[Sat Jun 17 04:57:57 EDT 2017] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/MM_M3_hist.pdf INPUT=MM_M3_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/MM_M3_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 [Sat Jun 17 04:57:57 EDT 2017] Executing as kkarri@scc-tk4.scc.bu.edu on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater INFO 2017-06-17 04:58:01 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:86,999,957 INFO 2017-06-17 04:58:03 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:170,426,938 INFO 2017-06-17 04:58:05 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:238,260,927 INFO 2017-06-17 04:58:08 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr10:35,802,324 INFO 2017-06-17 04:58:11 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr10:89,177,730 INFO 2017-06-17 04:58:13 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr11:81,649,323 INFO 2017-06-17 04:58:14 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr12:40,498,467 INFO 2017-06-17 04:58:16 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr13:91,080,917 INFO 2017-06-17 04:58:19 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr14:19,177,514 INFO 2017-06-17 04:58:23 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr14:19,179,848 INFO 2017-06-17 04:58:27 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr14:19,186,005 INFO 2017-06-17 04:58:30 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr14:19,190,989 INFO 2017-06-17 04:58:33 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr14:77,095,419 INFO 2017-06-17 04:58:35 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr16:6,976,516 INFO 2017-06-17 04:58:37 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr17:8,403,752 INFO 2017-06-17 04:58:39 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr18:48,702,880 INFO 2017-06-17 04:58:42 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr19:52,081,863 INFO 2017-06-17 04:58:44 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr2:104,788,275 INFO 2017-06-17 04:58:46 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr2:197,906,879 INFO 2017-06-17 04:58:49 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr20:12,327,761 INFO 2017-06-17 04:58:51 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr3:93,380,433 INFO 2017-06-17 04:58:54 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr4:50,159,292 INFO 2017-06-17 04:58:56 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr4:154,553,727 INFO 2017-06-17 04:58:59 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr4:180,899,053 INFO 2017-06-17 04:59:02 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr5:128,660,976 INFO 2017-06-17 04:59:05 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr6:47,902,324 INFO 2017-06-17 04:59:07 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr6:128,001,463 INFO 2017-06-17 04:59:09 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr7:34,356,062 INFO 2017-06-17 04:59:11 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr7:144,836,179 INFO 2017-06-17 04:59:13 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr8:78,344,875 INFO 2017-06-17 04:59:15 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr8:111,705,557 INFO 2017-06-17 04:59:17 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr8:117,465,013 INFO 2017-06-17 04:59:19 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr9:52,894,936 INFO 2017-06-17 04:59:21 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chrM:5,913 INFO 2017-06-17 04:59:24 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chrM:8,273 INFO 2017-06-17 04:59:27 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chrX:80,312,033 INFO 2017-06-17 04:59:53 RExecutor Executing R script via command: Rscript /tmp/kkarri/script8416572574926703969.R /scratch/9394918.1.linga/CollectInsertSizeMetrics/MM_M3_metrics /scratch/9394918.1.linga/CollectInsertSizeMetrics/MM_M3_hist.pdf MM_M3_primary_unique.bam INFO 2017-06-17 04:59:53 ProcessExecutor null device INFO 2017-06-17 04:59:53 ProcessExecutor 1 [Sat Jun 17 04:59:53 EDT 2017] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 1.94 minutes. Runtime.totalMemory()=1478688768