[Mon Apr 29 09:59:13 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=PB_LivTum2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/PB_LivTum2_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 [Mon Apr 29 09:59:13 EDT 2019] Executing as kkarri@scc-kb7.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 2019-04-29 09:59:14 CollectRnaSeqMetrics Loaded 23628 genes. INFO 2019-04-29 09:59:25 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 10s. Last read position: chr1:71,632,321 INFO 2019-04-29 09:59:38 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 12s. Last read position: chr1:104,524,812 INFO 2019-04-29 09:59:44 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 6s. Last read position: chr1:155,755,181 INFO 2019-04-29 09:59:51 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 6s. Last read position: chr1:167,704,040 INFO 2019-04-29 09:59:56 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 5s. Last read position: chr1:177,590,885 INFO 2019-04-29 10:00:03 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 7s. Last read position: chr10:59,764,526 INFO 2019-04-29 10:00:12 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 8s. Last read position: chr10:79,517,579 INFO 2019-04-29 10:00:20 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 7s. Last read position: chr10:86,984,677 INFO 2019-04-29 10:00:27 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 7s. Last read position: chr10:127,525,395 INFO 2019-04-29 10:00:33 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 6s. Last read position: chr11:6,319,570 INFO 2019-04-29 10:00:40 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 6s. Last read position: chr11:54,683,740 INFO 2019-04-29 10:00:48 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 7s. Last read position: chr11:70,468,006 INFO 2019-04-29 10:00:56 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 7s. Last read position: chr11:80,285,039 INFO 2019-04-29 10:01:02 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 6s. Last read position: chr11:100,345,079 INFO 2019-04-29 10:01:09 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 7s. Last read position: chr11:110,093,501 INFO 2019-04-29 10:01:16 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 6s. Last read position: chr12:4,249,735 INFO 2019-04-29 10:01:24 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 8s. Last read position: chr12:70,406,774 INFO 2019-04-29 10:01:32 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 7s. Last read position: chr12:104,968,532 INFO 2019-04-29 10:01:38 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: chr12:114,660,323 INFO 2019-04-29 10:01:57 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 19s. Last read position: chr13:49,474,866 INFO 2019-04-29 10:02:04 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 6s. Last read position: chr13:97,947,866 INFO 2019-04-29 10:02:13 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 9s. Last read position: chr14:32,475,435 INFO 2019-04-29 10:02:20 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 6s. Last read position: chr14:56,228,325 INFO 2019-04-29 10:02:27 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 6s. Last read position: chr14:73,764,406 INFO 2019-04-29 10:02:34 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 7s. Last read position: chr15:31,203,734 INFO 2019-04-29 10:02:41 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 7s. Last read position: chr15:78,230,184 INFO 2019-04-29 10:02:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 6s. Last read position: chr15:88,988,422 INFO 2019-04-29 10:02:56 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 8s. Last read position: chr16:4,706,772 INFO 2019-04-29 10:03:04 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 7s. Last read position: chr16:22,894,401 INFO 2019-04-29 10:03:14 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 9s. Last read position: chr16:27,450,575 INFO 2019-04-29 10:03:20 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 6s. Last read position: chr16:90,225,394 INFO 2019-04-29 10:03:27 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 6s. Last read position: chr17:24,876,471 INFO 2019-04-29 10:03:34 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 7s. Last read position: chr17:34,249,218 INFO 2019-04-29 10:03:41 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 7s. Last read position: chr17:39,983,315 INFO 2019-04-29 10:03:44 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr17:39,983,638 INFO 2019-04-29 10:03:47 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 3s. Last read position: chr17:39,984,047 INFO 2019-04-29 10:03:51 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 3s. Last read position: chr17:39,984,417 INFO 2019-04-29 10:03:54 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 3s. Last read position: chr17:39,984,636 INFO 2019-04-29 10:03:57 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 3s. Last read position: chr17:39,984,854 INFO 2019-04-29 10:04:01 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 4s. Last read position: chr17:46,862,911 INFO 2019-04-29 10:04:09 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 7s. Last read position: chr17:57,362,339 INFO 2019-04-29 10:04:17 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 8s. Last read position: chr18:20,824,007 INFO 2019-04-29 10:04:23 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 5s. Last read position: chr18:46,875,349 INFO 2019-04-29 10:04:29 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 6s. Last read position: chr19:3,385,021 INFO 2019-04-29 10:04:36 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 7s. Last read position: chr19:10,057,340 INFO 2019-04-29 10:04:43 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 6s. Last read position: chr19:31,983,292 INFO 2019-04-29 10:04:49 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 5s. Last read position: chr19:39,384,229 INFO 2019-04-29 10:04:55 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 6s. Last read position: chr19:39,717,891 INFO 2019-04-29 10:05:01 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 5s. Last read position: chr19:44,477,743 INFO 2019-04-29 10:05:08 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 7s. Last read position: chr2:24,829,736 INFO 2019-04-29 10:05:17 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 8s. Last read position: chr2:32,817,319 INFO 2019-04-29 10:05:25 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 8s. Last read position: chr2:90,235,294 INFO 2019-04-29 10:05:32 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 7s. Last read position: chr2:121,258,071 INFO 2019-04-29 10:05:40 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 8s. Last read position: chr2:146,836,188 INFO 2019-04-29 10:05:47 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 7s. Last read position: chr2:165,274,233 INFO 2019-04-29 10:05:54 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 7s. Last read position: chr3:19,874,883 INFO 2019-04-29 10:06:02 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 7s. Last read position: chr3:82,847,225 INFO 2019-04-29 10:06:09 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 7s. Last read position: chr3:95,792,992 INFO 2019-04-29 10:06:16 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 6s. Last read position: chr3:107,788,981 INFO 2019-04-29 10:06:21 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 5s. Last read position: chr3:108,067,987 INFO 2019-04-29 10:06:28 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 6s. Last read position: chr3:154,284,455 INFO 2019-04-29 10:06:35 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 6s. Last read position: chr4:62,804,399 INFO 2019-04-29 10:06:42 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 7s. Last read position: chr4:107,851,550 INFO 2019-04-29 10:06:49 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 7s. Last read position: chr4:135,522,324 INFO 2019-04-29 10:06:57 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 7s. Last read position: chr5:8,909,103 INFO 2019-04-29 10:07:04 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 7s. Last read position: chr5:76,642,005 INFO 2019-04-29 10:07:10 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 6s. Last read position: chr5:90,889,941 INFO 2019-04-29 10:07:15 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 4s. Last read position: chr5:90,891,738 INFO 2019-04-29 10:07:21 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 5s. Last read position: chr5:90,893,954 INFO 2019-04-29 10:07:27 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 6s. Last read position: chr5:90,897,642 INFO 2019-04-29 10:07:34 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 7s. Last read position: chr5:90,901,161 INFO 2019-04-29 10:07:42 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 7s. Last read position: chr5:90,903,715 INFO 2019-04-29 10:07:49 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 7s. Last read position: chr5:116,009,548 INFO 2019-04-29 10:07:56 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 6s. Last read position: chr5:130,360,006 INFO 2019-04-29 10:08:03 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 6s. Last read position: chr5:146,671,967 INFO 2019-04-29 10:08:08 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 5s. Last read position: chr6:5,204,558 INFO 2019-04-29 10:08:15 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 7s. Last read position: chr6:71,818,786 INFO 2019-04-29 10:08:22 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 6s. Last read position: chr6:116,602,370 INFO 2019-04-29 10:08:29 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 7s. Last read position: chr6:128,441,605 INFO 2019-04-29 10:08:37 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 7s. Last read position: chr7:4,828,743 INFO 2019-04-29 10:08:42 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 5s. Last read position: chr7:20,281,751 INFO 2019-04-29 10:08:47 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 4s. Last read position: chr7:20,282,837 INFO 2019-04-29 10:08:52 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 5s. Last read position: chr7:26,711,178 INFO 2019-04-29 10:08:59 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 6s. Last read position: chr7:31,278,685 INFO 2019-04-29 10:09:05 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 6s. Last read position: chr7:52,713,999 INFO 2019-04-29 10:09:11 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 6s. Last read position: chr7:73,194,539 INFO 2019-04-29 10:09:18 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 6s. Last read position: chr7:112,740,322 INFO 2019-04-29 10:09:24 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 6s. Last read position: chr7:125,258,378 INFO 2019-04-29 10:09:30 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 6s. Last read position: chr7:147,297,621 INFO 2019-04-29 10:09:36 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 6s. Last read position: chr7:148,112,591 INFO 2019-04-29 10:09:43 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 6s. Last read position: chr8:26,784,130 INFO 2019-04-29 10:09:50 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 6s. Last read position: chr8:86,096,133 INFO 2019-04-29 10:09:56 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 6s. Last read position: chr8:98,388,228 INFO 2019-04-29 10:10:02 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 6s. Last read position: chr8:112,515,416 INFO 2019-04-29 10:10:10 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 7s. Last read position: chr9:21,725,701 INFO 2019-04-29 10:10:16 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 6s. Last read position: chr9:46,037,068 INFO 2019-04-29 10:10:21 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 5s. Last read position: chr9:46,038,339 INFO 2019-04-29 10:10:26 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 5s. Last read position: chr9:56,773,369 INFO 2019-04-29 10:10:33 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 6s. Last read position: chr9:77,634,599 INFO 2019-04-29 10:10:38 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 5s. Last read position: chr9:103,111,393 INFO 2019-04-29 10:10:43 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 5s. Last read position: chr9:103,122,208 INFO 2019-04-29 10:10:51 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 7s. Last read position: chr9:103,130,309 INFO 2019-04-29 10:10:58 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 6s. Last read position: chr9:113,884,900 INFO 2019-04-29 10:11:02 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 4s. Last read position: chrM:2,825 INFO 2019-04-29 10:11:06 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 3s. Last read position: chrM:5,907 INFO 2019-04-29 10:11:09 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 3s. Last read position: chrX:7,469,949 INFO 2019-04-29 10:11:16 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 6s. Last read position: chrX:71,518,287 [Mon Apr 29 10:11:22 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 12.15 minutes. Runtime.totalMemory()=2002780160