[Sun Jul 15 18:16:32 EDT 2018] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G167_M5_hist.pdf INPUT=G167_M5_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G167_M5_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
[Sun Jul 15 18:16:32 EDT 2018] Executing as kkarri@scc-ka3.scc.bu.edu on Linux 2.6.32-696.28.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater
INFO	2018-07-15 18:16:40	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr10:87,030,097
INFO	2018-07-15 18:16:45	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    5s.  Last read position: chr12:8,022,202
INFO	2018-07-15 18:16:50	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    5s.  Last read position: chr13:64,466,577
INFO	2018-07-15 18:16:55	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    5s.  Last read position: chr15:78,270,445
INFO	2018-07-15 18:17:00	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    4s.  Last read position: chr17:35,611,176
INFO	2018-07-15 18:17:05	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr19:10,059,143
INFO	2018-07-15 18:17:10	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    5s.  Last read position: chr2:155,953,402
INFO	2018-07-15 18:17:15	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    4s.  Last read position: chr4:49,549,564
INFO	2018-07-15 18:17:20	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr4:60,964,433
INFO	2018-07-15 18:17:24	SinglePassSamProgram	Processed    10,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    4s.  Last read position: chr4:137,869,969
INFO	2018-07-15 18:17:29	SinglePassSamProgram	Processed    11,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    4s.  Last read position: chr5:123,621,891
INFO	2018-07-15 18:17:33	SinglePassSamProgram	Processed    12,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    4s.  Last read position: chr6:143,156,368
INFO	2018-07-15 18:17:38	SinglePassSamProgram	Processed    13,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    4s.  Last read position: chr7:117,122,317
INFO	2018-07-15 18:17:43	SinglePassSamProgram	Processed    14,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    5s.  Last read position: chr9:43,030,270
INFO	2018-07-15 18:17:48	SinglePassSamProgram	Processed    15,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    4s.  Last read position: chr9:123,370,946
INFO	2018-07-15 18:18:35	RExecutor	Executing R script via command: Rscript /tmp/kkarri/script7301620868805946036.R /scratch/6944806.1.linga/CollectInsertSizeMetrics/G167_M5_metrics /scratch/6944806.1.linga/CollectInsertSizeMetrics/G167_M5_hist.pdf G167_M5_primary_unique.bam
INFO	2018-07-15 18:18:35	ProcessExecutor	null device 
INFO	2018-07-15 18:18:35	ProcessExecutor	          1 
[Sun Jul 15 18:18:35 EDT 2018] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 2.06 minutes.
Runtime.totalMemory()=1787494400