[Tue Apr 30 04:18:25 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=CV_CO1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/CV_CO1_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 04:18:25 EDT 2019] Executing as kkarri@scc-tl2.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 04:18:26 CollectRnaSeqMetrics Loaded 23628 genes. INFO 2019-04-30 04:18:34 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:38,054,968 INFO 2019-04-30 04:18:40 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 6s. Last read position: chr1:66,899,851 INFO 2019-04-30 04:18:49 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 8s. Last read position: chr1:71,659,109 INFO 2019-04-30 04:18:57 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 8s. Last read position: chr1:88,502,187 INFO 2019-04-30 04:19:02 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 5s. Last read position: chr1:123,374,449 INFO 2019-04-30 04:19:07 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 4s. Last read position: chr1:141,671,096 INFO 2019-04-30 04:19:11 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 4s. Last read position: chr1:162,925,513 INFO 2019-04-30 04:19:16 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 4s. Last read position: chr1:173,155,236 INFO 2019-04-30 04:19:20 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr1:173,156,389 INFO 2019-04-30 04:19:24 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 4s. Last read position: chr1:182,930,021 INFO 2019-04-30 04:19:29 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 5s. Last read position: chr10:23,506,611 INFO 2019-04-30 04:19:35 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 5s. Last read position: chr10:60,892,137 INFO 2019-04-30 04:19:39 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 4s. Last read position: chr10:76,516,030 INFO 2019-04-30 04:19:44 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 4s. Last read position: chr10:79,865,847 INFO 2019-04-30 04:19:49 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 5s. Last read position: chr10:86,156,872 INFO 2019-04-30 04:19:55 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 5s. Last read position: chr10:111,047,257 INFO 2019-04-30 04:19:59 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 4s. Last read position: chr10:127,321,495 INFO 2019-04-30 04:20:04 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 4s. Last read position: chr10:128,005,968 INFO 2019-04-30 04:20:10 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 5s. Last read position: chr11:6,315,916 INFO 2019-04-30 04:20:16 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 5s. Last read position: chr11:48,617,724 INFO 2019-04-30 04:20:19 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: chr11:59,026,650 INFO 2019-04-30 04:20:24 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 4s. Last read position: chr11:69,826,703 INFO 2019-04-30 04:20:28 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 4s. Last read position: chr11:75,250,949 INFO 2019-04-30 04:20:32 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 4s. Last read position: chr11:78,315,298 INFO 2019-04-30 04:20:37 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 5s. Last read position: chr11:93,986,105 INFO 2019-04-30 04:20:42 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 5s. Last read position: chr11:98,913,223 INFO 2019-04-30 04:20:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 5s. Last read position: chr11:106,257,255 INFO 2019-04-30 04:20:53 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 4s. Last read position: chr11:115,469,660 INFO 2019-04-30 04:20:57 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: chr11:119,970,847 INFO 2019-04-30 04:21:02 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 4s. Last read position: chr12:3,895,734 INFO 2019-04-30 04:21:10 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 8s. Last read position: chr12:8,022,207 INFO 2019-04-30 04:21:15 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 4s. Last read position: chr12:56,519,243 INFO 2019-04-30 04:21:19 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr12:85,382,879 INFO 2019-04-30 04:21:23 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 4s. Last read position: chr12:104,966,596 INFO 2019-04-30 04:21:26 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr12:105,092,881 INFO 2019-04-30 04:21:29 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr12:105,186,290 INFO 2019-04-30 04:21:31 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr12:105,576,717 INFO 2019-04-30 04:21:34 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr12:105,581,397 INFO 2019-04-30 04:21:37 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr12:105,632,344 INFO 2019-04-30 04:21:41 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chr13:4,456,445 INFO 2019-04-30 04:21:45 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 4s. Last read position: chr13:38,605,012 INFO 2019-04-30 04:21:49 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 3s. Last read position: chr13:62,966,169 INFO 2019-04-30 04:21:52 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr13:94,387,405 INFO 2019-04-30 04:21:56 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 3s. Last read position: chr14:9,069,370 INFO 2019-04-30 04:22:01 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 4s. Last read position: chr14:31,708,638 INFO 2019-04-30 04:22:08 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 6s. Last read position: chr14:35,147,407 INFO 2019-04-30 04:22:11 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 3s. Last read position: chr14:41,972,773 INFO 2019-04-30 04:22:15 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 3s. Last read position: chr14:56,248,008 INFO 2019-04-30 04:22:18 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 3s. Last read position: chr14:66,616,501 INFO 2019-04-30 04:22:22 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 4s. Last read position: chr14:78,914,720 INFO 2019-04-30 04:22:26 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 4s. Last read position: chr15:3,229,508 INFO 2019-04-30 04:22:31 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 4s. Last read position: chr15:10,263,873 INFO 2019-04-30 04:22:35 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 4s. Last read position: chr15:57,973,073 INFO 2019-04-30 04:22:39 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 4s. Last read position: chr15:78,274,612 INFO 2019-04-30 04:22:44 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 5s. Last read position: chr15:82,285,907 INFO 2019-04-30 04:22:50 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 5s. Last read position: chr15:96,826,614 INFO 2019-04-30 04:22:59 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 8s. Last read position: chr15:101,920,726 INFO 2019-04-30 04:23:06 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 7s. Last read position: chr16:17,331,533 INFO 2019-04-30 04:23:13 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 6s. Last read position: chr16:22,892,287 INFO 2019-04-30 04:23:18 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 5s. Last read position: chr16:22,899,217 INFO 2019-04-30 04:23:23 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 4s. Last read position: chr16:23,079,867 INFO 2019-04-30 04:23:27 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 4s. Last read position: chr16:43,179,731 INFO 2019-04-30 04:23:31 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 3s. Last read position: chr16:98,080,689 INFO 2019-04-30 04:23:35 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 3s. Last read position: chr17:21,163,175 INFO 2019-04-30 04:23:38 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 3s. Last read position: chr17:27,890,768 INFO 2019-04-30 04:23:43 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 4s. Last read position: chr17:34,136,299 INFO 2019-04-30 04:23:48 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 4s. Last read position: chr17:35,403,221 INFO 2019-04-30 04:23:52 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 4s. Last read position: chr17:46,775,818 INFO 2019-04-30 04:23:55 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 3s. Last read position: chr17:57,343,529 INFO 2019-04-30 04:23:59 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 3s. Last read position: chr17:57,355,350 INFO 2019-04-30 04:24:06 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 7s. Last read position: chr17:57,367,449 INFO 2019-04-30 04:24:12 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 5s. Last read position: chr18:9,353,462 INFO 2019-04-30 04:24:16 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 3s. Last read position: chr18:20,828,570 INFO 2019-04-30 04:24:19 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 3s. Last read position: chr18:35,102,829 INFO 2019-04-30 04:24:22 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 3s. Last read position: chr18:56,720,450 INFO 2019-04-30 04:24:26 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 3s. Last read position: chr18:78,017,959 INFO 2019-04-30 04:24:29 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 3s. Last read position: chr19:4,617,714 INFO 2019-04-30 04:24:33 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 4s. Last read position: chr19:8,989,758 INFO 2019-04-30 04:24:37 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 3s. Last read position: chr19:12,720,855 INFO 2019-04-30 04:24:41 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr19:32,026,761 INFO 2019-04-30 04:24:45 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 4s. Last read position: chr19:39,361,765 INFO 2019-04-30 04:24:49 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 4s. Last read position: chr19:41,992,507 INFO 2019-04-30 04:24:52 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 3s. Last read position: chr19:44,470,384 INFO 2019-04-30 04:24:55 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr19:46,158,726 INFO 2019-04-30 04:25:00 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 4s. Last read position: chr2:4,857,090 INFO 2019-04-30 04:25:05 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 4s. Last read position: chr2:25,480,864 INFO 2019-04-30 04:25:09 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 4s. Last read position: chr2:31,330,244 INFO 2019-04-30 04:25:15 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 5s. Last read position: chr2:34,838,979 INFO 2019-04-30 04:25:20 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 5s. Last read position: chr2:71,725,507 INFO 2019-04-30 04:25:25 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 4s. Last read position: chr2:91,470,311 INFO 2019-04-30 04:25:28 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 3s. Last read position: chr2:103,615,801 INFO 2019-04-30 04:25:32 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 4s. Last read position: chr2:122,082,670 INFO 2019-04-30 04:25:37 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 4s. Last read position: chr2:132,362,462 INFO 2019-04-30 04:25:41 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 3s. Last read position: chr2:155,479,349 INFO 2019-04-30 04:25:45 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 4s. Last read position: chr2:172,180,223 INFO 2019-04-30 04:25:51 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 5s. Last read position: chr3:14,871,569 INFO 2019-04-30 04:25:55 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 4s. Last read position: chr3:57,568,205 INFO 2019-04-30 04:25:58 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 3s. Last read position: chr3:82,814,443 INFO 2019-04-30 04:26:02 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 4s. Last read position: chr3:82,835,553 INFO 2019-04-30 04:26:06 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: chr3:85,942,980 INFO 2019-04-30 04:26:11 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 4s. Last read position: chr3:94,839,240 INFO 2019-04-30 04:26:15 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 4s. Last read position: chr3:98,113,497 INFO 2019-04-30 04:26:19 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 3s. Last read position: chr3:107,819,509 INFO 2019-04-30 04:26:22 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 3s. Last read position: chr3:130,399,041 INFO 2019-04-30 04:26:26 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 3s. Last read position: chr3:142,454,633 INFO 2019-04-30 04:26:29 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 3s. Last read position: chr4:21,669,850 INFO 2019-04-30 04:26:33 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 3s. Last read position: chr4:49,512,602 INFO 2019-04-30 04:26:36 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 3s. Last read position: chr4:60,081,820 INFO 2019-04-30 04:26:39 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 3s. Last read position: chr4:61,712,937 INFO 2019-04-30 04:26:42 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr4:61,745,892 INFO 2019-04-30 04:26:46 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 3s. Last read position: chr4:62,813,742 INFO 2019-04-30 04:26:50 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 4s. Last read position: chr4:104,489,743 INFO 2019-04-30 04:26:53 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 3s. Last read position: chr4:107,765,435 INFO 2019-04-30 04:26:57 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 4s. Last read position: chr4:116,365,511 INFO 2019-04-30 04:27:01 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 3s. Last read position: chr4:132,086,710 INFO 2019-04-30 04:27:06 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 5s. Last read position: chr4:140,522,515 INFO 2019-04-30 04:27:10 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 3s. Last read position: chr4:151,699,980 INFO 2019-04-30 04:27:14 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 3s. Last read position: chr5:30,447,330 INFO 2019-04-30 04:27:17 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 3s. Last read position: chr5:53,133,094 INFO 2019-04-30 04:27:21 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 3s. Last read position: chr5:87,566,230 INFO 2019-04-30 04:27:24 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 3s. Last read position: chr5:89,870,599 INFO 2019-04-30 04:27:27 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 2s. Last read position: chr5:90,889,974 INFO 2019-04-30 04:27:29 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr5:90,891,746 INFO 2019-04-30 04:27:32 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr5:90,893,015 INFO 2019-04-30 04:27:35 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr5:90,893,136 INFO 2019-04-30 04:27:38 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr5:90,893,917 INFO 2019-04-30 04:27:41 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 3s. Last read position: chr5:90,894,933 INFO 2019-04-30 04:27:45 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 3s. Last read position: chr5:90,896,442 INFO 2019-04-30 04:27:48 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 3s. Last read position: chr5:90,897,574 INFO 2019-04-30 04:27:52 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 3s. Last read position: chr5:90,897,699 INFO 2019-04-30 04:27:55 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 3s. Last read position: chr5:90,898,630 INFO 2019-04-30 04:27:59 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 3s. Last read position: chr5:90,899,860 INFO 2019-04-30 04:28:02 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 3s. Last read position: chr5:90,901,135 INFO 2019-04-30 04:28:06 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 3s. Last read position: chr5:90,901,541 INFO 2019-04-30 04:28:11 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 5s. Last read position: chr5:90,901,639 INFO 2019-04-30 04:28:15 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 4s. Last read position: chr5:90,903,621 INFO 2019-04-30 04:28:21 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 5s. Last read position: chr5:90,903,720 INFO 2019-04-30 04:28:25 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 4s. Last read position: chr5:90,905,552 INFO 2019-04-30 04:28:29 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 4s. Last read position: chr5:114,839,074 INFO 2019-04-30 04:28:34 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 4s. Last read position: chr5:122,026,556 INFO 2019-04-30 04:28:38 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 3s. Last read position: chr5:130,363,090 INFO 2019-04-30 04:28:44 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 5s. Last read position: chr5:138,602,629 INFO 2019-04-30 04:28:47 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 3s. Last read position: chr5:146,672,053 INFO 2019-04-30 04:28:52 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 4s. Last read position: chr5:151,585,637 INFO 2019-04-30 04:28:55 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 3s. Last read position: chr6:38,553,509 INFO 2019-04-30 04:29:00 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 4s. Last read position: chr6:71,149,889 INFO 2019-04-30 04:29:04 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 3s. Last read position: chr6:82,602,700 INFO 2019-04-30 04:29:08 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 3s. Last read position: chr6:90,509,359 INFO 2019-04-30 04:29:12 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 4s. Last read position: chr6:119,304,504 INFO 2019-04-30 04:29:16 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 4s. Last read position: chr6:121,999,760 INFO 2019-04-30 04:29:20 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 3s. Last read position: chr6:125,307,777 INFO 2019-04-30 04:29:25 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 4s. Last read position: chr6:128,462,353 INFO 2019-04-30 04:29:29 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 3s. Last read position: chr6:138,105,059 INFO 2019-04-30 04:29:34 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 5s. Last read position: chr7:13,576,575 INFO 2019-04-30 04:29:38 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 3s. Last read position: chr7:20,277,308 INFO 2019-04-30 04:29:42 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 4s. Last read position: chr7:20,281,909 INFO 2019-04-30 04:29:45 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 2s. Last read position: chr7:20,282,335 INFO 2019-04-30 04:29:49 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 3s. Last read position: chr7:20,283,574 INFO 2019-04-30 04:29:52 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 3s. Last read position: chr7:28,959,591 INFO 2019-04-30 04:29:56 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 3s. Last read position: chr7:50,707,856 INFO 2019-04-30 04:29:59 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr7:52,715,038 INFO 2019-04-30 04:30:04 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 5s. Last read position: chr7:87,408,574 INFO 2019-04-30 04:30:07 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 3s. Last read position: chr7:108,492,446 INFO 2019-04-30 04:30:11 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 3s. Last read position: chr7:112,748,356 INFO 2019-04-30 04:30:14 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 3s. Last read position: chr7:133,615,852 INFO 2019-04-30 04:30:19 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 4s. Last read position: chr7:147,298,392 INFO 2019-04-30 04:30:21 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 2s. Last read position: chr7:147,959,583 INFO 2019-04-30 04:30:26 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 4s. Last read position: chr7:151,705,065 INFO 2019-04-30 04:30:29 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 3s. Last read position: chr8:34,726,183 INFO 2019-04-30 04:30:34 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 4s. Last read position: chr8:63,991,244 INFO 2019-04-30 04:30:37 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 3s. Last read position: chr8:87,366,503 INFO 2019-04-30 04:30:41 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 3s. Last read position: chr8:95,644,196 INFO 2019-04-30 04:30:45 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 3s. Last read position: chr8:98,388,950 INFO 2019-04-30 04:30:50 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 4s. Last read position: chr8:108,467,153 INFO 2019-04-30 04:30:53 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 2s. Last read position: chr8:112,516,703 INFO 2019-04-30 04:30:56 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 3s. Last read position: chr8:125,416,545 INFO 2019-04-30 04:31:01 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 4s. Last read position: chr9:21,897,312 INFO 2019-04-30 04:31:04 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 3s. Last read position: chr9:44,196,632 INFO 2019-04-30 04:31:07 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 3s. Last read position: chr9:46,037,960 INFO 2019-04-30 04:31:11 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 3s. Last read position: chr9:46,042,784 INFO 2019-04-30 04:31:14 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 3s. Last read position: chr9:59,405,120 INFO 2019-04-30 04:31:19 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 5s. Last read position: chr9:77,826,650 INFO 2019-04-30 04:31:23 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 3s. Last read position: chr9:78,328,216 INFO 2019-04-30 04:31:27 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 3s. Last read position: chr9:103,111,392 INFO 2019-04-30 04:31:30 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 2s. Last read position: chr9:103,118,172 INFO 2019-04-30 04:31:33 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 3s. Last read position: chr9:103,123,370 INFO 2019-04-30 04:31:37 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 3s. Last read position: chr9:103,128,409 INFO 2019-04-30 04:31:41 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 3s. Last read position: chr9:106,355,187 INFO 2019-04-30 04:31:44 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 3s. Last read position: chr9:108,652,380 INFO 2019-04-30 04:31:48 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 3s. Last read position: chr9:121,824,330 INFO 2019-04-30 04:31:50 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 2s. Last read position: chrM:3,288 INFO 2019-04-30 04:31:52 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chrM:4,307 INFO 2019-04-30 04:31:54 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chrM:5,431 INFO 2019-04-30 04:31:56 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chrM:5,824 INFO 2019-04-30 04:31:57 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chrM:6,079 INFO 2019-04-30 04:31:59 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chrM:6,340 INFO 2019-04-30 04:32:01 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chrM:11,147 INFO 2019-04-30 04:32:03 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chrM:12,895 INFO 2019-04-30 04:32:05 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chrM:14,447 INFO 2019-04-30 04:32:07 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chrM:14,979 INFO 2019-04-30 04:32:09 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 2s. Last read position: chrX:20,134,825 INFO 2019-04-30 04:32:13 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 3s. Last read position: chrX:69,068,013 INFO 2019-04-30 04:32:17 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 3s. Last read position: chrX:103,398,734 [Tue Apr 30 04:32:20 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 13.91 minutes. Runtime.totalMemory()=1979711488