[Wed Aug 30 20:37:02 EDT 2017] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G160_M33_hist.pdf INPUT=G160_M33_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G160_M33_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Aug 30 20:37:02 EDT 2017] Executing as kkarri@scc-kb2.scc.bu.edu on Linux 2.6.32-696.10.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater INFO 2017-08-30 20:37:07 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:75,211,650 INFO 2017-08-30 20:37:11 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:145,478,461 INFO 2017-08-30 20:37:15 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr10:9,118,363 INFO 2017-08-30 20:37:18 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr10:77,729,820 INFO 2017-08-30 20:37:23 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 4s. Last read position: chr11:4,006,050 INFO 2017-08-30 20:37:27 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 4s. Last read position: chr11:73,158,191 INFO 2017-08-30 20:37:31 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 4s. Last read position: chr11:109,947,927 INFO 2017-08-30 20:37:35 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 4s. Last read position: chr12:41,942,771 INFO 2017-08-30 20:37:39 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 4s. Last read position: chr12:92,912,056 INFO 2017-08-30 20:37:43 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: chr13:36,535,492 INFO 2017-08-30 20:37:47 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: chr13:105,079,021 INFO 2017-08-30 20:37:50 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr14:31,835,638 INFO 2017-08-30 20:37:54 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr14:100,382,655 INFO 2017-08-30 20:37:57 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr15:39,619,862 INFO 2017-08-30 20:38:01 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr15:96,861,378 INFO 2017-08-30 20:38:04 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr16:31,707,397 INFO 2017-08-30 20:38:08 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr17:3,237,894 INFO 2017-08-30 20:38:11 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: chr17:39,980,702 INFO 2017-08-30 20:38:15 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr17:39,983,821 INFO 2017-08-30 20:38:18 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr17:53,758,245 INFO 2017-08-30 20:38:22 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 4s. Last read position: chr18:21,122,872 INFO 2017-08-30 20:38:26 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 4s. Last read position: chr18:76,446,583 INFO 2017-08-30 20:38:31 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 4s. Last read position: chr19:8,417,894 INFO 2017-08-30 20:38:35 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 4s. Last read position: chr19:44,133,606 INFO 2017-08-30 20:38:39 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 4s. Last read position: chr2:30,105,082 INFO 2017-08-30 20:38:43 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 4s. Last read position: chr2:80,254,208 INFO 2017-08-30 20:38:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 4s. Last read position: chr2:147,786,409 INFO 2017-08-30 20:38:52 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 4s. Last read position: chr3:40,777,800 INFO 2017-08-30 20:38:56 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 4s. Last read position: chr3:107,732,118 INFO 2017-08-30 20:39:01 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 4s. Last read position: chr3:154,239,284 INFO 2017-08-30 20:39:05 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 4s. Last read position: chr4:82,179,776 INFO 2017-08-30 20:39:09 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 4s. Last read position: chr4:132,345,571 INFO 2017-08-30 20:39:13 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr5:33,752,275 INFO 2017-08-30 20:39:17 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr5:90,905,554 INFO 2017-08-30 20:39:21 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 4s. Last read position: chr5:145,031,236 INFO 2017-08-30 20:39:25 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr6:32,752,425 INFO 2017-08-30 20:39:29 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 4s. Last read position: chr6:97,246,330 INFO 2017-08-30 20:39:33 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 4s. Last read position: chr6:141,610,748 INFO 2017-08-30 20:39:37 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr7:37,987,176 INFO 2017-08-30 20:39:41 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 4s. Last read position: chr7:122,920,602 INFO 2017-08-30 20:39:45 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chr8:28,090,105 INFO 2017-08-30 20:39:48 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: chr8:95,737,300 INFO 2017-08-30 20:39:51 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 3s. Last read position: chr9:42,228,008 INFO 2017-08-30 20:39:55 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr9:77,937,965 INFO 2017-08-30 20:39:58 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 3s. Last read position: chr9:123,371,133 INFO 2017-08-30 20:40:01 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: chrX:100,658,388 INFO 2017-08-30 20:41:18 RExecutor Executing R script via command: Rscript /tmp/kkarri/script590286586238992197.R /scratch/473926.1.linga/CollectInsertSizeMetrics/G160_M33_metrics /scratch/473926.1.linga/CollectInsertSizeMetrics/G160_M33_hist.pdf G160_M33_primary_unique.bam INFO 2017-08-30 20:41:19 ProcessExecutor null device INFO 2017-08-30 20:41:19 ProcessExecutor 1 [Wed Aug 30 20:41:19 EDT 2017] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 4.28 minutes. Runtime.totalMemory()=1769537536