[Wed Aug 30 20:37:09 EDT 2017] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G160_M11_hist.pdf INPUT=G160_M11_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G160_M11_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 20:37:09 EDT 2017] Executing as kkarri@scc-tm4.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 20:37:13 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:136,521,301 INFO 2017-08-30 20:37:14 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr10:53,330,100 INFO 2017-08-30 20:37:16 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr11:29,102,122 INFO 2017-08-30 20:37:18 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr11:110,048,434 INFO 2017-08-30 20:37:20 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr12:85,772,119 INFO 2017-08-30 20:37:21 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr13:94,387,232 INFO 2017-08-30 20:37:23 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr14:69,867,590 INFO 2017-08-30 20:37:26 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr15:82,980,120 INFO 2017-08-30 20:37:28 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr16:30,356,869 INFO 2017-08-30 20:37:31 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr17:34,099,679 INFO 2017-08-30 20:37:33 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr17:39,983,807 INFO 2017-08-30 20:37:35 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr17:46,848,490 INFO 2017-08-30 20:37:37 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr18:65,382,993 INFO 2017-08-30 20:37:39 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr19:23,401,480 INFO 2017-08-30 20:37:41 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr2:34,662,218 INFO 2017-08-30 20:37:44 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr2:146,275,378 INFO 2017-08-30 20:37:45 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr3:82,835,853 INFO 2017-08-30 20:37:47 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr4:19,942,984 INFO 2017-08-30 20:37:50 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr4:131,926,941 INFO 2017-08-30 20:37:51 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr5:90,893,047 INFO 2017-08-30 20:37:54 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr5:147,072,581 INFO 2017-08-30 20:37:56 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr6:88,679,510 INFO 2017-08-30 20:37:58 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr7:20,283,481 INFO 2017-08-30 20:38:00 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr7:147,937,290 INFO 2017-08-30 20:38:01 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr8:107,581,986 INFO 2017-08-30 20:38:03 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr9:77,777,951 INFO 2017-08-30 20:38:05 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr9:123,513,118 INFO 2017-08-30 20:38:07 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chrM:1,955 INFO 2017-08-30 20:38:09 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chrX:103,068,394 INFO 2017-08-30 20:38:32 RExecutor Executing R script via command: Rscript /tmp/kkarri/script797057607381908340.R /scratch/473922.1.linga/CollectInsertSizeMetrics/G160_M11_metrics /scratch/473922.1.linga/CollectInsertSizeMetrics/G160_M11_hist.pdf G160_M11_primary_unique.bam INFO 2017-08-30 20:38:32 ProcessExecutor null device INFO 2017-08-30 20:38:32 ProcessExecutor 1 [Wed Aug 30 20:38:32 EDT 2017] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 1.39 minutes. Runtime.totalMemory()=1790509056