[Tue Apr 30 04:20:00 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=WT2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WT2_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 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
[Tue Apr 30 04:20:01 EDT 2019] Executing as kkarri@scc-kb5.scc.bu.edu on Linux 2.6.32-754.6.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater
INFO	2019-04-30 04:20:02	CollectRnaSeqMetrics	Loaded 23628 genes.
INFO	2019-04-30 04:20:12	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr11:102,265,424
INFO	2019-04-30 04:20:19	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    7s.  Last read position: chr15:31,519,539
INFO	2019-04-30 04:20:26	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    6s.  Last read position: chr17:39,984,211
INFO	2019-04-30 04:20:32	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    5s.  Last read position: chr2:10,050,867
INFO	2019-04-30 04:20:39	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    7s.  Last read position: chr4:115,164,186
INFO	2019-04-30 04:20:46	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    7s.  Last read position: chr5:118,450,473
INFO	2019-04-30 04:20:53	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    6s.  Last read position: chr7:117,062,859
INFO	2019-04-30 04:21:00	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    6s.  Last read position: chr9:120,866,296
[Tue Apr 30 04:21:03 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 1.05 minutes.
Runtime.totalMemory()=2084044800