[Tue Apr 30 04:27:12 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=WT1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WT1_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 04:27:13 EDT 2019] Executing as kkarri@scc-ka4.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 04:27:14	CollectRnaSeqMetrics	Loaded 23628 genes.
INFO	2019-04-30 04:27:22	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr11:107,472,245
INFO	2019-04-30 04:27:29	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    6s.  Last read position: chr15:58,284,551
INFO	2019-04-30 04:27:34	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr17:39,984,296
INFO	2019-04-30 04:27:39	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    5s.  Last read position: chr2:31,375,979
INFO	2019-04-30 04:27:47	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    7s.  Last read position: chr4:125,933,310
INFO	2019-04-30 04:27:53	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    6s.  Last read position: chr5:138,224,656
INFO	2019-04-30 04:28:00	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    6s.  Last read position: chr7:147,955,589
INFO	2019-04-30 04:28:05	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    5s.  Last read position: chrM:3,969
[Tue Apr 30 04:28:08 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.93 minutes.
Runtime.totalMemory()=2083520512