[Sun Jul 15 18:16:31 EDT 2018] picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G167_M2_hist.pdf INPUT=G167_M2_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G167_M2_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 18:16:31 EDT 2018] Executing as kkarri@scc-kb7.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 18:16:38	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr10:79,322,420
INFO	2018-07-15 18:16:43	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    5s.  Last read position: chr11:100,985,820
INFO	2018-07-15 18:16:48	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    4s.  Last read position: chr12:105,581,408
INFO	2018-07-15 18:16:52	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    4s.  Last read position: chr14:123,091,476
INFO	2018-07-15 18:16:56	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    4s.  Last read position: chr16:31,446,736
INFO	2018-07-15 18:17:00	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    4s.  Last read position: chr17:84,238,221
INFO	2018-07-15 18:17:05	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    4s.  Last read position: chr2:4,857,062
INFO	2018-07-15 18:17:09	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    4s.  Last read position: chr3:14,871,677
INFO	2018-07-15 18:17:14	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    4s.  Last read position: chr4:60,081,068
INFO	2018-07-15 18:17:19	SinglePassSamProgram	Processed    10,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr4:61,745,601
INFO	2018-07-15 18:17:23	SinglePassSamProgram	Processed    11,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    4s.  Last read position: chr5:90,890,035
INFO	2018-07-15 18:17:27	SinglePassSamProgram	Processed    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    4s.  Last read position: chr5:146,673,984
INFO	2018-07-15 18:17:32	SinglePassSamProgram	Processed    13,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    4s.  Last read position: chr7:20,274,916
INFO	2018-07-15 18:17:36	SinglePassSamProgram	Processed    14,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    4s.  Last read position: chr7:134,416,528
INFO	2018-07-15 18:17:41	SinglePassSamProgram	Processed    15,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    4s.  Last read position: chr9:40,611,342
INFO	2018-07-15 18:17:46	SinglePassSamProgram	Processed    16,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    5s.  Last read position: chr9:108,458,341
INFO	2018-07-15 18:17:51	SinglePassSamProgram	Processed    17,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    4s.  Last read position: chrX:82,948,170
INFO	2018-07-15 18:18:33	RExecutor	Executing R script via command: Rscript /tmp/kkarri/script7497176370893697452.R /scratch/6944803.1.linga/CollectInsertSizeMetrics/G167_M2_metrics /scratch/6944803.1.linga/CollectInsertSizeMetrics/G167_M2_hist.pdf G167_M2_primary_unique.bam
INFO	2018-07-15 18:18:33	ProcessExecutor	null device 
INFO	2018-07-15 18:18:33	ProcessExecutor	          1 
[Sun Jul 15 18:18:33 EDT 2018] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 2.04 minutes.
Runtime.totalMemory()=1828978688