[Thu Jun 15 06:20:30 EDT 2017] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/C_IP6_hist.pdf INPUT=C_IP6_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/C_IP6_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 [Thu Jun 15 06:20:30 EDT 2017] Executing as kkarri@scc-kb4.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 2017-06-15 06:20:37 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:100,850,327 INFO 2017-06-15 06:20:41 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 4s. Last read position: chr1:213,521,929 INFO 2017-06-15 06:20:45 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:263,787,082 INFO 2017-06-15 06:20:49 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 4s. Last read position: chr10:71,720,081 INFO 2017-06-15 06:20:53 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr11:81,649,170 INFO 2017-06-15 06:20:57 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr12:41,620,393 INFO 2017-06-15 06:21:01 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr13:99,281,827 INFO 2017-06-15 06:21:04 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr14:19,178,196 INFO 2017-06-15 06:21:08 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr14:19,181,087 INFO 2017-06-15 06:21:12 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr14:19,187,047 INFO 2017-06-15 06:21:15 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: chr14:22,529,804 INFO 2017-06-15 06:21:19 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 4s. Last read position: chr16:2,115,028 INFO 2017-06-15 06:21:23 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 4s. Last read position: chr17:42,115,134 INFO 2017-06-15 06:21:27 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: chr19:21,400,997 INFO 2017-06-15 06:21:31 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 4s. Last read position: chr2:53,115,975 INFO 2017-06-15 06:21:36 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 4s. Last read position: chr2:197,789,445 INFO 2017-06-15 06:21:41 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 4s. Last read position: chr20:46,261,587 INFO 2017-06-15 06:21:45 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 4s. Last read position: chr3:147,238,440 INFO 2017-06-15 06:21:49 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 4s. Last read position: chr4:149,273,619 INFO 2017-06-15 06:21:53 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 4s. Last read position: chr5:8,893,989 INFO 2017-06-15 06:21:57 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr5:127,508,564 INFO 2017-06-15 06:22:01 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 4s. Last read position: chr6:95,480,765 INFO 2017-06-15 06:22:05 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 4s. Last read position: chr6:128,080,388 INFO 2017-06-15 06:22:09 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 4s. Last read position: chr7:117,307,744 INFO 2017-06-15 06:22:13 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr8:46,529,009 INFO 2017-06-15 06:22:17 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr8:111,698,314 INFO 2017-06-15 06:22:20 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr9:9,746,738 INFO 2017-06-15 06:22:24 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chrM:5,676 INFO 2017-06-15 06:22:27 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chrM:8,248 INFO 2017-06-15 06:22:31 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: chrX:75,449,183 INFO 2017-06-15 06:23:22 RExecutor Executing R script via command: Rscript /tmp/kkarri/script3577269461573560181.R /scratch/9332931.1.linga/CollectInsertSizeMetrics/C_IP6_metrics /scratch/9332931.1.linga/CollectInsertSizeMetrics/C_IP6_hist.pdf C_IP6_primary_unique.bam INFO 2017-06-15 06:23:22 ProcessExecutor null device INFO 2017-06-15 06:23:22 ProcessExecutor 1 [Thu Jun 15 06:23:22 EDT 2017] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 2.88 minutes. Runtime.totalMemory()=1703215104