[Tue Apr 30 04:23:59 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=WT7_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WT7_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 04:24:01 EDT 2019] Executing as kkarri@scc-kb1.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 04:24:02	CollectRnaSeqMetrics	Loaded 23628 genes.
INFO	2019-04-30 04:24:10	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr11:78,068,534
INFO	2019-04-30 04:24:17	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    6s.  Last read position: chr14:47,939,170
INFO	2019-04-30 04:24:23	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    6s.  Last read position: chr17:39,983,635
INFO	2019-04-30 04:24:27	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    4s.  Last read position: chr19:39,723,466
INFO	2019-04-30 04:24:33	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    5s.  Last read position: chr3:153,585,602
INFO	2019-04-30 04:24:38	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    5s.  Last read position: chr5:90,897,647
INFO	2019-04-30 04:24:44	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    5s.  Last read position: chr6:138,103,686
INFO	2019-04-30 04:24:49	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    5s.  Last read position: chr8:112,099,899
INFO	2019-04-30 04:24:54	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    4s.  Last read position: chrM:12,971
[Tue Apr 30 04:24:56 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.95 minutes.
Runtime.totalMemory()=2093481984