[Wed Aug 30 20:25:54 EDT 2017] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G160_M11_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G160_M11_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 [Wed Aug 30 20:25:54 EDT 2017] Executing as kkarri@scc-kb4.scc.bu.edu on Linux 2.6.32-696.10.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater INFO 2017-08-30 20:25:57 CollectRnaSeqMetrics Loaded 23628 genes. INFO 2017-08-30 20:26:14 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 17s. Last read position: chr1:136,521,301 INFO 2017-08-30 20:26:24 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 9s. Last read position: chr10:53,330,100 INFO 2017-08-30 20:26:34 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 10s. Last read position: chr11:29,102,122 INFO 2017-08-30 20:26:45 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 10s. Last read position: chr11:110,048,434 INFO 2017-08-30 20:26:57 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 12s. Last read position: chr12:85,772,119 INFO 2017-08-30 20:27:07 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 10s. Last read position: chr13:94,387,232 INFO 2017-08-30 20:27:17 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 9s. Last read position: chr14:69,867,590 INFO 2017-08-30 20:27:27 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 10s. Last read position: chr15:82,980,120 INFO 2017-08-30 20:27:35 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 7s. Last read position: chr16:30,356,869 INFO 2017-08-30 20:27:44 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 8s. Last read position: chr17:34,099,679 INFO 2017-08-30 20:27:49 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 5s. Last read position: chr17:39,983,807 INFO 2017-08-30 20:27:54 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 5s. Last read position: chr17:46,848,490 INFO 2017-08-30 20:28:06 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 11s. Last read position: chr18:65,382,993 INFO 2017-08-30 20:28:17 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 10s. Last read position: chr19:23,401,480 INFO 2017-08-30 20:28:31 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 14s. Last read position: chr2:34,662,218 INFO 2017-08-30 20:28:45 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 14s. Last read position: chr2:146,275,378 INFO 2017-08-30 20:28:56 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 10s. Last read position: chr3:82,835,853 INFO 2017-08-30 20:29:08 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 12s. Last read position: chr4:19,942,984 INFO 2017-08-30 20:29:20 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 12s. Last read position: chr4:131,926,941 INFO 2017-08-30 20:29:33 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 12s. Last read position: chr5:90,893,047 INFO 2017-08-30 20:29:45 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 12s. Last read position: chr5:147,072,581 INFO 2017-08-30 20:29:55 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 10s. Last read position: chr6:88,679,510 INFO 2017-08-30 20:30:08 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 13s. Last read position: chr7:20,283,481 INFO 2017-08-30 20:30:21 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 12s. Last read position: chr7:147,937,290 INFO 2017-08-30 20:30:33 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 12s. Last read position: chr8:107,581,986 INFO 2017-08-30 20:30:44 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 11s. Last read position: chr9:77,777,951 INFO 2017-08-30 20:30:54 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 9s. Last read position: chr9:123,513,118 INFO 2017-08-30 20:30:59 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 5s. Last read position: chrM:1,955 INFO 2017-08-30 20:31:09 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 9s. Last read position: chrX:103,068,394 [Wed Aug 30 20:31:12 EDT 2017] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 5.30 minutes. Runtime.totalMemory()=2137194496