/Users/strigg/Desktop/20200416/20200416_qualimap_CollectWgsMetrics.sh /Users/strigg/Desktop/20200416/20200416_qualimap_CollectWgsMetrics.sh: line 1: fg: no job control ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap multi-bamqc -d /Users/strigg/Desktop/20200416/Mcap/multibamQC/multiBamqc_data_paths.txt -outdir /Users/strigg/Desktop/20200416/Mcap/multibamQC/ -r Java memory size is set to 1200M Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: multi-bamqc Thu Apr 16 14:03:21 PDT 2020 WARNING Output folder already exists, the results will be saved there Running BAM QC on given samples Started processing /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 3442 Chunk of reads size: 1000 Number of threads: 4 Processed 344 out of 3442 windows... Processed 688 out of 3442 windows... Processed 1032 out of 3442 windows... Processed 1376 out of 3442 windows... Processed 1720 out of 3442 windows... Processed 2064 out of 3442 windows... Processed 2408 out of 3442 windows... Processed 2752 out of 3442 windows... Processed 3096 out of 3442 windows... Processed 3440 out of 3442 windows... Total processed windows:3442 Number of reads: 25173110 Number of valid reads: 25173110 Number of correct strand reads:0 Inside of regions... Num mapped reads: 25173110 Num mapped first of pair: 12586555 Num mapped second of pair: 12586555 Num singletons: 0 Time taken to analyze reads: 235 Computing descriptors... numberOfMappedBases: 2802249284 referenceSize: 885704498 numberOfSequencedBases: 2791954846 numberOfAs: 1095325325 Computing per chromosome statistics... Computing histograms... Overall analysis time: 241 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 3442 Chunk of reads size: 1000 Number of threads: 4 Processed 344 out of 3442 windows... Processed 688 out of 3442 windows... Processed 1032 out of 3442 windows... Processed 1376 out of 3442 windows... Processed 1720 out of 3442 windows... Processed 2064 out of 3442 windows... Processed 2408 out of 3442 windows... Processed 2752 out of 3442 windows... Processed 3096 out of 3442 windows... Processed 3440 out of 3442 windows... Total processed windows:3442 Number of reads: 24620938 Number of valid reads: 24620938 Number of correct strand reads:0 Inside of regions... Num mapped reads: 24620938 Num mapped first of pair: 12310469 Num mapped second of pair: 12310469 Num singletons: 0 Time taken to analyze reads: 239 Computing descriptors... numberOfMappedBases: 2795884956 referenceSize: 885704498 numberOfSequencedBases: 2786043715 numberOfAs: 1091867936 Computing per chromosome statistics... Computing histograms... Overall analysis time: 245 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 3442 Chunk of reads size: 1000 Number of threads: 4 Processed 344 out of 3442 windows... Processed 688 out of 3442 windows... Processed 1032 out of 3442 windows... Processed 1376 out of 3442 windows... Processed 1720 out of 3442 windows... Processed 2064 out of 3442 windows... Processed 2408 out of 3442 windows... Processed 2752 out of 3442 windows... Processed 3096 out of 3442 windows... Processed 3440 out of 3442 windows... Total processed windows:3442 Number of reads: 36913682 Number of valid reads: 36913682 Number of correct strand reads:0 Inside of regions... Num mapped reads: 36913682 Num mapped first of pair: 18456841 Num mapped second of pair: 18456841 Num singletons: 0 Time taken to analyze reads: 389 Computing descriptors... numberOfMappedBases: 4263943800 referenceSize: 885704498 numberOfSequencedBases: 4248418891 numberOfAs: 1670273745 Computing per chromosome statistics... Computing histograms... Overall analysis time: 398 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 3442 Chunk of reads size: 1000 Number of threads: 4 Processed 344 out of 3442 windows... Processed 688 out of 3442 windows... Processed 1032 out of 3442 windows... Processed 1376 out of 3442 windows... Processed 1720 out of 3442 windows... Processed 2064 out of 3442 windows... Processed 2408 out of 3442 windows... Processed 2752 out of 3442 windows... Processed 3096 out of 3442 windows... Processed 3440 out of 3442 windows... Total processed windows:3442 Number of reads: 110001612 Number of valid reads: 110001612 Number of correct strand reads:0 Inside of regions... Num mapped reads: 110001612 Num mapped first of pair: 55000806 Num mapped second of pair: 55000806 Num singletons: 0 Time taken to analyze reads: 1387 Computing descriptors... numberOfMappedBases: 13112318325 referenceSize: 885704498 numberOfSequencedBases: 13094725561 numberOfAs: 5114834199 Computing per chromosome statistics... Computing histograms... WARNING: out of memory! Qualimap allows to set RAM size using special argument: --java-mem-size Check more details using --help command or read the manual. ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap multi-bamqc -d /Users/strigg/Desktop/20200416/Pact/multibamQC/multiBamqc_data_paths.txt -outdir /Users/strigg/Desktop/20200416/Pact/multibamQC/ -r Java memory size is set to 1200M Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: multi-bamqc Thu Apr 16 14:41:34 PDT 2020 WARNING Output folder already exists, the results will be saved there Running BAM QC on given samples Started processing /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 168864 Chunk of reads size: 1000 Number of threads: 4 Processed 16886 out of 168864 windows... Processed 33772 out of 168864 windows... Processed 50658 out of 168864 windows... Processed 67544 out of 168864 windows... Processed 84430 out of 168864 windows... Processed 101316 out of 168864 windows... Processed 118202 out of 168864 windows... Processed 135088 out of 168864 windows... Processed 151974 out of 168864 windows... Processed 168860 out of 168864 windows... Total processed windows:168864 Number of reads: 32297506 Number of valid reads: 32297506 Number of correct strand reads:0 Inside of regions... Num mapped reads: 32297506 Num mapped first of pair: 16148753 Num mapped second of pair: 16148753 Num singletons: 0 Time taken to analyze reads: 399 Computing descriptors... numberOfMappedBases: 3604572906 referenceSize: 352019984 numberOfSequencedBases: 3589534990 numberOfAs: 1431412077 Computing per chromosome statistics... Computing histograms... Overall analysis time: 411 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 168864 Chunk of reads size: 1000 Number of threads: 4 Processed 16886 out of 168864 windows... Processed 33772 out of 168864 windows... Processed 50658 out of 168864 windows... Processed 67544 out of 168864 windows... Processed 84430 out of 168864 windows... Processed 101316 out of 168864 windows... Processed 118202 out of 168864 windows... Processed 135088 out of 168864 windows... Processed 151974 out of 168864 windows... Processed 168860 out of 168864 windows... Total processed windows:168864 Number of reads: 45341734 Number of valid reads: 45341734 Number of correct strand reads:0 Inside of regions... Num mapped reads: 45341734 Num mapped first of pair: 22670867 Num mapped second of pair: 22670867 Num singletons: 0 Time taken to analyze reads: 510 Computing descriptors... numberOfMappedBases: 4958626850 referenceSize: 352019984 numberOfSequencedBases: 4938342678 numberOfAs: 1965767042 Computing per chromosome statistics... Computing histograms... Overall analysis time: 523 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 168864 Chunk of reads size: 1000 Number of threads: 4 Processed 16886 out of 168864 windows... Processed 33772 out of 168864 windows... Processed 50658 out of 168864 windows... Processed 67544 out of 168864 windows... Processed 84430 out of 168864 windows... Processed 101316 out of 168864 windows... Processed 118202 out of 168864 windows... Processed 135088 out of 168864 windows... Processed 151974 out of 168864 windows... Processed 168860 out of 168864 windows... Total processed windows:168864 Number of reads: 36877600 Number of valid reads: 36877600 Number of correct strand reads:0 Inside of regions... Num mapped reads: 36877600 Num mapped first of pair: 18438800 Num mapped second of pair: 18438800 Num singletons: 0 Time taken to analyze reads: 431 Computing descriptors... numberOfMappedBases: 4097650178 referenceSize: 352019984 numberOfSequencedBases: 4081120164 numberOfAs: 1623928079 Computing per chromosome statistics... Computing histograms... Overall analysis time: 441 HTML report created successfully Finished processing /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam BAM QC results are saved to /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats Started processing /Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 168864 Chunk of reads size: 1000 Number of threads: 4 ^Cbash-3.2$ d/Users/strigg/Desktop/20200416/20200416_CollectWgsMetrics.sh chmod +x  [4@at 20200416_qualimap hmod +x 20200416 [4@at 20200416_qualimap hmod +x 20200416 [22@/Users/strigg/Desktop/20200416/ INFO 2020-04-16 15:26:35 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 ********** 15:26:36.828 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Thu Apr 16 15:26:36 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 [Thu Apr 16 15:26:36 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 2020-04-16 15:26:45 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 2020-04-16 15:26:53 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 2020-04-16 15:27:01 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:24s. Time for last 10,000,000: 7s. Last read position: 15:1,277,111 INFO 2020-04-16 15:27:08 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 2020-04-16 15:27:15 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 2020-04-16 15:27:23 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 2020-04-16 15:27:31 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 2020-04-16 15:27:39 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 2020-04-16 15:27:45 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 2020-04-16 15:27:53 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 2020-04-16 15:28:00 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 2020-04-16 15:28:08 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 2020-04-16 15:28:15 CollectWgsMetrics Processed 130,000,000 loci. Elapsed time: 00:01:38s. Time for last 10,000,000: 7s. Last read position: 80:1,003,826 INFO 2020-04-16 15:28:23 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 2020-04-16 15:28:30 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 2020-04-16 15:28:38 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 2020-04-16 15:28:45 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 2020-04-16 15:28:53 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:16s. Time for last 10,000,000: 7s. Last read position: 124:300,378 INFO 2020-04-16 15:29:00 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 2020-04-16 15:29:08 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 7s. Last read position: 143:937,913 INFO 2020-04-16 15:29:14 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 6s. Last read position: 154:196,816 INFO 2020-04-16 15:29:21 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 7s. Last read position: 164:946,097 INFO 2020-04-16 15:29:29 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 7s. Last read position: 176:142,662 INFO 2020-04-16 15:29:36 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 7s. Last read position: 186:787,532 INFO 2020-04-16 15:29:43 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:06s. Time for last 10,000,000: 6s. Last read position: 197:551,543 INFO 2020-04-16 15:29:50 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:03:13s. Time for last 10,000,000: 7s. Last read position: 210:166,366 INFO 2020-04-16 15:29:57 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:20s. Time for last 10,000,000: 6s. Last read position: 221:702,430 INFO 2020-04-16 15:30:04 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:27s. Time for last 10,000,000: 6s. Last read position: 234:821,523 INFO 2020-04-16 15:30:10 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:33s. Time for last 10,000,000: 6s. Last read position: 247:449,458 INFO 2020-04-16 15:30:17 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:40s. Time for last 10,000,000: 6s. Last read position: 259:701,369 INFO 2020-04-16 15:30:24 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:47s. Time for last 10,000,000: 6s. Last read position: 273:137,205 INFO 2020-04-16 15:30:30 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:54s. Time for last 10,000,000: 6s. Last read position: 287:177,113 INFO 2020-04-16 15:30:37 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:04:00s. Time for last 10,000,000: 6s. Last read position: 300:416,946 INFO 2020-04-16 15:30:44 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 6s. Last read position: 314:424,834 INFO 2020-04-16 15:30:50 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:04:13s. Time for last 10,000,000: 6s. Last read position: 330:127 INFO 2020-04-16 15:30:57 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:04:20s. Time for last 10,000,000: 6s. Last read position: 344:423,663 INFO 2020-04-16 15:31:03 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:04:26s. Time for last 10,000,000: 6s. Last read position: 359:634,934 INFO 2020-04-16 15:31:09 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 2020-04-16 15:31:16 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:04:39s. Time for last 10,000,000: 6s. Last read position: 392:532,908 INFO 2020-04-16 15:31:22 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:04:46s. Time for last 10,000,000: 6s. Last read position: 409:150,400 INFO 2020-04-16 15:31:30 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:04:53s. Time for last 10,000,000: 7s. Last read position: 426:510,191 INFO 2020-04-16 15:31:36 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:04:59s. Time for last 10,000,000: 6s. Last read position: 444:356,488 INFO 2020-04-16 15:31:43 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:05:06s. Time for last 10,000,000: 6s. Last read position: 462:132,483 INFO 2020-04-16 15:31:49 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:05:13s. Time for last 10,000,000: 6s. Last read position: 480:476,684 INFO 2020-04-16 15:31:56 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:05:19s. Time for last 10,000,000: 6s. Last read position: 499:472,487 INFO 2020-04-16 15:32:02 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:05:26s. Time for last 10,000,000: 6s. Last read position: 520:167,314 INFO 2020-04-16 15:32:09 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 2020-04-16 15:32:16 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:05:39s. Time for last 10,000,000: 6s. Last read position: 561:89,787 INFO 2020-04-16 15:32:22 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 6s. Last read position: 581:275,897 INFO 2020-04-16 15:32:28 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:05:51s. Time for last 10,000,000: 5s. Last read position: 605:50,138 INFO 2020-04-16 15:32:34 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:05:57s. Time for last 10,000,000: 6s. Last read position: 626:305,229 INFO 2020-04-16 15:32:40 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 2020-04-16 15:32:46 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:06:09s. Time for last 10,000,000: 5s. Last read position: 671:195,673 INFO 2020-04-16 15:32:53 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:06:16s. Time for last 10,000,000: 6s. Last read position: 695:85,112 INFO 2020-04-16 15:32:59 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:06:22s. Time for last 10,000,000: 5s. Last read position: 720:113,488 INFO 2020-04-16 15:33:05 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:06:28s. Time for last 10,000,000: 6s. Last read position: 748:34,007 INFO 2020-04-16 15:33:11 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 2020-04-16 15:33:17 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 2020-04-16 15:33:23 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 2020-04-16 15:33:28 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 2020-04-16 15:33:34 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 2020-04-16 15:33:40 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:07:03s. Time for last 10,000,000: 6s. Last read position: 918:326,056 INFO 2020-04-16 15:33:45 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:07:09s. Time for last 10,000,000: 5s. Last read position: 951:37,914 INFO 2020-04-16 15:33:51 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:07:14s. Time for last 10,000,000: 5s. Last read position: 984:126,977 INFO 2020-04-16 15:33:57 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 5s. Last read position: 1017:167,455 INFO 2020-04-16 15:34:01 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 2020-04-16 15:34:06 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 2020-04-16 15:34:12 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 2020-04-16 15:34:18 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:07:41s. Time for last 10,000,000: 5s. Last read position: 1168:8,743 INFO 2020-04-16 15:34:23 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:07:46s. Time for last 10,000,000: 5s. Last read position: 1210:48,462 INFO 2020-04-16 15:34:28 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 2020-04-16 15:34:33 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 2020-04-16 15:34:38 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:08:02s. Time for last 10,000,000: 5s. Last read position: 1347:42,922 INFO 2020-04-16 15:34:44 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:08:07s. Time for last 10,000,000: 5s. Last read position: 1397:45,967 INFO 2020-04-16 15:34:49 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:08:12s. Time for last 10,000,000: 5s. Last read position: 1450:5,557 INFO 2020-04-16 15:34:53 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 2020-04-16 15:34:58 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 2020-04-16 15:35:03 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:08:26s. Time for last 10,000,000: 4s. Last read position: 1631:39,335 INFO 2020-04-16 15:35:08 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:08:31s. Time for last 10,000,000: 4s. Last read position: 1698:107,239 INFO 2020-04-16 15:35:13 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:08:36s. Time for last 10,000,000: 4s. Last read position: 1774:115,449 INFO 2020-04-16 15:35:17 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:08:40s. Time for last 10,000,000: 4s. Last read position: 1853:95,173 INFO 2020-04-16 15:35:22 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:08:45s. Time for last 10,000,000: 4s. Last read position: 1942:62,123 INFO 2020-04-16 15:35:26 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:08:49s. Time for last 10,000,000: 4s. Last read position: 2039:16,006 INFO 2020-04-16 15:35:30 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:08:53s. Time for last 10,000,000: 4s. Last read position: 2147:65,939 INFO 2020-04-16 15:35:35 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:08:58s. Time for last 10,000,000: 4s. Last read position: 2269:65,204 INFO 2020-04-16 15:35:39 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:09:03s. Time for last 10,000,000: 4s. Last read position: 2409:16,999 INFO 2020-04-16 15:35:43 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:09:07s. Time for last 10,000,000: 3s. Last read position: 2580:1,672 INFO 2020-04-16 15:35:47 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:09:10s. Time for last 10,000,000: 3s. Last read position: 2825:574 INFO 2020-04-16 15:35:49 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-16 15:35:49 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-16 15:35:49 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-16 15:35:51 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-16 15:35:53 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-16 15:35:55 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-16 15:35:56 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-16 15:35:58 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-16 15:36:00 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-16 15:36:01 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-16 15:36:03 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-16 15:36:05 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-16 15:36:06 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 16 15:36:07 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 9.52 minutes. Runtime.totalMemory()=805306368 INFO 2020-04-16 15:36:08 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 ********** 15:36:09.240 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Thu Apr 16 15:36:09 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 [Thu Apr 16 15:36:09 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 2020-04-16 15:36:18 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:09s. Time for last 10,000,000: 9s. Last read position: 4:2,571,827 INFO 2020-04-16 15:36:26 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:00:17s. Time for last 10,000,000: 7s. Last read position: 9:2,185,583 INFO 2020-04-16 15:36:33 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:00:24s. Time for last 10,000,000: 7s. Last read position: 15:1,277,111 INFO 2020-04-16 15:36:41 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 2020-04-16 15:36:48 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:00:39s. Time for last 10,000,000: 7s. Last read position: 26:192,822 INFO 2020-04-16 15:36:56 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:00:47s. Time for last 10,000,000: 7s. Last read position: 31:1,345,614 INFO 2020-04-16 15:37:04 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 2020-04-16 15:37:11 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 2020-04-16 15:37:18 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 2020-04-16 15:37:26 CollectWgsMetrics Processed 100,000,000 loci. Elapsed time: 00:01:17s. Time for last 10,000,000: 7s. Last read position: 57:1,126,989 INFO 2020-04-16 15:37:33 CollectWgsMetrics Processed 110,000,000 loci. Elapsed time: 00:01:24s. Time for last 10,000,000: 7s. Last read position: 64:1,029,276 INFO 2020-04-16 15:37:40 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 2020-04-16 15:37:48 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 2020-04-16 15:37:56 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:01:47s. Time for last 10,000,000: 7s. Last read position: 88:693,929 INFO 2020-04-16 15:38:03 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:01:54s. Time for last 10,000,000: 7s. Last read position: 97:654,820 INFO 2020-04-16 15:38:11 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:02:02s. Time for last 10,000,000: 8s. Last read position: 106:954,050 INFO 2020-04-16 15:38:18 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:09s. Time for last 10,000,000: 7s. Last read position: 115:314,973 INFO 2020-04-16 15:38:25 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:16s. Time for last 10,000,000: 7s. Last read position: 124:300,378 INFO 2020-04-16 15:38:33 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:02:24s. Time for last 10,000,000: 7s. Last read position: 134:346,484 INFO 2020-04-16 15:38:40 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:02:31s. Time for last 10,000,000: 7s. Last read position: 143:937,913 INFO 2020-04-16 15:38:47 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 6s. Last read position: 154:196,816 INFO 2020-04-16 15:38:54 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:02:45s. Time for last 10,000,000: 7s. Last read position: 164:946,097 INFO 2020-04-16 15:39:01 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:02:52s. Time for last 10,000,000: 7s. Last read position: 176:142,662 INFO 2020-04-16 15:39:08 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:02:59s. Time for last 10,000,000: 7s. Last read position: 186:787,532 INFO 2020-04-16 15:39:16 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:07s. Time for last 10,000,000: 7s. Last read position: 197:551,543 INFO 2020-04-16 15:39:23 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 7s. Last read position: 210:166,366 INFO 2020-04-16 15:39:30 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:03:21s. Time for last 10,000,000: 6s. Last read position: 221:702,430 INFO 2020-04-16 15:39:37 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:03:27s. Time for last 10,000,000: 6s. Last read position: 234:821,523 INFO 2020-04-16 15:39:43 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:03:33s. Time for last 10,000,000: 5s. Last read position: 247:449,458 INFO 2020-04-16 15:39:49 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:03:40s. Time for last 10,000,000: 6s. Last read position: 259:701,369 INFO 2020-04-16 15:39:56 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:03:47s. Time for last 10,000,000: 6s. Last read position: 273:137,205 INFO 2020-04-16 15:40:03 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:03:54s. Time for last 10,000,000: 6s. Last read position: 287:177,113 INFO 2020-04-16 15:40:10 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:04:01s. Time for last 10,000,000: 6s. Last read position: 300:416,946 INFO 2020-04-16 15:40:17 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 6s. Last read position: 314:424,834 INFO 2020-04-16 15:40:23 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:04:14s. Time for last 10,000,000: 6s. Last read position: 330:127 INFO 2020-04-16 15:40:30 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:04:20s. Time for last 10,000,000: 6s. Last read position: 344:423,663 INFO 2020-04-16 15:40:36 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:04:27s. Time for last 10,000,000: 6s. Last read position: 359:634,934 INFO 2020-04-16 15:40:42 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:04:33s. Time for last 10,000,000: 6s. Last read position: 377:83,616 INFO 2020-04-16 15:40:48 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:04:39s. Time for last 10,000,000: 6s. Last read position: 392:532,908 INFO 2020-04-16 15:40:55 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:04:46s. Time for last 10,000,000: 6s. Last read position: 409:150,400 INFO 2020-04-16 15:41:02 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:04:53s. Time for last 10,000,000: 7s. Last read position: 426:510,191 INFO 2020-04-16 15:41:09 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:05:00s. Time for last 10,000,000: 6s. Last read position: 444:356,488 INFO 2020-04-16 15:41:16 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:05:07s. Time for last 10,000,000: 6s. Last read position: 462:132,483 INFO 2020-04-16 15:41:22 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:05:13s. Time for last 10,000,000: 6s. Last read position: 480:476,684 INFO 2020-04-16 15:41:28 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:05:19s. Time for last 10,000,000: 6s. Last read position: 499:472,487 INFO 2020-04-16 15:41:35 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 2020-04-16 15:41:41 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 2020-04-16 15:41:48 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:05:39s. Time for last 10,000,000: 6s. Last read position: 561:89,787 INFO 2020-04-16 15:41:54 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:05:45s. Time for last 10,000,000: 6s. Last read position: 581:275,897 INFO 2020-04-16 15:42:00 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:05:51s. Time for last 10,000,000: 6s. Last read position: 605:50,138 INFO 2020-04-16 15:42:07 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:05:58s. Time for last 10,000,000: 6s. Last read position: 626:305,229 INFO 2020-04-16 15:42:13 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:06:04s. Time for last 10,000,000: 6s. Last read position: 648:244,080 INFO 2020-04-16 15:42:19 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:06:10s. Time for last 10,000,000: 6s. Last read position: 671:195,673 INFO 2020-04-16 15:42:26 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:06:17s. Time for last 10,000,000: 6s. Last read position: 695:85,112 INFO 2020-04-16 15:42:31 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:06:22s. Time for last 10,000,000: 5s. Last read position: 720:113,488 INFO 2020-04-16 15:42:38 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:06:29s. Time for last 10,000,000: 6s. Last read position: 748:34,007 INFO 2020-04-16 15:42:44 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:06:35s. Time for last 10,000,000: 6s. Last read position: 774:112,571 INFO 2020-04-16 15:42:50 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:06:41s. Time for last 10,000,000: 5s. Last read position: 801:129,443 INFO 2020-04-16 15:42:56 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 2020-04-16 15:43:01 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 2020-04-16 15:43:07 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 2020-04-16 15:43:13 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:07:03s. Time for last 10,000,000: 6s. Last read position: 918:326,056 INFO 2020-04-16 15:43:18 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:07:09s. Time for last 10,000,000: 5s. Last read position: 951:37,914 INFO 2020-04-16 15:43:24 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:07:14s. Time for last 10,000,000: 5s. Last read position: 984:126,977 INFO 2020-04-16 15:43:29 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:07:20s. Time for last 10,000,000: 5s. Last read position: 1017:167,455 INFO 2020-04-16 15:43:34 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:07:25s. Time for last 10,000,000: 4s. Last read position: 1052:230,503 INFO 2020-04-16 15:43:39 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:07:30s. Time for last 10,000,000: 5s. Last read position: 1090:74,736 INFO 2020-04-16 15:43:45 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:07:36s. Time for last 10,000,000: 5s. Last read position: 1128:19,199 INFO 2020-04-16 15:43:50 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:07:41s. Time for last 10,000,000: 5s. Last read position: 1168:8,743 INFO 2020-04-16 15:43:56 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:07:46s. Time for last 10,000,000: 5s. Last read position: 1210:48,462 INFO 2020-04-16 15:44:01 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:07:52s. Time for last 10,000,000: 5s. Last read position: 1252:73,681 INFO 2020-04-16 15:44:06 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:07:57s. Time for last 10,000,000: 4s. Last read position: 1298:135,654 INFO 2020-04-16 15:44:11 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:08:02s. Time for last 10,000,000: 5s. Last read position: 1347:42,922 INFO 2020-04-16 15:44:16 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:08:07s. Time for last 10,000,000: 4s. Last read position: 1397:45,967 INFO 2020-04-16 15:44:21 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:08:12s. Time for last 10,000,000: 5s. Last read position: 1450:5,557 INFO 2020-04-16 15:44:26 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:08:17s. Time for last 10,000,000: 4s. Last read position: 1505:129,718 INFO 2020-04-16 15:44:31 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:08:22s. Time for last 10,000,000: 4s. Last read position: 1568:3,714 INFO 2020-04-16 15:44:36 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:08:26s. Time for last 10,000,000: 4s. Last read position: 1631:39,335 INFO 2020-04-16 15:44:40 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:08:31s. Time for last 10,000,000: 4s. Last read position: 1698:107,239 INFO 2020-04-16 15:44:45 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:08:36s. Time for last 10,000,000: 4s. Last read position: 1774:115,449 INFO 2020-04-16 15:44:49 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:08:40s. Time for last 10,000,000: 4s. Last read position: 1853:95,173 INFO 2020-04-16 15:44:54 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 2020-04-16 15:44:58 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:08:49s. Time for last 10,000,000: 4s. Last read position: 2039:16,006 INFO 2020-04-16 15:45:02 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:08:53s. Time for last 10,000,000: 4s. Last read position: 2147:65,939 INFO 2020-04-16 15:45:07 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:08:57s. Time for last 10,000,000: 4s. Last read position: 2269:65,204 INFO 2020-04-16 15:45:11 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:09:02s. Time for last 10,000,000: 4s. Last read position: 2409:16,999 INFO 2020-04-16 15:45:15 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:09:06s. Time for last 10,000,000: 3s. Last read position: 2580:1,672 INFO 2020-04-16 15:45:18 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:09:09s. Time for last 10,000,000: 3s. Last read position: 2825:574 INFO 2020-04-16 15:45:20 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-16 15:45:20 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-16 15:45:20 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-16 15:45:22 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-16 15:45:24 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-16 15:45:26 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-16 15:45:27 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-16 15:45:29 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-16 15:45:31 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-16 15:45:32 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-16 15:45:34 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-16 15:45:36 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-16 15:45:37 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 16 15:45:38 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 9.49 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-16 15:45:39 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 ********** 15:45:40.953 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Thu Apr 16 15:45:41 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 [Thu Apr 16 15:45:41 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 2020-04-16 15:45:53 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:12s. Time for last 10,000,000: 11s. Last read position: 4:2,571,827 INFO 2020-04-16 15:46:03 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 2020-04-16 15:46:12 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 2020-04-16 15:46:21 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 2020-04-16 15:46:31 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 2020-04-16 15:46:41 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 2020-04-16 15:46:51 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 2020-04-16 15:47:01 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 2020-04-16 15:47:10 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 2020-04-16 15:47:20 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 2020-04-16 15:47:29 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 2020-04-16 15:47:38 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 2020-04-16 15:47:48 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 2020-04-16 15:47:58 CollectWgsMetrics Processed 140,000,000 loci. Elapsed time: 00:02:17s. Time for last 10,000,000: 10s. Last read position: 88:693,929 INFO 2020-04-16 15:48:07 CollectWgsMetrics Processed 150,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 9s. Last read position: 97:654,820 INFO 2020-04-16 15:48:18 CollectWgsMetrics Processed 160,000,000 loci. Elapsed time: 00:02:37s. Time for last 10,000,000: 10s. Last read position: 106:954,050 INFO 2020-04-16 15:48:27 CollectWgsMetrics Processed 170,000,000 loci. Elapsed time: 00:02:46s. Time for last 10,000,000: 8s. Last read position: 115:314,973 INFO 2020-04-16 15:48:36 CollectWgsMetrics Processed 180,000,000 loci. Elapsed time: 00:02:55s. Time for last 10,000,000: 9s. Last read position: 124:300,378 INFO 2020-04-16 15:48:46 CollectWgsMetrics Processed 190,000,000 loci. Elapsed time: 00:03:05s. Time for last 10,000,000: 9s. Last read position: 134:346,484 INFO 2020-04-16 15:48:55 CollectWgsMetrics Processed 200,000,000 loci. Elapsed time: 00:03:14s. Time for last 10,000,000: 9s. Last read position: 143:937,913 INFO 2020-04-16 15:49:03 CollectWgsMetrics Processed 210,000,000 loci. Elapsed time: 00:03:22s. Time for last 10,000,000: 7s. Last read position: 154:196,816 INFO 2020-04-16 15:49:11 CollectWgsMetrics Processed 220,000,000 loci. Elapsed time: 00:03:30s. Time for last 10,000,000: 8s. Last read position: 164:946,097 INFO 2020-04-16 15:49:20 CollectWgsMetrics Processed 230,000,000 loci. Elapsed time: 00:03:39s. Time for last 10,000,000: 8s. Last read position: 176:142,662 INFO 2020-04-16 15:49:30 CollectWgsMetrics Processed 240,000,000 loci. Elapsed time: 00:03:49s. Time for last 10,000,000: 9s. Last read position: 186:787,532 INFO 2020-04-16 15:49:39 CollectWgsMetrics Processed 250,000,000 loci. Elapsed time: 00:03:57s. Time for last 10,000,000: 8s. Last read position: 197:551,543 INFO 2020-04-16 15:49:48 CollectWgsMetrics Processed 260,000,000 loci. Elapsed time: 00:04:07s. Time for last 10,000,000: 9s. Last read position: 210:166,366 INFO 2020-04-16 15:49:56 CollectWgsMetrics Processed 270,000,000 loci. Elapsed time: 00:04:15s. Time for last 10,000,000: 8s. Last read position: 221:702,430 INFO 2020-04-16 15:50:05 CollectWgsMetrics Processed 280,000,000 loci. Elapsed time: 00:04:24s. Time for last 10,000,000: 8s. Last read position: 234:821,523 INFO 2020-04-16 15:50:13 CollectWgsMetrics Processed 290,000,000 loci. Elapsed time: 00:04:32s. Time for last 10,000,000: 7s. Last read position: 247:449,458 INFO 2020-04-16 15:50:21 CollectWgsMetrics Processed 300,000,000 loci. Elapsed time: 00:04:40s. Time for last 10,000,000: 8s. Last read position: 259:701,369 INFO 2020-04-16 15:50:30 CollectWgsMetrics Processed 310,000,000 loci. Elapsed time: 00:04:49s. Time for last 10,000,000: 8s. Last read position: 273:137,205 INFO 2020-04-16 15:50:39 CollectWgsMetrics Processed 320,000,000 loci. Elapsed time: 00:04:58s. Time for last 10,000,000: 8s. Last read position: 287:177,113 INFO 2020-04-16 15:50:48 CollectWgsMetrics Processed 330,000,000 loci. Elapsed time: 00:05:06s. Time for last 10,000,000: 8s. Last read position: 300:416,946 INFO 2020-04-16 15:50:56 CollectWgsMetrics Processed 340,000,000 loci. Elapsed time: 00:05:15s. Time for last 10,000,000: 8s. Last read position: 314:424,834 INFO 2020-04-16 15:51:04 CollectWgsMetrics Processed 350,000,000 loci. Elapsed time: 00:05:23s. Time for last 10,000,000: 8s. Last read position: 330:127 INFO 2020-04-16 15:51:13 CollectWgsMetrics Processed 360,000,000 loci. Elapsed time: 00:05:32s. Time for last 10,000,000: 8s. Last read position: 344:423,663 INFO 2020-04-16 15:51:21 CollectWgsMetrics Processed 370,000,000 loci. Elapsed time: 00:05:40s. Time for last 10,000,000: 8s. Last read position: 359:634,934 INFO 2020-04-16 15:51:30 CollectWgsMetrics Processed 380,000,000 loci. Elapsed time: 00:05:49s. Time for last 10,000,000: 8s. Last read position: 377:83,616 INFO 2020-04-16 15:51:38 CollectWgsMetrics Processed 390,000,000 loci. Elapsed time: 00:05:57s. Time for last 10,000,000: 8s. Last read position: 392:532,908 INFO 2020-04-16 15:51:47 CollectWgsMetrics Processed 400,000,000 loci. Elapsed time: 00:06:05s. Time for last 10,000,000: 8s. Last read position: 409:150,400 INFO 2020-04-16 15:51:55 CollectWgsMetrics Processed 410,000,000 loci. Elapsed time: 00:06:14s. Time for last 10,000,000: 8s. Last read position: 426:510,191 INFO 2020-04-16 15:52:04 CollectWgsMetrics Processed 420,000,000 loci. Elapsed time: 00:06:23s. Time for last 10,000,000: 8s. Last read position: 444:356,488 INFO 2020-04-16 15:52:12 CollectWgsMetrics Processed 430,000,000 loci. Elapsed time: 00:06:31s. Time for last 10,000,000: 8s. Last read position: 462:132,483 INFO 2020-04-16 15:52:20 CollectWgsMetrics Processed 440,000,000 loci. Elapsed time: 00:06:39s. Time for last 10,000,000: 7s. Last read position: 480:476,684 INFO 2020-04-16 15:52:28 CollectWgsMetrics Processed 450,000,000 loci. Elapsed time: 00:06:47s. Time for last 10,000,000: 8s. Last read position: 499:472,487 INFO 2020-04-16 15:52:36 CollectWgsMetrics Processed 460,000,000 loci. Elapsed time: 00:06:55s. Time for last 10,000,000: 7s. Last read position: 520:167,314 INFO 2020-04-16 15:52:44 CollectWgsMetrics Processed 470,000,000 loci. Elapsed time: 00:07:03s. Time for last 10,000,000: 8s. Last read position: 541:218,900 INFO 2020-04-16 15:52:52 CollectWgsMetrics Processed 480,000,000 loci. Elapsed time: 00:07:11s. Time for last 10,000,000: 8s. Last read position: 561:89,787 INFO 2020-04-16 15:53:00 CollectWgsMetrics Processed 490,000,000 loci. Elapsed time: 00:07:19s. Time for last 10,000,000: 7s. Last read position: 581:275,897 INFO 2020-04-16 15:53:07 CollectWgsMetrics Processed 500,000,000 loci. Elapsed time: 00:07:26s. Time for last 10,000,000: 7s. Last read position: 605:50,138 INFO 2020-04-16 15:53:15 CollectWgsMetrics Processed 510,000,000 loci. Elapsed time: 00:07:34s. Time for last 10,000,000: 7s. Last read position: 626:305,229 INFO 2020-04-16 15:53:23 CollectWgsMetrics Processed 520,000,000 loci. Elapsed time: 00:07:42s. Time for last 10,000,000: 7s. Last read position: 648:244,080 INFO 2020-04-16 15:53:30 CollectWgsMetrics Processed 530,000,000 loci. Elapsed time: 00:07:49s. Time for last 10,000,000: 7s. Last read position: 671:195,673 INFO 2020-04-16 15:53:38 CollectWgsMetrics Processed 540,000,000 loci. Elapsed time: 00:07:57s. Time for last 10,000,000: 7s. Last read position: 695:85,112 INFO 2020-04-16 15:53:45 CollectWgsMetrics Processed 550,000,000 loci. Elapsed time: 00:08:04s. Time for last 10,000,000: 7s. Last read position: 720:113,488 INFO 2020-04-16 15:53:53 CollectWgsMetrics Processed 560,000,000 loci. Elapsed time: 00:08:12s. Time for last 10,000,000: 7s. Last read position: 748:34,007 INFO 2020-04-16 15:54:01 CollectWgsMetrics Processed 570,000,000 loci. Elapsed time: 00:08:20s. Time for last 10,000,000: 8s. Last read position: 774:112,571 INFO 2020-04-16 15:54:08 CollectWgsMetrics Processed 580,000,000 loci. Elapsed time: 00:08:27s. Time for last 10,000,000: 7s. Last read position: 801:129,443 INFO 2020-04-16 15:54:15 CollectWgsMetrics Processed 590,000,000 loci. Elapsed time: 00:08:34s. Time for last 10,000,000: 7s. Last read position: 830:46,237 INFO 2020-04-16 15:54:22 CollectWgsMetrics Processed 600,000,000 loci. Elapsed time: 00:08:41s. Time for last 10,000,000: 6s. Last read position: 858:343,631 INFO 2020-04-16 15:54:29 CollectWgsMetrics Processed 610,000,000 loci. Elapsed time: 00:08:48s. Time for last 10,000,000: 7s. Last read position: 888:3,547 INFO 2020-04-16 15:54:37 CollectWgsMetrics Processed 620,000,000 loci. Elapsed time: 00:08:56s. Time for last 10,000,000: 7s. Last read position: 918:326,056 INFO 2020-04-16 15:54:43 CollectWgsMetrics Processed 630,000,000 loci. Elapsed time: 00:09:02s. Time for last 10,000,000: 6s. Last read position: 951:37,914 INFO 2020-04-16 15:54:50 CollectWgsMetrics Processed 640,000,000 loci. Elapsed time: 00:09:08s. Time for last 10,000,000: 6s. Last read position: 984:126,977 INFO 2020-04-16 15:54:57 CollectWgsMetrics Processed 650,000,000 loci. Elapsed time: 00:09:16s. Time for last 10,000,000: 7s. Last read position: 1017:167,455 INFO 2020-04-16 15:55:02 CollectWgsMetrics Processed 660,000,000 loci. Elapsed time: 00:09:21s. Time for last 10,000,000: 5s. Last read position: 1052:230,503 INFO 2020-04-16 15:55:09 CollectWgsMetrics Processed 670,000,000 loci. Elapsed time: 00:09:28s. Time for last 10,000,000: 6s. Last read position: 1090:74,736 INFO 2020-04-16 15:55:16 CollectWgsMetrics Processed 680,000,000 loci. Elapsed time: 00:09:35s. Time for last 10,000,000: 7s. Last read position: 1128:19,199 INFO 2020-04-16 15:55:23 CollectWgsMetrics Processed 690,000,000 loci. Elapsed time: 00:09:42s. Time for last 10,000,000: 6s. Last read position: 1168:8,743 INFO 2020-04-16 15:55:30 CollectWgsMetrics Processed 700,000,000 loci. Elapsed time: 00:09:49s. Time for last 10,000,000: 6s. Last read position: 1210:48,462 INFO 2020-04-16 15:55:37 CollectWgsMetrics Processed 710,000,000 loci. Elapsed time: 00:09:55s. Time for last 10,000,000: 6s. Last read position: 1252:73,681 INFO 2020-04-16 15:55:42 CollectWgsMetrics Processed 720,000,000 loci. Elapsed time: 00:10:01s. Time for last 10,000,000: 5s. Last read position: 1298:135,654 INFO 2020-04-16 15:55:49 CollectWgsMetrics Processed 730,000,000 loci. Elapsed time: 00:10:08s. Time for last 10,000,000: 6s. Last read position: 1347:42,922 INFO 2020-04-16 15:55:55 CollectWgsMetrics Processed 740,000,000 loci. Elapsed time: 00:10:14s. Time for last 10,000,000: 6s. Last read position: 1397:45,967 INFO 2020-04-16 15:56:01 CollectWgsMetrics Processed 750,000,000 loci. Elapsed time: 00:10:20s. Time for last 10,000,000: 6s. Last read position: 1450:5,557 INFO 2020-04-16 15:56:07 CollectWgsMetrics Processed 760,000,000 loci. Elapsed time: 00:10:26s. Time for last 10,000,000: 5s. Last read position: 1505:129,718 INFO 2020-04-16 15:56:12 CollectWgsMetrics Processed 770,000,000 loci. Elapsed time: 00:10:31s. Time for last 10,000,000: 5s. Last read position: 1568:3,714 INFO 2020-04-16 15:56:18 CollectWgsMetrics Processed 780,000,000 loci. Elapsed time: 00:10:37s. Time for last 10,000,000: 5s. Last read position: 1631:39,335 INFO 2020-04-16 15:56:24 CollectWgsMetrics Processed 790,000,000 loci. Elapsed time: 00:10:43s. Time for last 10,000,000: 5s. Last read position: 1698:107,239 INFO 2020-04-16 15:56:29 CollectWgsMetrics Processed 800,000,000 loci. Elapsed time: 00:10:48s. Time for last 10,000,000: 5s. Last read position: 1774:115,449 INFO 2020-04-16 15:56:34 CollectWgsMetrics Processed 810,000,000 loci. Elapsed time: 00:10:53s. Time for last 10,000,000: 5s. Last read position: 1853:95,173 INFO 2020-04-16 15:56:40 CollectWgsMetrics Processed 820,000,000 loci. Elapsed time: 00:10:58s. Time for last 10,000,000: 5s. Last read position: 1942:62,123 INFO 2020-04-16 15:56:45 CollectWgsMetrics Processed 830,000,000 loci. Elapsed time: 00:11:04s. Time for last 10,000,000: 5s. Last read position: 2039:16,006 INFO 2020-04-16 15:56:50 CollectWgsMetrics Processed 840,000,000 loci. Elapsed time: 00:11:09s. Time for last 10,000,000: 5s. Last read position: 2147:65,939 INFO 2020-04-16 15:56:55 CollectWgsMetrics Processed 850,000,000 loci. Elapsed time: 00:11:14s. Time for last 10,000,000: 5s. Last read position: 2269:65,204 INFO 2020-04-16 15:57:00 CollectWgsMetrics Processed 860,000,000 loci. Elapsed time: 00:11:19s. Time for last 10,000,000: 5s. Last read position: 2409:16,999 INFO 2020-04-16 15:57:05 CollectWgsMetrics Processed 870,000,000 loci. Elapsed time: 00:11:24s. Time for last 10,000,000: 4s. Last read position: 2580:1,672 INFO 2020-04-16 15:57:09 CollectWgsMetrics Processed 880,000,000 loci. Elapsed time: 00:11:28s. Time for last 10,000,000: 4s. Last read position: 2825:574 INFO 2020-04-16 15:57:11 TheoreticalSensitivity Creating Roulette Wheel INFO 2020-04-16 15:57:11 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2020-04-16 15:57:11 TheoreticalSensitivity 0 sampling iterations completed INFO 2020-04-16 15:57:13 TheoreticalSensitivity 1000 sampling iterations completed INFO 2020-04-16 15:57:15 TheoreticalSensitivity 2000 sampling iterations completed INFO 2020-04-16 15:57:16 TheoreticalSensitivity 3000 sampling iterations completed INFO 2020-04-16 15:57:18 TheoreticalSensitivity 4000 sampling iterations completed INFO 2020-04-16 15:57:20 TheoreticalSensitivity 5000 sampling iterations completed INFO 2020-04-16 15:57:22 TheoreticalSensitivity 6000 sampling iterations completed INFO 2020-04-16 15:57:23 TheoreticalSensitivity 7000 sampling iterations completed INFO 2020-04-16 15:57:25 TheoreticalSensitivity 8000 sampling iterations completed INFO 2020-04-16 15:57:27 TheoreticalSensitivity 9000 sampling iterations completed INFO 2020-04-16 15:57:28 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 16 15:57:29 PDT 2020] picard.analysis.CollectWgsMetrics done. Elapsed time: 11.81 minutes. Runtime.totalMemory()=966787072 INFO 2020-04-16 15:57:30 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/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 ********** 15:57:31.047 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Thu Apr 16 15:57:31 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 [Thu Apr 16 15:57:31 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 2020-04-16 15:58:00 CollectWgsMetrics Processed 10,000,000 loci. Elapsed time: 00:00:29s. Time for last 10,000,000: 28s. Last read position: 4:2,571,827 INFO 2020-04-16 15:58:32 CollectWgsMetrics Processed 20,000,000 loci. Elapsed time: 00:01:00s. Time for last 10,000,000: 31s. Last read position: 9:2,185,583 INFO 2020-04-16 15:58:59 CollectWgsMetrics Processed 30,000,000 loci. Elapsed time: 00:01:28s. Time for last 10,000,000: 27s. Last read position: 15:1,277,111 INFO 2020-04-16 15:59:29 CollectWgsMetrics Processed 40,000,000 loci. Elapsed time: 00:01:58s. Time for last 10,000,000: 29s. Last read position: 20:430,949 INFO 2020-04-16 15:59:57 CollectWgsMetrics Processed 50,000,000 loci. Elapsed time: 00:02:26s. Time for last 10,000,000: 28s. Last read position: 26:192,822 INFO 2020-04-16 16:00:29 CollectWgsMetrics Processed 60,000,000 loci. Elapsed time: 00:02:57s. Time for last 10,000,000: 31s. Last read position: 31:1,345,614 INFO 2020-04-16 16:00:54 CollectWgsMetrics Processed 70,000,000 loci. Elapsed time: 00:03:23s. Time for last 10,000,000: 25s. Last read position: 37:1,212,527 INFO 2020-04-16 16:01:24 CollectWgsMetrics Processed 80,000,000 loci. Elapsed time: 00:03:53s. Time for last 10,000,000: 29s. Last read position: 44:228,145 ^CINFO 2020-04-16 16:01:27 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/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 ********** 16:01:27.868 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/strigg/anaconda3/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Thu Apr 16 16:01:27 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 [Thu Apr 16 16:01:27 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 ^C^Cbash-3.2$ bash-3.2$ bash-3.2$ bash-3.2$ /gsUsers/strigg/Desktop/20200416/ 20200416_CollectWgsMetrics.sh 20200416_rsync_md5check.sh Pact_C1/ 20200416_qualimap.sh Mcap/ 20200416_qualimap_CollectWgsMetrics.sh Pact/ bash-3.2$ /Users/strigg/Desktop/20200416/20200416_CollectWgsMetrics.sh 20200416_CollectWgsMetrics.sh d