[Tue Apr 30 04:20:56 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=KI3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/KI3_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 04:20:57 EDT 2019] Executing as kkarri@scc-kb6.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 04:20:58	CollectRnaSeqMetrics	Loaded 23628 genes.
INFO	2019-04-30 04:21:09	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:   10s.  Last read position: chr11:69,481,074
INFO	2019-04-30 04:21:24	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:   15s.  Last read position: chr14:25,312,622
INFO	2019-04-30 04:21:42	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   17s.  Last read position: chr17:32,470,863
INFO	2019-04-30 04:21:53	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:   10s.  Last read position: chr2:5,218,886
INFO	2019-04-30 04:22:08	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:   15s.  Last read position: chr4:49,549,463
INFO	2019-04-30 04:22:22	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:   14s.  Last read position: chr5:90,898,594
INFO	2019-04-30 04:22:38	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:   16s.  Last read position: chr6:128,472,197
INFO	2019-04-30 04:22:49	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:   10s.  Last read position: chr8:88,036,198
INFO	2019-04-30 04:23:00	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:   11s.  Last read position: chrM:5,846
[Tue Apr 30 04:23:06 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 2.17 minutes.
Runtime.totalMemory()=1670905856