39:43 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:04s. Time for last 10,000,000: 3s. Last read position: 124:300,378 INFO 2020-04-17 10:39:47 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:07s. Time for last 10,000,000: 3s. Last read position: 134:346,484 INFO 2020-04-17 10:39:50 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:10s. Time for last 10,000,000: 3s. Last read position: 143:937,913 INFO 2020-04-17 10:39:53 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 3s. Last read position: 154:196,816 INFO 2020-04-17 10:39:56 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:17s. Time for last 10,000,000: 3s. Last read position: 164:946,097 INFO 2020-04-17 10:40:00 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:20s. Time for last 10,000,000: 3s. Last read position: 176:142,662 INFO 2020-04-17 10:40:03 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:24s. Time for last 10,000,000: 3s. Last read position: 186:787,532 INFO 2020-04-17 10:40:07 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 3s. Last read position: 197:551,543 INFO 2020-04-17 10:40:10 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:30s. Time for last 10,000,000: 3s. Last read position: 210:166,366 INFO 2020-04-17 10:40:13 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:34s. Time for last 10,000,000: 3s. Last read position: 221:702,430 INFO 2020-04-17 10:40:17 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:37s. Time for last 10,000,000: 3s. Last read position: 234:821,523 INFO 2020-04-17 10:40:20 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:40s. Time for last 10,000,000: 3s. Last read position: 247:449,458 INFO 2020-04-17 10:40:23 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:43s. Time for last 10,000,000: 3s. Last read position: 259:701,369 INFO 2020-04-17 10:40:26 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 3s. Last read position: 273:137,205 INFO 2020-04-17 10:40:29 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 3s. Last read position: 287:177,113 INFO 2020-04-17 10:40:33 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:53s. Time for last 10,000,000: 3s. Last read position: 300:416,946 INFO 2020-04-17 10:40:36 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:01:57s. Time for last 10,000,000: 3s. Last read position: 314:424,834 INFO 2020-04-17 10:40:39 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:00s. Time for last 10,000,000: 3s. Last read position: 330:127 INFO 2020-04-17 10:40:43 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:03s. Time for last 10,000,000: 3s. Last read position: 344:423,663 INFO 2020-04-17 10:40:46 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:06s. Time for last 10,000,000: 3s. Last read position: 359:634,934 INFO 2020-04-17 10:40:49 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:09s. Time for last 10,000,000: 3s. Last read position: 377:83,616 INFO 2020-04-17 10:40:52 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:13s. Time for last 10,000,000: 3s. Last read position: 392:532,908 INFO 2020-04-17 10:40:55 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:16s. Time for last 10,000,000: 3s. Last read position: 409:150,400 INFO 2020-04-17 10:40:59 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:02:19s. Time for last 10,000,000: 3s. Last read position: 426:510,191 INFO 2020-04-17 10:41:02 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 3s. Last read position: 444:356,488 INFO 2020-04-17 10:41:05 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 3s. Last read position: 462:132,483 INFO 2020-04-17 10:41:08 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:29s. Time for last 10,000,000: 3s. Last read position: 480:476,684 INFO 2020-04-17 10:41:12 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:32s. Time for last 10,000,000: 3s. Last read position: 499:472,487 INFO 2020-04-17 10:41:15 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:35s. Time for last 10,000,000: 3s. Last read position: 520:167,314 INFO 2020-04-17 10:41:18 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:38s. Time for last 10,000,000: 3s. Last read position: 541:218,900 INFO 2020-04-17 10:41:21 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:42s. Time for last 10,000,000: 3s. Last read position: 561:89,787 INFO 2020-04-17 10:41:24 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 3s. Last read position: 581:275,897 INFO 2020-04-17 10:41:27 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:48s. Time for last 10,000,000: 3s. Last read position: 605:50,138 INFO 2020-04-17 10:41:31 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 3s. Last read position: 626:305,229 INFO 2020-04-17 10:41:34 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:02:54s. Time for last 10,000,000: 3s. Last read position: 648:244,080 INFO 2020-04-17 10:41:37 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:02:57s. Time for last 10,000,000: 3s. Last read position: 671:195,673 INFO 2020-04-17 10:41:40 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 3s. Last read position: 695:85,112 INFO 2020-04-17 10:41:43 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 3s. Last read position: 720:113,488 INFO 2020-04-17 10:41:46 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 3s. Last read position: 748:34,007 INFO 2020-04-17 10:41:49 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 3s. Last read position: 774:112,571 INFO 2020-04-17 10:41:52 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 3s. Last read position: 801:129,443 INFO 2020-04-17 10:41:55 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 3s. Last read position: 830:46,237 INFO 2020-04-17 10:41:58 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 2s. Last read position: 858:343,631 INFO 2020-04-17 10:42:01 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 3s. Last read position: 888:3,547 INFO 2020-04-17 10:42:04 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:03:25s. Time for last 10,000,000: 3s. Last read position: 918:326,056 INFO 2020-04-17 10:42:07 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:28s. Time for last 10,000,000: 2s. Last read position: 951:37,914 INFO 2020-04-17 10:42:10 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 2s. Last read position: 984:126,977 INFO 2020-04-17 10:42:13 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 3s. Last read position: 1017:167,455 INFO 2020-04-17 10:42:16 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:36s. Time for last 10,000,000: 2s. Last read position: 1052:230,503 INFO 2020-04-17 10:42:19 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 2s. Last read position: 1090:74,736 INFO 2020-04-17 10:42:22 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:42s. Time for last 10,000,000: 3s. Last read position: 1128:19,199 INFO 2020-04-17 10:42:25 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 2s. Last read position: 1168:8,743 INFO 2020-04-17 10:42:28 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 2s. Last read position: 1210:48,462 INFO 2020-04-17 10:42:31 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:03:51s. Time for last 10,000,000: 2s. Last read position: 1252:73,681 INFO 2020-04-17 10:42:34 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:03:54s. Time for last 10,000,000: 2s. Last read position: 1298:135,654 INFO 2020-04-17 10:42:37 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:03:57s. Time for last 10,000,000: 2s. Last read position: 1347:42,922 INFO 2020-04-17 10:42:39 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 2s. Last read position: 1397:45,967 INFO 2020-04-17 10:42:42 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:04:03s. Time for last 10,000,000: 2s. Last read position: 1450:5,557 INFO 2020-04-17 10:42:45 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:04:05s. Time for last 10,000,000: 2s. Last read position: 1505:129,718 INFO 2020-04-17 10:42:48 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 2s. Last read position: 1568:3,714 INFO 2020-04-17 10:42:51 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 2s. Last read position: 1631:39,335 INFO 2020-04-17 10:42:53 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:04:14s. Time for last 10,000,000: 2s. Last read position: 1698:107,239 INFO 2020-04-17 10:42:56 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 2s. Last read position: 1774:115,449 INFO 2020-04-17 10:42:59 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 2s. Last read position: 1853:95,173 INFO 2020-04-17 10:43:01 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:04:22s. Time for last 10,000,000: 2s. Last read position: 1942:62,123 INFO 2020-04-17 10:43:04 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 2s. Last read position: 2039:16,006 INFO 2020-04-17 10:43:07 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:27s. Time for last 10,000,000: 2s. Last read position: 2147:65,939 INFO 2020-04-17 10:43:10 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:30s. Time for last 10,000,000: 2s. Last read position: 2269:65,204 INFO 2020-04-17 10:43:12 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:33s. Time for last 10,000,000: 2s. Last read position: 2409:16,999 INFO 2020-04-17 10:43:15 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:35s. Time for last 10,000,000: 2s. Last read position: 2580:1,672 INFO 2020-04-17 10:43:17 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:38s. Time for last 10,000,000: 2s. Last read position: 2825:574 INFO 2020-04-17 10:43:19 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 10:43:19 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 10:43:19 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 10:43:21 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 10:43:22 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 10:43:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 10:43:26 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 10:43:27 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 10:43:29 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 10:43:31 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 10:43:33 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 10:43:34 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 10:43:36 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 10:43:37 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 4.96 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-17 10:43:37 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 10:43:38.613 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 10:43:38 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 10:43:38 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 10:44:01 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 19s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 10:44:19 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:40s. Time for last 10,000,000: 17s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 10:44:36 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:57s. Time for last 10,000,000: 17s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 10:44:53 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 16s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 10:45:10 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:31s. Time for last 10,000,000: 16s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 10:45:27 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:01:48s. Time for last 10,000,000: 16s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 10:45:43 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 16s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 10:46:01 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 17s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 10:46:18 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:02:39s. Time for last 10,000,000: 16s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 10:46:35 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 17s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 10:46:52 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 16s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 10:47:08 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:03:30s. Time for last 10,000,000: 16s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 10:47:25 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:03:46s. Time for last 10,000,000: 16s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 10:47:42 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:04:03s. Time for last 10,000,000: 16s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 10:47:58 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 16s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 10:48:14 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:04:35s. Time for last 10,000,000: 16s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 10:48:30 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:04:51s. Time for last 10,000,000: 15s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 10:48:45 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:05:07s. Time for last 10,000,000: 15s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 10:49:01 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:05:23s. Time for last 10,000,000: 15s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 10:49:16 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:05:38s. Time for last 10,000,000: 15s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 10:49:31 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:05:53s. Time for last 10,000,000: 14s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 10:49:45 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:06:06s. Time for last 10,000,000: 13s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 10:49:59 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:06:20s. Time for last 10,000,000: 13s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 10:50:11 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:06:32s. Time for last 10,000,000: 12s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 10:50:22 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:06:44s. Time for last 10,000,000: 11s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 10:50:34 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:06:55s. Time for last 10,000,000: 11s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 10:50:45 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:07:06s. Time for last 10,000,000: 10s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 10:50:56 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:07:17s. Time for last 10,000,000: 10s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 10:51:06 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:07:27s. Time for last 10,000,000: 10s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 10:51:16 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:07:37s. Time for last 10,000,000: 9s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 10:51:25 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:07:46s. Time for last 10,000,000: 9s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 10:51:41 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:08:03s. Time for last 10,000,000: 16s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 10:51:56 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:08:18s. Time for last 10,000,000: 14s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 10:52:10 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 10:52:10 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 10:52:10 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 10:52:12 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 10:52:14 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 10:52:15 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 10:52:17 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 10:52:19 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 10:52:20 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 10:52:22 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 10:52:24 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 10:52:25 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 10:52:27 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 10:52:28 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 8.83 minutes. Runtime.totalMemory()=2092957696 INFO 2020-04-17 10:52:29 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 10:52:30.815 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 10:52:30 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 10:52:30 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 10:52:58 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:27s. Time for last 10,000,000: 24s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 10:53:21 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:50s. Time for last 10,000,000: 22s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 10:53:43 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:01:13s. Time for last 10,000,000: 22s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 10:54:06 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:35s. Time for last 10,000,000: 22s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 10:54:27 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 21s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 10:54:49 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 22s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 10:55:11 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:02:40s. Time for last 10,000,000: 21s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 10:55:34 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 22s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 10:55:57 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 22s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 10:56:19 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 22s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 10:56:42 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 22s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 10:57:03 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:04:32s. Time for last 10,000,000: 21s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 10:57:25 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:04:54s. Time for last 10,000,000: 21s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 10:57:46 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:05:15s. Time for last 10,000,000: 21s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 10:58:07 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:05:37s. Time for last 10,000,000: 21s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 10:58:29 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:05:58s. Time for last 10,000,000: 21s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 10:58:50 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:06:19s. Time for last 10,000,000: 20s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 10:59:10 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:06:39s. Time for last 10,000,000: 20s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 10:59:31 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:07:00s. Time for last 10,000,000: 20s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 10:59:50 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 19s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 11:00:10 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:07:39s. Time for last 10,000,000: 19s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 11:00:27 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:07:57s. Time for last 10,000,000: 17s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 11:00:45 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:08:14s. Time for last 10,000,000: 17s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 11:01:01 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:08:30s. Time for last 10,000,000: 15s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 11:01:15 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:08:45s. Time for last 10,000,000: 14s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 11:01:30 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:09:00s. Time for last 10,000,000: 14s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 11:01:44 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:09:13s. Time for last 10,000,000: 13s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 11:01:58 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:09:27s. Time for last 10,000,000: 13s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 11:02:11 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:09:40s. Time for last 10,000,000: 13s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 11:02:23 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:09:52s. Time for last 10,000,000: 12s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 11:02:35 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:10:04s. Time for last 10,000,000: 11s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 11:02:57 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:10:26s. Time for last 10,000,000: 21s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 11:03:16 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:10:45s. Time for last 10,000,000: 19s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 11:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 11:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 11:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 11:03:36 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 11:03:37 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 11:03:39 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 11:03:41 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 11:03:42 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 11:03:44 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 11:03:46 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 11:03:47 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 11:03:49 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 11:03:51 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 11:03:52 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 11.35 minutes. Runtime.totalMemory()=1824522240 INFO 2020-04-17 11:03:52 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 11:03:54.481 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 11:03:54 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 11:03:54 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 11:04:18 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 20s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 11:04:37 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:42s. Time for last 10,000,000: 19s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 11:04:56 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:01:01s. Time for last 10,000,000: 18s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 11:05:14 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 18s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 11:05:32 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 18s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 11:05:51 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 18s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 11:06:09 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:02:14s. Time for last 10,000,000: 18s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 11:06:28 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:02:34s. Time for last 10,000,000: 19s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 11:06:47 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 18s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 11:07:06 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:03:11s. Time for last 10,000,000: 18s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 11:07:24 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:03:30s. Time for last 10,000,000: 18s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 11:07:42 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 17s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 11:08:01 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:04:06s. Time for last 10,000,000: 18s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 11:08:19 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 18s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 11:08:37 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:04:42s. Time for last 10,000,000: 17s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 11:08:55 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:05:00s. Time for last 10,000,000: 17s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 11:09:12 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:05:17s. Time for last 10,000,000: 17s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 11:09:29 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:05:34s. Time for last 10,000,000: 16s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 11:09:46 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:05:52s. Time for last 10,000,000: 17s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 11:10:03 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:06:08s. Time for last 10,000,000: 16s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 11:10:19 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:06:24s. Time for last 10,000,000: 16s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 11:10:34 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:06:39s. Time for last 10,000,000: 14s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 11:10:48 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:06:54s. Time for last 10,000,000: 14s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 11:11:02 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:07:07s. Time for last 10,000,000: 13s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 11:11:14 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 12s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 11:11:27 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:07:32s. Time for last 10,000,000: 12s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 11:11:38 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:07:44s. Time for last 10,000,000: 11s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 11:11:50 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:07:56s. Time for last 10,000,000: 11s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 11:12:01 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:08:07s. Time for last 10,000,000: 11s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 11:12:12 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:08:17s. Time for last 10,000,000: 10s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 11:12:22 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:08:27s. Time for last 10,000,000: 9s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 11:12:40 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:08:45s. Time for last 10,000,000: 18s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 11:12:56 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:09:02s. Time for last 10,000,000: 16s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 11:13:12 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 11:13:12 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 11:13:12 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 11:13:13 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 11:13:15 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 11:13:17 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 11:13:18 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 11:13:20 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 11:13:22 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 11:13:23 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 11:13:25 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 11:13:27 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 11:13:29 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 11:13:29 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 9.59 minutes. Runtime.totalMemory()=1939865600 INFO 2020-04-17 11:13:30 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 11:13:31.315 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 11:13:31 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 11:13:31 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 11:15:14 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:01:43s. Time for last 10,000,000: 99s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 11:16:37 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 82s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 11:18:20 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:04:49s. Time for last 10,000,000: 103s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 11:19:47 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:06:16s. Time for last 10,000,000: 86s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 11:21:16 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:07:45s. Time for last 10,000,000: 89s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 11:22:38 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:09:07s. Time for last 10,000,000: 82s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 11:24:08 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:10:36s. Time for last 10,000,000: 89s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 11:25:41 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:12:09s. Time for last 10,000,000: 93s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 11:27:09 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:13:37s. Time for last 10,000,000: 88s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 11:28:47 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:15:15s. Time for last 10,000,000: 97s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 11:30:21 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:16:49s. Time for last 10,000,000: 93s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 11:31:50 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:18:18s. Time for last 10,000,000: 89s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 11:33:24 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:19:52s. Time for last 10,000,000: 94s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 11:34:49 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:21:17s. Time for last 10,000,000: 85s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 11:36:16 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:22:44s. Time for last 10,000,000: 86s. Last read position: scaffold4238_cov95:138,603 WARNING 2020-04-17 11:37:29 AbstractLocusIterator We have encountered greater than 100000 reads at position scaffold4845_cov90:44 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 11:37:46 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:24:15s. Time for last 10,000,000: 90s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 11:39:09 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:25:38s. Time for last 10,000,000: 82s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 11:40:45 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:27:14s. Time for last 10,000,000: 95s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 11:42:05 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:28:34s. Time for last 10,000,000: 79s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 11:43:31 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:30:00s. Time for last 10,000,000: 85s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 11:45:26 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:31:54s. Time for last 10,000,000: 114s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 11:46:47 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:33:16s. Time for last 10,000,000: 81s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 11:47:59 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:34:28s. Time for last 10,000,000: 71s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 11:49:18 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:35:47s. Time for last 10,000,000: 78s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 11:50:28 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:36:57s. Time for last 10,000,000: 70s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 11:51:58 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:38:27s. Time for last 10,000,000: 89s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 11:53:27 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:39:55s. Time for last 10,000,000: 88s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 11:54:44 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:41:13s. Time for last 10,000,000: 77s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 11:55:48 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:42:16s. Time for last 10,000,000: 63s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 11:56:53 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:43:22s. Time for last 10,000,000: 65s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 11:58:01 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:44:30s. Time for last 10,000,000: 68s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 11:59:39 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:46:08s. Time for last 10,000,000: 97s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 12:01:01 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:47:30s. Time for last 10,000,000: 81s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 12:03:41 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 12:03:41 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 12:03:41 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 12:03:43 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 12:03:45 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 12:03:46 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 12:03:48 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 12:03:50 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 12:03:51 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 12:03:53 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 12:03:55 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 12:03:56 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 12:03:58 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 12:03:59 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 50.47 minutes. Runtime.totalMemory()=6788481024 INFO 2020-04-17 12:04:00 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth5_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 12:04:01.406 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 12:04:01 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth5_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 12:04:01 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 12:08:13 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 248s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 12:11:29 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:07:28s. Time for last 10,000,000: 196s. Last read position: scaffold378_cov109:513,118 WARNING 2020-04-17 12:13:17 AbstractLocusIterator We have encountered greater than 100000 reads at position scaffold458_cov114:451017 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 12:15:11 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:11:09s. Time for last 10,000,000: 221s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 12:18:35 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:14:34s. Time for last 10,000,000: 204s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 12:21:57 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:17:56s. Time for last 10,000,000: 201s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 12:25:16 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:21:15s. Time for last 10,000,000: 199s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 12:28:49 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:24:48s. Time for last 10,000,000: 213s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 12:32:34 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:28:32s. Time for last 10,000,000: 224s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 12:36:07 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:32:06s. Time for last 10,000,000: 213s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 12:40:05 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:36:03s. Time for last 10,000,000: 237s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 12:43:51 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:39:50s. Time for last 10,000,000: 226s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 12:47:17 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:43:15s. Time for last 10,000,000: 205s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 12:50:47 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:46:46s. Time for last 10,000,000: 210s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 12:54:03 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:50:02s. Time for last 10,000,000: 195s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 12:57:29 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:53:27s. Time for last 10,000,000: 205s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 13:00:47 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:56:46s. Time for last 10,000,000: 198s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 13:04:01 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 01:00:00s. Time for last 10,000,000: 193s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 13:07:41 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 01:03:40s. Time for last 10,000,000: 219s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 13:10:45 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 01:06:44s. Time for last 10,000,000: 183s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 13:13:56 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 01:09:55s. Time for last 10,000,000: 191s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 13:17:46 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 01:13:45s. Time for last 10,000,000: 229s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 13:20:48 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 01:16:46s. Time for last 10,000,000: 181s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 13:23:33 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 01:19:31s. Time for last 10,000,000: 165s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 13:26:42 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 01:22:41s. Time for last 10,000,000: 189s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 13:29:18 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 01:25:17s. Time for last 10,000,000: 155s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 13:32:41 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 01:28:40s. Time for last 10,000,000: 202s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 13:35:42 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 01:31:40s. Time for last 10,000,000: 180s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 13:38:18 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 01:34:16s. Time for last 10,000,000: 156s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 13:40:43 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 01:36:42s. Time for last 10,000,000: 145s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 13:42:59 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 01:38:57s. Time for last 10,000,000: 135s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 13:45:21 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 01:41:19s. Time for last 10,000,000: 141s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 13:48:58 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 01:44:57s. Time for last 10,000,000: 217s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 13:52:12 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 01:48:11s. Time for last 10,000,000: 193s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 13:56:19 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 13:56:19 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 13:56:19 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 13:56:20 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 13:56:22 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 13:56:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 13:56:25 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 13:56:27 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 13:56:29 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 13:56:30 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 13:56:32 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 13:56:34 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 13:56:35 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 13:56:36 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 112.59 minutes. Runtime.totalMemory()=7398752256 INFO 2020-04-17 13:56:38 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth6_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 13:56:40.432 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 13:56:40 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth6_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 13:56:40 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 13:58:16 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:01:35s. Time for last 10,000,000: 91s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 13:59:32 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 76s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 14:01:05 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 93s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 14:02:25 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 80s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 14:03:48 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:07:07s. Time for last 10,000,000: 82s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 14:05:05 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:08:24s. Time for last 10,000,000: 76s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 14:06:28 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:09:47s. Time for last 10,000,000: 82s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 14:07:53 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:11:13s. Time for last 10,000,000: 85s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 14:09:15 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:12:35s. Time for last 10,000,000: 81s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 14:10:46 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:14:06s. Time for last 10,000,000: 91s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 14:12:14 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:15:33s. Time for last 10,000,000: 87s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 14:13:36 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:16:55s. Time for last 10,000,000: 81s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 14:15:02 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:18:21s. Time for last 10,000,000: 86s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 14:16:20 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:19:39s. Time for last 10,000,000: 78s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 14:17:40 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:20:59s. Time for last 10,000,000: 79s. Last read position: scaffold4238_cov95:138,603 WARNING 2020-04-17 14:18:47 AbstractLocusIterator We have encountered greater than 100000 reads at position scaffold4845_cov90:44 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 14:19:03 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:22:22s. Time for last 10,000,000: 83s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 14:20:18 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:23:38s. Time for last 10,000,000: 75s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 14:21:45 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:25:05s. Time for last 10,000,000: 86s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 14:22:59 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:26:19s. Time for last 10,000,000: 74s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 14:24:18 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:27:37s. Time for last 10,000,000: 78s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 14:26:04 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:29:24s. Time for last 10,000,000: 106s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 14:27:20 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:30:40s. Time for last 10,000,000: 75s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 14:28:28 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:31:47s. Time for last 10,000,000: 67s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 14:29:42 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:33:01s. Time for last 10,000,000: 73s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 14:30:46 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:34:06s. Time for last 10,000,000: 64s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 14:32:07 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:35:27s. Time for last 10,000,000: 80s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 14:33:33 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:36:53s. Time for last 10,000,000: 85s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 14:34:46 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:38:06s. Time for last 10,000,000: 73s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 14:35:46 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:39:06s. Time for last 10,000,000: 60s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 14:36:48 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:40:07s. Time for last 10,000,000: 61s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 14:37:50 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:41:10s. Time for last 10,000,000: 62s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 14:39:22 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:42:41s. Time for last 10,000,000: 91s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 14:40:37 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:43:57s. Time for last 10,000,000: 75s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 14:43:18 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 14:43:18 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 14:43:18 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 14:43:20 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 14:43:22 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 14:43:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 14:43:25 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 14:43:27 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 14:43:29 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 14:43:30 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 14:43:32 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 14:43:34 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 14:43:35 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 14:43:36 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 46.94 minutes. Runtime.totalMemory()=7738490880 INFO 2020-04-17 14:43:38 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 14:43:39.668 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 14:43:39 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 14:43:39 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 14:43:58 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 15s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 14:44:12 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:32s. Time for last 10,000,000: 14s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 14:44:26 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:47s. Time for last 10,000,000: 14s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 14:44:40 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 13s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 14:44:54 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 14s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 14:45:08 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 14s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 14:45:21 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 12s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 14:45:35 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 14s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 14:45:49 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:02:09s. Time for last 10,000,000: 13s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 14:46:04 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:02:24s. Time for last 10,000,000: 14s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 14:46:17 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 13s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 14:46:31 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 13s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 14:46:45 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 13s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 14:46:58 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:03:18s. Time for last 10,000,000: 12s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 14:47:11 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 13s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 14:47:24 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:03:44s. Time for last 10,000,000: 13s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 14:47:38 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:03:58s. Time for last 10,000,000: 13s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 14:47:51 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 12s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 14:48:04 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 13s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 14:48:16 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:04:36s. Time for last 10,000,000: 11s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 14:48:30 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:04:50s. Time for last 10,000,000: 14s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 14:48:42 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:05:03s. Time for last 10,000,000: 12s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 14:48:54 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:05:14s. Time for last 10,000,000: 11s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 14:49:05 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:05:25s. Time for last 10,000,000: 10s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 14:49:16 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:05:37s. Time for last 10,000,000: 11s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 14:49:29 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:05:49s. Time for last 10,000,000: 12s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 14:49:39 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:05:59s. Time for last 10,000,000: 10s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 14:49:49 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:06:10s. Time for last 10,000,000: 10s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 14:50:00 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:06:20s. Time for last 10,000,000: 10s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 14:50:10 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:06:30s. Time for last 10,000,000: 10s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 14:50:20 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:06:40s. Time for last 10,000,000: 9s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 14:50:34 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:06:55s. Time for last 10,000,000: 14s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 14:50:47 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:07:07s. Time for last 10,000,000: 12s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 14:51:04 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 14:51:04 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 14:51:04 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 14:51:05 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 14:51:07 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 14:51:09 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 14:51:11 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 14:51:12 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 14:51:14 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 14:51:16 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 14:51:17 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 14:51:19 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 14:51:21 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 14:51:21 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 7.71 minutes. Runtime.totalMemory()=2038431744 INFO 2020-04-17 14:51:22 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 14:51:23.491 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 14:51:23 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 14:51:23 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 14:51:36 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 9s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 14:51:44 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:21s. Time for last 10,000,000: 7s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 14:51:52 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:28s. Time for last 10,000,000: 7s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 14:51:59 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:36s. Time for last 10,000,000: 7s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 14:52:07 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 7s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 14:52:15 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:51s. Time for last 10,000,000: 7s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 14:52:22 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:58s. Time for last 10,000,000: 6s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 14:52:30 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:07s. Time for last 10,000,000: 8s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 14:52:38 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:01:14s. Time for last 10,000,000: 7s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 14:52:46 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:01:22s. Time for last 10,000,000: 8s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 14:52:53 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 7s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 14:53:01 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 8s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 14:53:09 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:45s. Time for last 10,000,000: 7s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 14:53:16 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:52s. Time for last 10,000,000: 6s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 14:53:23 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:59s. Time for last 10,000,000: 7s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 14:53:30 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:02:07s. Time for last 10,000,000: 7s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 14:53:38 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 8s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 14:53:46 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 7s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 14:53:53 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:02:30s. Time for last 10,000,000: 7s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 14:54:00 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:36s. Time for last 10,000,000: 6s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 14:54:07 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:44s. Time for last 10,000,000: 7s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 14:54:15 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 7s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 14:54:22 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:58s. Time for last 10,000,000: 6s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 14:54:28 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:03:04s. Time for last 10,000,000: 6s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 14:54:35 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:11s. Time for last 10,000,000: 6s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 14:54:42 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 7s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 14:54:48 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:25s. Time for last 10,000,000: 6s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 14:54:55 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 6s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 14:55:02 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:38s. Time for last 10,000,000: 6s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 14:55:08 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 6s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 14:55:14 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:51s. Time for last 10,000,000: 5s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 14:55:23 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 8s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 14:55:30 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:04:06s. Time for last 10,000,000: 6s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 14:55:41 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 14:55:41 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 14:55:41 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 14:55:42 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 14:55:44 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 14:55:46 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 14:55:48 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 14:55:49 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 14:55:51 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 14:55:53 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 14:55:54 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 14:55:56 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 14:55:58 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 14:55:58 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 4.59 minutes. Runtime.totalMemory()=2956984320 INFO 2020-04-17 14:55:59 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta ********** 14:56:01.328 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 14:56:01 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/Pact_Genome/Pocillopora_acuta_genome_v1.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 14:56:01 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 14:56:20 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 15s. Last read position: scaffold174_cov103:82,005 INFO 2020-04-17 14:56:33 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:32s. Time for last 10,000,000: 13s. Last read position: scaffold378_cov109:513,118 INFO 2020-04-17 14:56:47 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 13s. Last read position: scaffold543_cov112:282,336 INFO 2020-04-17 14:57:00 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:59s. Time for last 10,000,000: 12s. Last read position: scaffold733_cov100:67,264 INFO 2020-04-17 14:57:13 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 13s. Last read position: scaffold933_cov100:105,041 INFO 2020-04-17 14:57:27 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:01:26s. Time for last 10,000,000: 13s. Last read position: scaffold1105_cov104:582,009 INFO 2020-04-17 14:57:39 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 12s. Last read position: scaffold1389_cov93:344,014 INFO 2020-04-17 14:57:53 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:01:52s. Time for last 10,000,000: 13s. Last read position: scaffold1608_cov101:380,242 INFO 2020-04-17 14:58:06 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:02:04s. Time for last 10,000,000: 12s. Last read position: scaffold1888_cov75:7,343 INFO 2020-04-17 14:58:20 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 13s. Last read position: scaffold2117_cov101:80,202 INFO 2020-04-17 14:58:33 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 12s. Last read position: scaffold2469_cov109:277,544 INFO 2020-04-17 14:58:46 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:02:44s. Time for last 10,000,000: 13s. Last read position: scaffold2810_cov55:521 INFO 2020-04-17 14:58:59 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:02:57s. Time for last 10,000,000: 13s. Last read position: scaffold3152_cov102:209,393 INFO 2020-04-17 14:59:11 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 12s. Last read position: scaffold3617_cov101:140,299 INFO 2020-04-17 14:59:24 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 12s. Last read position: scaffold4238_cov95:138,603 INFO 2020-04-17 14:59:36 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:03:35s. Time for last 10,000,000: 12s. Last read position: scaffold4918_cov108:109,118 INFO 2020-04-17 14:59:49 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:03:47s. Time for last 10,000,000: 12s. Last read position: scaffold5793_cov102:357,192 INFO 2020-04-17 15:00:01 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 12s. Last read position: scaffold6744_cov56:225 INFO 2020-04-17 15:00:13 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:04:12s. Time for last 10,000,000: 12s. Last read position: scaffold8110_cov105:164,417 INFO 2020-04-17 15:00:25 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:04:23s. Time for last 10,000,000: 11s. Last read position: scaffold9716_cov97:37,251 INFO 2020-04-17 15:00:37 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:04:36s. Time for last 10,000,000: 12s. Last read position: scaffold12136_cov60:862 INFO 2020-04-17 15:00:48 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:04:47s. Time for last 10,000,000: 11s. Last read position: scaffold15966_cov78:7,894 INFO 2020-04-17 15:00:59 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:04:57s. Time for last 10,000,000: 10s. Last read position: scaffold19936_cov57:767 INFO 2020-04-17 15:01:08 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:05:07s. Time for last 10,000,000: 9s. Last read position: scaffold26698_cov85:79 INFO 2020-04-17 15:01:18 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:05:17s. Time for last 10,000,000: 9s. Last read position: scaffold34819_cov59:11,716 INFO 2020-04-17 15:01:29 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:05:27s. Time for last 10,000,000: 10s. Last read position: scaffold45645_cov87:5,091 INFO 2020-04-17 15:01:37 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:05:36s. Time for last 10,000,000: 8s. Last read position: scaffold58876_cov115:175 INFO 2020-04-17 15:01:47 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 9s. Last read position: scaffold74197_cov108:432 INFO 2020-04-17 15:01:56 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:05:54s. Time for last 10,000,000: 8s. Last read position: scaffold92694_cov107:177,918 INFO 2020-04-17 15:02:04 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:06:03s. Time for last 10,000,000: 8s. Last read position: scaffold115807_cov63:295 INFO 2020-04-17 15:02:13 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:06:11s. Time for last 10,000,000: 8s. Last read position: scaffold144853_cov90:1,383 INFO 2020-04-17 15:02:26 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:06:25s. Time for last 10,000,000: 13s. Last read position: scaffold150336_cov100:44,078 INFO 2020-04-17 15:02:38 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:06:37s. Time for last 10,000,000: 11s. Last read position: scaffold159416_cov103:1,227 INFO 2020-04-17 15:02:52 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:02:52 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:02:52 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:02:54 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:02:55 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:02:57 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:02:59 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:03:00 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:03:02 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:03:04 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:03:05 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:03:07 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:03:09 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:03:09 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 7.14 minutes. Runtime.totalMemory()=2216689664 INFO 2020-04-17 15:03:10 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:03:11.634 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:03:11 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:03:11 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:03:15 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:03:18 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:03:20 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:09s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:03:23 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:03:25 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:14s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:03:28 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:17s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:03:31 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:03:34 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:03:37 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:25s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:03:40 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:28s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:03:43 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:31s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:03:46 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:34s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:03:49 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:37s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:03:52 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:40s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:03:54 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:03:57 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:04:00 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:00:48s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:04:03 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:00:51s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:04:06 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:00:54s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:04:09 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:00:57s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:04:12 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:04:15 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:04:18 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:04:21 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:09s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:04:24 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:04:27 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:15s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:04:30 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:18s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:04:33 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:21s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:04:35 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:24s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 15:04:38 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:04:41 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:04:44 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:32s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:04:47 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:35s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:04:50 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:04:53 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:04:56 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:01:44s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:04:59 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:05:02 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:05:05 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:01:53s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:05:08 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:05:11 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:01:59s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:05:14 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:02s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:05:17 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:05:20 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:05:22 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:05:25 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:14s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:05:28 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:17s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:05:31 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:05:34 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:05:37 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:25s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:05:40 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:02:28s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:05:43 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:05:46 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:02:34s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:05:49 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:05:52 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:02:40s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:05:55 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:02:43s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:05:58 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:02:46s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:06:01 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:02:49s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:06:04 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:06:07 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:06:10 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:02:58s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:06:13 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:03:01s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:06:16 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:04s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:06:18 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:06:21 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:06:24 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:06:27 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:06:30 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:06:34 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:06:37 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:03:25s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:06:39 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:03:28s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:06:42 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:06:45 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:06:48 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:03:37s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:06:51 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:03:40s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:06:54 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:03:43s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:06:58 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:03:46s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:07:01 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:03:49s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:07:04 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:07:07 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:03:55s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:07:10 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:03:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:07:13 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:04:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:07:16 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:07:19 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:07:22 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:07:25 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:07:28 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:07:31 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:07:33 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:04:21s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:07:35 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:07:35 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:07:35 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:07:37 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:07:38 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:07:40 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:07:42 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:07:43 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:07:45 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:07:47 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:07:48 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:07:50 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:07:52 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:07:53 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 4.69 minutes. Runtime.totalMemory()=1673527296 INFO 2020-04-17 15:07:54 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:07:54.719 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:07:54 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:07:54 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:07:58 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:08:00 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:05s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:08:02 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:08:05 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:08:07 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:12s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:08:10 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:15s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:08:12 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:08:15 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:20s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:08:18 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:08:21 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:26s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:08:24 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:08:26 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:32s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:08:29 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:35s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:08:32 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:37s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:08:35 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:40s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:08:38 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:08:41 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:08:44 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:00:49s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:08:47 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:00:52s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:08:49 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:00:55s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:08:52 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:00:58s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:08:55 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:08:58 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:09:01 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:09:04 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:09s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:09:07 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:09:10 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:15s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:09:13 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:18s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:09:15 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:21s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 15:09:18 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:23s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:09:21 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:26s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:09:24 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:09:27 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:32s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:09:30 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:01:35s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:09:33 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:09:36 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:09:39 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:01:44s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:09:41 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:09:44 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:09:47 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:01:52s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:09:50 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:01:55s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:09:53 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:09:56 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:09:59 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:04s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:10:02 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:10:05 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:10:07 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:10:10 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:10:13 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:10:16 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:21s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:10:19 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:02:24s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:10:22 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:02:27s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:10:25 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:02:30s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:10:28 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:02:33s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:10:31 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:02:36s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:10:34 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:02:39s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:10:36 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:02:42s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:10:39 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:10:42 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:02:48s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:10:45 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:02:50s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:10:48 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:02:53s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:10:51 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:10:54 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:10:57 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:02s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:11:00 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:11:03 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:11:06 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:11:09 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:11:12 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:03:17s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:11:15 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:11:18 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:11:21 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:11:23 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:03:29s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:11:26 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:03:32s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:11:29 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:03:35s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:11:32 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:03:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:11:35 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:03:41s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:11:38 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:03:44s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:11:41 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:03:47s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:11:45 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:03:50s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:11:48 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:03:53s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:11:51 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:03:56s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:11:54 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:11:57 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:02s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:12:00 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:05s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:12:02 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:12:05 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:12:08 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:12:10 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:12:12 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:12:12 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:12:12 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:12:14 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:12:16 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:12:17 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:12:19 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:12:21 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:12:22 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:12:24 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:12:26 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:12:27 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:12:29 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:12:30 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 4.59 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-17 15:12:31 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:12:31.849 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:12:31 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:12:31 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:12:35 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:12:38 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:12:40 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:12:42 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:12:45 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:12:48 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:12:51 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:12:53 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:21s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:12:56 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:24s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:12:59 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:27s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:13:02 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:30s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:13:05 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:33s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:13:08 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:36s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:13:11 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:39s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:13:13 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:42s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:13:16 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:44s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:13:19 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:00:47s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:13:22 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:00:50s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:13:25 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:00:53s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:13:28 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:00:56s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:13:31 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:00:59s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:13:34 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:13:36 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:05s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:13:39 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:13:42 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:13:45 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:13:48 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:13:51 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:13:54 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:22s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 15:13:57 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:25s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:14:00 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:28s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:14:02 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:31s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:14:05 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:34s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:14:08 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:01:36s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:14:11 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:01:39s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:14:14 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:01:42s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:14:17 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:01:45s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:14:20 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:01:48s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:14:23 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:01:51s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:14:26 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:14:29 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:01:57s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:14:32 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:00s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:14:35 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:14:38 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:14:40 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:14:43 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:14:46 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:14s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:14:49 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:17s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:14:52 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:20s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:14:55 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:23s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:14:58 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:15:01 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:02:29s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:15:04 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:02:32s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:15:07 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:02:35s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:15:10 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:02:38s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:15:13 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:02:41s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:15:16 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:02:44s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:15:19 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:02:47s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:15:21 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:02:50s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:15:24 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:15:27 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:15:30 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:02:58s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:15:33 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:01s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:15:36 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:04s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:15:39 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:15:42 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:15:45 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:15:48 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:15:51 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:15:54 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:15:57 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:03:25s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:16:00 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:03:28s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:16:03 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:16:06 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:16:09 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:03:37s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:16:12 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:03:40s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:16:15 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:03:43s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:16:18 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:03:46s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:16:21 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:03:49s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:16:24 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:16:27 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:03:55s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:16:30 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:03:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:16:33 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:16:36 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:16:39 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:16:42 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:10s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:16:45 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:16:48 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:16:50 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:16:52 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:16:52 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:16:52 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:16:54 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:16:56 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:16:57 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:16:59 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:17:01 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:17:03 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:17:04 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:17:06 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:17:08 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:17:09 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:17:10 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 4.65 minutes. Runtime.totalMemory()=1673527296 INFO 2020-04-17 15:17:11 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth4_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:17:12.314 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:17:12 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth4_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:17:12 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:17:17 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:17:19 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:17:22 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:17:25 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:17:28 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:15s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:17:31 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:17:34 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:17:37 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:25s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:17:41 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:28s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:17:44 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:31s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:17:47 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:17:50 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:17:53 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:17:57 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:45s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:18:01 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:18:04 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:18:07 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:00:55s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:18:11 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:00:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:18:14 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:18:18 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:05s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:18:21 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:09s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:18:25 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:18:28 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:15s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:18:31 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:18:35 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:23s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:18:39 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:26s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:18:42 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:29s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:18:45 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:33s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:18:48 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:36s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1311:52,950 WARNING 2020-04-17 15:18:52 AbstractLocusIterator We have encountered greater than 100000 reads at position SymbC1.scaffold1384:18113 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 15:18:53 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:18:57 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:44s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:19:00 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:19:03 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:51s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:19:07 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:19:10 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:19:13 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:19:17 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:19:20 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:19:23 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:19:27 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:19:30 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:19:33 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:21s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:19:37 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:25s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:19:40 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:28s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:19:44 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:19:47 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:19:50 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:19:53 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:19:57 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:20:00 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:20:04 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:02:51s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:20:07 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:02:54s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:20:10 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:02:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:20:13 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:03:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:20:17 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:03:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:20:20 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:03:07s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:20:23 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:03:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:20:26 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:20:29 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:03:17s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:20:33 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:20:36 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:20:39 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:03:27s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:20:43 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:20:47 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:20:50 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:20:54 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:42s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:20:58 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:21:01 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:21:04 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:21:07 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:03:55s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:21:10 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:03:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:21:14 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:04:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:21:17 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:21:20 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:21:23 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:04:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:21:27 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:04:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:21:30 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:04:18s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:21:33 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:04:21s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:21:37 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:21:40 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:04:28s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:21:43 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:04:31s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:21:47 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:04:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:21:50 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:21:53 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:21:57 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:22:03 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:04:51s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:22:06 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:04:54s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:22:10 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:04:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:22:13 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:05:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:23:24 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:23:24 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:23:24 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:23:26 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:23:28 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:23:29 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:23:31 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:23:33 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:23:34 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:23:36 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:23:38 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:23:40 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:23:41 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:23:42 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 6.51 minutes. Runtime.totalMemory()=6016729088 INFO 2020-04-17 15:23:44 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth5_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:23:45.331 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:23:45 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth5_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:23:45 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:23:50 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:05s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:23:53 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:23:56 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:23:59 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:24:03 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:17s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:24:07 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:21s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:24:11 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:25s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:24:15 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:30s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:24:20 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:35s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:24:24 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:39s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:24:28 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:24:33 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:47s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:24:37 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:52s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:24:42 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:57s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:24:47 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:02s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:24:52 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:07s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:24:57 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:11s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:25:01 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:16s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:25:06 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:20s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:25:12 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:26s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:25:17 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:32s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:25:22 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:37s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:25:27 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:25:31 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:46s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:25:37 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:51s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:25:41 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:25:45 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:02:00s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:25:50 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:25:54 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:02:09s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1311:52,950 WARNING 2020-04-17 15:25:59 AbstractLocusIterator We have encountered greater than 100000 reads at position SymbC1.scaffold1384:18113 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 15:26:00 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:26:05 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:02:20s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:26:10 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:02:24s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:26:14 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:02:29s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:26:18 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:33s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:26:22 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:26:27 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:41s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:26:31 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:46s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:26:35 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:50s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:26:40 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:26:44 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:26:49 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:26:53 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:03:08s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:26:58 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:27:02 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:03:17s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:27:06 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:03:21s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:27:11 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:03:25s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:27:15 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:03:29s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:27:19 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:27:24 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:27:28 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:03:43s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:27:32 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:03:47s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:27:37 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:03:51s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:27:41 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:03:55s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:27:46 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:27:50 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:04:05s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:27:54 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:04:09s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:27:58 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:28:02 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:04:17s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:28:06 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:04:21s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:28:10 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:28:15 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:04:29s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:28:19 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:04:33s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:28:25 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:04:40s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:28:29 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:28:33 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:04:48s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:28:40 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:04:54s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:28:44 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:04:59s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:28:48 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:05:03s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:28:52 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:05:07s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:28:57 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:05:11s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:29:01 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:05:15s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:29:05 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:05:19s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:29:09 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:05:23s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:29:13 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:05:28s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:29:17 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:05:32s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:29:21 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:05:36s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:29:25 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:05:40s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:29:30 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:29:34 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:05:49s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:29:38 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:05:53s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:29:43 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:05:58s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:29:47 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:06:02s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:29:51 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:06:06s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:29:55 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:06:10s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:29:59 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:06:14s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:30:09 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:06:24s. Time for last 10,000,000: 10s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:30:13 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:06:28s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:30:18 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:06:32s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:30:22 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:06:36s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:31:58 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:31:58 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:31:58 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:32:00 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:32:01 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:32:03 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:32:05 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:32:07 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:32:08 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:32:10 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:32:12 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:32:14 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:32:16 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:32:16 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 8.53 minutes. Runtime.totalMemory()=7063207936 INFO 2020-04-17 15:32:18 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth6_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:32:19.655 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:32:19 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth6_R1_001_val_1_bismark_bt2_pe.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:32:19 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:32:24 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:04s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:32:27 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:07s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:32:29 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:09s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:32:32 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:12s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:32:35 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:15s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:32:38 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:32:41 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:22s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:32:45 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:25s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:32:48 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:32:51 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:32s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:32:55 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:35s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:32:58 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:33:01 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:42s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:33:05 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:00:45s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:33:09 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:00:49s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:33:12 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:00:53s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:33:16 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:00:56s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:33:19 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:33:23 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:03s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:33:27 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:07s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:33:31 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:11s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:33:35 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:15s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:33:39 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:33:42 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:22s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:33:47 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:33:50 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:01:31s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:33:54 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:01:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:33:57 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:34:01 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:01:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1311:52,950 WARNING 2020-04-17 15:34:05 AbstractLocusIterator We have encountered greater than 100000 reads at position SymbC1.scaffold1384:18113 and will ignore the remaining reads at this position. Note that further warnings will be suppressed. INFO 2020-04-17 15:34:06 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:34:10 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:34:14 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:34:17 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:01:57s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:34:21 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:34:24 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:05s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:34:28 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:02:08s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:34:32 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:02:12s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:34:35 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:34:39 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:02:19s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:34:42 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:02:23s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:34:46 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:34:50 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:02:30s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:34:54 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:02:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:34:57 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:35:01 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:02:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:35:04 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:35:08 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:02:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:35:12 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:35:16 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:02:56s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:35:19 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:35:23 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:35:26 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:35:29 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:35:33 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:35:36 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:03:17s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:35:40 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:35:43 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:35:46 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:03:27s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:35:50 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:03:30s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:35:53 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:03:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:35:57 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:03:37s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:36:01 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:03:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:36:05 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:36:09 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:03:49s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:36:12 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:36:16 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:03:57s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:36:20 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:36:23 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:04:03s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:36:27 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:36:30 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:04:10s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:36:33 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:04:14s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:36:37 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:04:17s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:36:40 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:04:20s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:36:43 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:36:47 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:04:27s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:36:50 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:04:31s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:36:54 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:04:34s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:36:57 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:04:38s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:37:01 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:04:41s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:37:04 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:04:44s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:37:07 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:04:48s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:37:11 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:04:51s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:37:14 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:04:55s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:37:18 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:04:58s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:37:21 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:05:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:37:28 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:05:08s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:37:31 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:05:11s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:37:34 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:05:15s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:37:37 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:05:18s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:38:54 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:38:54 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:38:54 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:38:56 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:38:58 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:38:59 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:39:01 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:39:03 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:39:04 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:39:06 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:39:08 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:39:10 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:39:11 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:39:12 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 6.88 minutes. Runtime.totalMemory()=7696547840 INFO 2020-04-17 15:39:14 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:39:15.370 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:39:15 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:39:15 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:39:19 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:39:21 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:39:23 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:39:26 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:10s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:39:28 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:39:33 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:39:39 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:39:44 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:39:50 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:35s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:39:56 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:40s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:40:02 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:46s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:40:08 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:52s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:40:14 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:58s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:40:20 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:04s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:40:25 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:10s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:40:31 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:16s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:40:37 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:21s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:40:42 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:40:48 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:33s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:40:54 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:39s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:41:00 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:45s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:41:06 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:41:11 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:56s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:41:17 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:41:23 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:02:07s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:41:28 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:02:13s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:41:34 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:02:18s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:41:40 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:02:24s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:41:46 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:02:30s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 15:41:51 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:02:36s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:41:57 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:02:42s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:42:03 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:02:47s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:42:09 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:02:53s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:42:14 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:42:20 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:42:26 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:42:31 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:03:16s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:42:37 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:42:43 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:03:27s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:42:49 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:03:33s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:42:54 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:43:00 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:03:45s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:43:06 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:03:51s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:43:12 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:03:56s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:43:18 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:04:02s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:43:23 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:43:29 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:04:14s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:43:35 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:04:19s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:43:41 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:43:46 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:04:31s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:43:52 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:04:37s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:43:58 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:04:42s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:44:04 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:04:48s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:44:10 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:04:55s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:44:16 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:05:00s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:44:22 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:05:06s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:44:28 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:05:12s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:44:34 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:05:18s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:44:40 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:05:24s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:44:46 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:05:30s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:44:52 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:05:36s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:44:58 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:05:42s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:45:03 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:05:48s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:45:09 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:05:54s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:45:15 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:05:59s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:45:20 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:06:05s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:45:26 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:06:11s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:45:32 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:06:17s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:45:38 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:06:22s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:45:44 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:06:28s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:45:50 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:06:34s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:45:56 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:06:41s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:46:02 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:06:47s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:46:08 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:06:52s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:46:13 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:06:58s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:46:19 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:07:04s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:46:25 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:07:09s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:46:30 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:07:15s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:46:36 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:46:41 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:07:26s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:46:47 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:07:31s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:46:52 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:07:37s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:46:58 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:07:42s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:47:04 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:07:48s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:47:08 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:07:53s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:47:13 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:07:57s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:47:17 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:08:01s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:47:20 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:08:05s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:47:24 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:08:09s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:47:27 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:47:27 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:47:27 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:47:28 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:47:30 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:47:32 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:47:34 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:47:35 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:47:37 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:47:39 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:47:40 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:47:42 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:47:44 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:47:44 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 8.49 minutes. Runtime.totalMemory()=1673527296 INFO 2020-04-17 15:47:45 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:47:46.654 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:47:46 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:47:46 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:47:50 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:47:53 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:47:55 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:47:57 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:48:00 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:48:07 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:20s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:48:14 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:27s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:48:21 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:34s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:48:28 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:42s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 15:48:36 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:49s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 15:48:43 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:56s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 15:48:51 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:01:04s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 15:48:59 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:12s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 15:49:06 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:19s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 15:49:14 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 15:49:22 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:35s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 15:49:29 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:42s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 15:49:37 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 15:49:45 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 15:49:54 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:07s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 15:50:02 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:15s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 15:50:10 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:23s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 15:50:18 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 15:50:26 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:39s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 15:50:34 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:02:47s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 15:50:41 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 15:50:49 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:03s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 15:50:57 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:11s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 15:51:05 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:19s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 15:51:13 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 15:51:22 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:35s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 15:51:30 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:43s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 15:51:39 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:03:52s. Time for last 10,000,000: 9s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 15:51:47 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 15:51:55 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:04:08s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 15:52:03 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:04:16s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 15:52:11 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 15:52:19 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:04:32s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 15:52:27 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:04:40s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 15:52:35 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:04:48s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 15:52:43 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:04:56s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 15:52:51 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:05:04s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 15:52:59 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:05:13s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 15:53:07 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:05:20s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 15:53:16 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:05:29s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 15:53:23 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:05:37s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 15:53:31 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 15:53:39 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:05:52s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 15:53:47 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:06:00s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 15:53:55 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:06:09s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 15:54:04 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:06:17s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 15:54:12 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:06:25s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 15:54:21 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:06:34s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 15:54:29 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:06:43s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 15:54:37 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:06:51s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 15:54:46 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:06:59s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 15:54:54 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:07:07s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 15:55:02 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:07:16s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 15:55:11 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:07:24s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 15:55:20 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:07:33s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 15:55:28 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:07:42s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 15:55:37 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:07:50s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 15:55:46 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:07:59s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 15:55:54 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:08:07s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 15:56:02 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:08:15s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 15:56:10 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:08:24s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 15:56:19 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:08:33s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 15:56:27 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:08:41s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 15:56:35 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:08:48s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 15:56:43 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:08:56s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 15:56:51 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:09:04s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 15:56:59 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:09:13s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 15:57:07 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:09:20s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 15:57:15 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:09:28s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 15:57:23 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:09:36s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 15:57:31 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:09:44s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 15:57:38 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:09:52s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 15:57:46 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:09:59s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 15:57:53 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:10:06s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 15:58:01 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:10:14s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 15:58:08 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:10:22s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 15:58:16 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:10:29s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 15:58:24 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:10:37s. Time for last 10,000,000: 8s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 15:58:31 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:10:45s. Time for last 10,000,000: 7s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 15:58:38 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:10:51s. Time for last 10,000,000: 6s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 15:58:44 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:10:57s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 15:58:49 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:11:02s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 15:58:54 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:11:07s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 15:58:59 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:11:13s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 15:59:06 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 15:59:06 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 15:59:06 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 15:59:07 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 15:59:09 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 15:59:11 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 15:59:12 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 15:59:14 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 15:59:16 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 15:59:18 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 15:59:19 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 15:59:21 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 15:59:23 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 15:59:23 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 11.62 minutes. Runtime.totalMemory()=1673527296 INFO 2020-04-17 15:59:24 CollectWgsMetrics ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** CollectWgsMetrics -I /Users/strigg/Desktop/20200416/Pact_C1/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam -O /Users/strigg/Desktop/20200416/Pact_C1/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt -R /Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta ********** 15:59:25.528 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Fri Apr 17 15:59:25 PDT 2020] CollectWgsMetrics INPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam OUTPUT=/Users/strigg/Desktop/20200416/Pact_C1/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.collect_wgs_metrics.txt REFERENCE_SEQUENCE=/Volumes/web/seashell/bu-mox/data/froger/C1_Genome/SymbC1.Genome.Scaffolds.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Apr 17 15:59:25 PDT 2020] Executing as strigg@ostrich on Mac OS X 10.11.6 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT INFO 2020-04-17 15:59:29 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:03s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold2:1,667,851 INFO 2020-04-17 15:59:31 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:06s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold4:4,334,950 INFO 2020-04-17 15:59:34 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:08s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold7:3,866,586 INFO 2020-04-17 15:59:36 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:00:11s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold16:177,862 INFO 2020-04-17 15:59:39 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:13s. Time for last 10,000,000: 2s. Last read position: SymbC1.scaffold23:1,022,107 INFO 2020-04-17 15:59:44 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:18s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold51:36,217 INFO 2020-04-17 15:59:48 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:00:23s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold82:143,437 INFO 2020-04-17 15:59:53 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:00:28s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold114:283,466 INFO 2020-04-17 15:59:58 CollectWgsMetrics Processed 90,000,000 loci. Elapsed time: 00:00:33s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold153:53,543 INFO 2020-04-17 16:00:03 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:00:38s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold193:33,806 INFO 2020-04-17 16:00:09 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:00:43s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold234:35,767 INFO 2020-04-17 16:00:14 CollectWgsMetrics Processed 120,000,000 loci. Elapsed time: 00:00:49s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold278:103,465 INFO 2020-04-17 16:00:20 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:00:54s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold324:122,765 INFO 2020-04-17 16:00:25 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold370:227,695 INFO 2020-04-17 16:00:30 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:05s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold420:43,063 INFO 2020-04-17 16:00:36 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:01:11s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold470:2,491 INFO 2020-04-17 16:00:41 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:01:16s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold522:140,354 INFO 2020-04-17 16:00:47 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:01:21s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold577:84,385 INFO 2020-04-17 16:00:53 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:01:27s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold635:121,664 INFO 2020-04-17 16:00:59 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:01:33s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold696:24,615 INFO 2020-04-17 16:01:04 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:01:39s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold757:40,526 INFO 2020-04-17 16:01:10 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:01:44s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold820:123,820 INFO 2020-04-17 16:01:15 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:01:50s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold885:49,750 INFO 2020-04-17 16:01:21 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:01:55s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold951:116,351 INFO 2020-04-17 16:01:26 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:02:01s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1019:106,039 INFO 2020-04-17 16:01:32 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:02:06s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1087:93,405 INFO 2020-04-17 16:01:37 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:02:12s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1160:140,085 INFO 2020-04-17 16:01:42 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:02:17s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1234:22,723 INFO 2020-04-17 16:01:48 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:02:22s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1311:52,950 INFO 2020-04-17 16:01:53 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:02:27s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1387:86,997 INFO 2020-04-17 16:01:58 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:02:33s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1469:20,787 INFO 2020-04-17 16:02:04 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:02:38s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1551:98,124 INFO 2020-04-17 16:02:09 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:02:44s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1635:99,488 INFO 2020-04-17 16:02:14 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:02:49s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1723:100,945 INFO 2020-04-17 16:02:20 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:02:54s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1812:19,243 INFO 2020-04-17 16:02:25 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:03:00s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1901:42,085 INFO 2020-04-17 16:02:30 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold1998:6,100 INFO 2020-04-17 16:02:36 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:03:10s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2096:30,185 INFO 2020-04-17 16:02:41 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:03:15s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2192:43,265 INFO 2020-04-17 16:02:46 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2295:44,302 INFO 2020-04-17 16:02:51 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:03:26s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2399:30,829 INFO 2020-04-17 16:02:57 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:03:31s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2507:69,437 INFO 2020-04-17 16:03:02 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:03:37s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2617:63,372 INFO 2020-04-17 16:03:08 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:03:42s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2731:16,849 INFO 2020-04-17 16:03:14 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:03:48s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2846:3,880 INFO 2020-04-17 16:03:19 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:03:53s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold2966:62,629 INFO 2020-04-17 16:03:24 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:03:59s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3092:38,782 INFO 2020-04-17 16:03:29 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:04:04s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3218:80,680 INFO 2020-04-17 16:03:35 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:04:10s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3348:35,770 INFO 2020-04-17 16:03:40 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:04:15s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3482:35,160 INFO 2020-04-17 16:03:46 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:04:20s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3623:83,442 INFO 2020-04-17 16:03:51 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:04:25s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3766:36,448 INFO 2020-04-17 16:03:56 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:04:31s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold3911:73,381 INFO 2020-04-17 16:04:01 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:04:36s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4058:25,380 INFO 2020-04-17 16:04:07 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:04:41s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4217:68,282 INFO 2020-04-17 16:04:12 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:04:46s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4382:22,977 INFO 2020-04-17 16:04:17 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:04:52s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4543:36,388 INFO 2020-04-17 16:04:22 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:04:57s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4714:56,724 INFO 2020-04-17 16:04:28 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:05:02s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold4888:43,216 INFO 2020-04-17 16:04:33 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:05:07s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5066:49,892 INFO 2020-04-17 16:04:38 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:05:13s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5257:94,615 INFO 2020-04-17 16:04:43 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:05:18s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5452:3,462 INFO 2020-04-17 16:04:49 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:05:23s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5655:52,006 INFO 2020-04-17 16:04:54 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:05:28s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold5872:23,131 INFO 2020-04-17 16:04:59 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:05:34s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6097:27,927 INFO 2020-04-17 16:05:05 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:05:39s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6327:30,719 INFO 2020-04-17 16:05:11 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6575:20,771 INFO 2020-04-17 16:05:16 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:05:50s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold6831:764 INFO 2020-04-17 16:05:21 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:05:55s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold7097:34,938 INFO 2020-04-17 16:05:26 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:06:00s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold7378:21,043 INFO 2020-04-17 16:05:31 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:06:05s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold7674:2,347 INFO 2020-04-17 16:05:36 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:06:11s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold7986:28,515 INFO 2020-04-17 16:05:41 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:06:16s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold8321:21,053 INFO 2020-04-17 16:05:46 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:06:21s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold8680:20,309 INFO 2020-04-17 16:05:51 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:06:26s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9064:23,295 INFO 2020-04-17 16:05:57 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:06:31s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9487:9,909 INFO 2020-04-17 16:06:02 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:06:36s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold9947:5,607 INFO 2020-04-17 16:06:07 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:06:41s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold10449:18,903 INFO 2020-04-17 16:06:12 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:06:46s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold11013:17,923 INFO 2020-04-17 16:06:17 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:06:51s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold11668:10,508 INFO 2020-04-17 16:06:21 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:06:56s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold12426:2,215 INFO 2020-04-17 16:06:26 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:07:01s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold13357:19,399 INFO 2020-04-17 16:06:31 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:07:06s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold14551:9,294 INFO 2020-04-17 16:06:36 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:07:11s. Time for last 10,000,000: 5s. Last read position: SymbC1.scaffold16106:2,566 INFO 2020-04-17 16:06:41 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:07:15s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold18132:4,133 INFO 2020-04-17 16:06:45 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:07:19s. Time for last 10,000,000: 4s. Last read position: SymbC1.scaffold20990:1,704 INFO 2020-04-17 16:06:49 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:07:23s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold25078:1,405 INFO 2020-04-17 16:06:52 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:07:27s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold31098:1,124 INFO 2020-04-17 16:06:56 CollectWgsMetrics Processed 890,000,000 loci. Elapsed time: 00:07:30s. Time for last 10,000,000: 3s. Last read position: SymbC1.scaffold39623:90 INFO 2020-04-17 16:06:58 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-17 16:06:58 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-17 16:06:58 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-17 16:07:00 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-17 16:07:02 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-17 16:07:03 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-17 16:07:05 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-17 16:07:07 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-17 16:07:08 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-17 16:07:10 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-17 16:07:12 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-17 16:07:14 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-17 16:07:15 TheoreticalSensitivity Calculating theoretical het sensitivity [Fri Apr 17 16:07:16 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 7.85 minutes. Runtime.totalMemory()=1673527296 bash-3.2$