[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=KI2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/KI2_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 04:20:14	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:   11s.  Last read position: chr11:69,787,506
INFO	2019-04-30 04:20:22	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    8s.  Last read position: chr14:31,703,301
INFO	2019-04-30 04:20:31	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    8s.  Last read position: chr17:34,133,188
INFO	2019-04-30 04:20:38	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    7s.  Last read position: chr2:13,448,316
INFO	2019-04-30 04:20:46	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    8s.  Last read position: chr4:49,556,693
INFO	2019-04-30 04:20:53	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    7s.  Last read position: chr5:90,899,816
INFO	2019-04-30 04:21:01	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    7s.  Last read position: chr6:142,979,318
INFO	2019-04-30 04:21:08	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    6s.  Last read position: chr8:95,716,792
INFO	2019-04-30 04:21:14	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    6s.  Last read position: chrM:6,312
[Tue Apr 30 04:21:17 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 1.27 minutes.
Runtime.totalMemory()=1936719872