/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 28, 2026 12:05:52 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu May 28 00:05:52 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_buD-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu May 28 00:05:52 GMT 2026] Executing as ?@nf-53ef2b239a835feab1789f6826bdd0ec-d03b8-sfj97 on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 20-internal-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.0
WARNING: BAM index file /tmp/nxf.XXXX976iZs/659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXX976iZs/659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:05:54 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:06:06 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:10,033,637
INFO 2026-05-28 00:06:17 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 11s. Last read position: chr1:19,129,061
INFO 2026-05-28 00:06:27 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 10s. Last read position: chr1:23,333,588
INFO 2026-05-28 00:06:34 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 7s. Last read position: chr1:30,873,251
INFO 2026-05-28 00:06:45 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 10s. Last read position: chr1:37,501,841
INFO 2026-05-28 00:07:16 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 31s. Last read position: chr1:43,591,461
INFO 2026-05-28 00:07:27 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 10s. Last read position: chr1:53,210,553
INFO 2026-05-28 00:07:38 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 10s. Last read position: chr1:86,903,064
INFO 2026-05-28 00:07:44 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 6s. Last read position: chr1:109,252,042
INFO 2026-05-28 00:07:55 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 10s. Last read position: chr1:116,401,221
INFO 2026-05-28 00:08:02 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 7s. Last read position: chr1:121,187,454
INFO 2026-05-28 00:08:08 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 5s. Last read position: chr1:148,545,717
INFO 2026-05-28 00:08:14 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 5s. Last read position: chr1:150,159,116
INFO 2026-05-28 00:08:22 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 7s. Last read position: chr1:151,423,455
INFO 2026-05-28 00:08:29 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 7s. Last read position: chr1:154,172,040
INFO 2026-05-28 00:08:45 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 16s. Last read position: chr1:155,192,143
INFO 2026-05-28 00:09:02 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 16s. Last read position: chr1:156,135,291
INFO 2026-05-28 00:09:15 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 12s. Last read position: chr1:159,929,955
INFO 2026-05-28 00:09:29 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 13s. Last read position: chr1:161,984,859
INFO 2026-05-28 00:09:36 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 7s. Last read position: chr1:178,458,067
INFO 2026-05-28 00:09:43 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 6s. Last read position: chr1:193,021,182
INFO 2026-05-28 00:09:52 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 9s. Last read position: chr1:204,257,701
INFO 2026-05-28 00:10:00 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 8s. Last read position: chr1:220,034,914
INFO 2026-05-28 00:10:15 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 14s. Last read position: chr1:235,455,630
INFO 2026-05-28 00:10:25 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 10s. Last read position: chr2:11,249,747
INFO 2026-05-28 00:10:34 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 8s. Last read position: chr2:27,222,243
INFO 2026-05-28 00:10:42 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 7s. Last read position: chr2:32,916,264
INFO 2026-05-28 00:10:47 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 5s. Last read position: chr2:36,905,575
INFO 2026-05-28 00:10:59 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 11s. Last read position: chr2:54,630,909
INFO 2026-05-28 00:11:23 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 23s. Last read position: chr2:71,078,323
INFO 2026-05-28 00:11:32 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 9s. Last read position: chr2:88,857,566
INFO 2026-05-28 00:11:43 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 10s. Last read position: chr2:108,751,315
INFO 2026-05-28 00:11:51 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 7s. Last read position: chr2:127,657,395
INFO 2026-05-28 00:12:03 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 11s. Last read position: chr2:165,759,363
INFO 2026-05-28 00:12:28 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 25s. Last read position: chr2:186,668,770
INFO 2026-05-28 00:12:38 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 9s. Last read position: chr2:190,924,581
INFO 2026-05-28 00:12:53 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 15s. Last read position: chr2:215,362,013
INFO 2026-05-28 00:13:33 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 39s. Last read position: chr2:215,408,168
INFO 2026-05-28 00:14:10 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 36s. Last read position: chr2:219,182,216
INFO 2026-05-28 00:14:24 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 14s. Last read position: chr2:237,336,136
INFO 2026-05-28 00:14:52 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 28s. Last read position: chr3:9,697,793
INFO 2026-05-28 00:15:03 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 11s. Last read position: chr3:25,612,638
INFO 2026-05-28 00:15:19 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 15s. Last read position: chr3:42,194,802
INFO 2026-05-28 00:15:30 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 11s. Last read position: chr3:49,122,165
INFO 2026-05-28 00:15:40 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 9s. Last read position: chr3:53,242,131
INFO 2026-05-28 00:15:53 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 12s. Last read position: chr3:105,693,491
INFO 2026-05-28 00:16:01 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 8s. Last read position: chr3:126,462,027
INFO 2026-05-28 00:16:12 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 11s. Last read position: chr3:141,963,868
INFO 2026-05-28 00:16:22 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 9s. Last read position: chr3:170,281,949
INFO 2026-05-28 00:16:41 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 19s. Last read position: chr3:184,575,883
INFO 2026-05-28 00:16:51 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 9s. Last read position: chr3:197,029,646
INFO 2026-05-28 00:17:08 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 16s. Last read position: chr4:15,442,596
INFO 2026-05-28 00:17:17 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 9s. Last read position: chr4:57,023,330
INFO 2026-05-28 00:17:33 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 15s. Last read position: chr4:86,101,110
INFO 2026-05-28 00:17:54 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 20s. Last read position: chr4:120,060,057
INFO 2026-05-28 00:18:11 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 16s. Last read position: chr4:154,490,710
INFO 2026-05-28 00:18:24 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 12s. Last read position: chr5:5,462,520
INFO 2026-05-28 00:18:41 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 16s. Last read position: chr5:38,918,924
INFO 2026-05-28 00:18:50 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 8s. Last read position: chr5:73,498,530
INFO 2026-05-28 00:19:04 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 14s. Last read position: chr5:102,950,809
INFO 2026-05-28 00:19:14 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 10s. Last read position: chr5:138,375,160
INFO 2026-05-28 00:19:22 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 7s. Last read position: chr5:141,672,587
INFO 2026-05-28 00:19:30 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 8s. Last read position: chr5:150,404,687
INFO 2026-05-28 00:19:38 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 7s. Last read position: chr5:151,674,641
INFO 2026-05-28 00:19:49 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 11s. Last read position: chr5:177,458,096
INFO 2026-05-28 00:20:02 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 12s. Last read position: chr6:6,145,636
INFO 2026-05-28 00:20:08 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 6s. Last read position: chr6:26,184,001
INFO 2026-05-28 00:20:12 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 4s. Last read position: chr6:30,884,682
INFO 2026-05-28 00:20:24 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 12s. Last read position: chr6:31,816,173
INFO 2026-05-28 00:20:31 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 6s. Last read position: chr6:32,978,124
INFO 2026-05-28 00:20:37 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 6s. Last read position: chr6:36,230,522
INFO 2026-05-28 00:20:47 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 10s. Last read position: chr6:44,149,909
INFO 2026-05-28 00:21:21 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 33s. Last read position: chr6:56,642,095
INFO 2026-05-28 00:21:38 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 16s. Last read position: chr6:89,083,789
INFO 2026-05-28 00:21:47 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 9s. Last read position: chr6:116,279,068
INFO 2026-05-28 00:22:00 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:16:06s. Time for last 1,000,000: 13s. Last read position: chr6:138,404,513
INFO 2026-05-28 00:22:15 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 14s. Last read position: chr6:158,977,613
INFO 2026-05-28 00:22:27 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 12s. Last read position: chr7:2,658,413
INFO 2026-05-28 00:22:35 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 7s. Last read position: chr7:10,933,569
INFO 2026-05-28 00:22:47 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 11s. Last read position: chr7:40,775,693
INFO 2026-05-28 00:22:56 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 8s. Last read position: chr7:65,884,550
INFO 2026-05-28 00:23:05 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:17:10s. Time for last 1,000,000: 8s. Last read position: chr7:76,048,180
INFO 2026-05-28 00:23:24 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 19s. Last read position: chr7:94,417,774
INFO 2026-05-28 00:23:37 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 13s. Last read position: chr7:100,356,721
INFO 2026-05-28 00:23:48 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 10s. Last read position: chr7:107,980,645
INFO 2026-05-28 00:24:04 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 15s. Last read position: chr7:128,657,525
INFO 2026-05-28 00:24:12 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:18:17s. Time for last 1,000,000: 7s. Last read position: chr7:140,834,686
INFO 2026-05-28 00:24:17 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:18:22s. Time for last 1,000,000: 4s. Last read position: chr7:149,874,124
INFO 2026-05-28 00:24:34 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 17s. Last read position: chr8:1,292,872
INFO 2026-05-28 00:24:51 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 16s. Last read position: chr8:27,604,994
INFO 2026-05-28 00:25:04 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:19:10s. Time for last 1,000,000: 13s. Last read position: chr8:42,314,387
INFO 2026-05-28 00:25:17 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:19:22s. Time for last 1,000,000: 12s. Last read position: chr8:70,113,614
INFO 2026-05-28 00:25:24 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 7s. Last read position: chr8:99,511,454
INFO 2026-05-28 00:25:45 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:19:50s. Time for last 1,000,000: 20s. Last read position: chr8:120,212,462
INFO 2026-05-28 00:25:57 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:20:02s. Time for last 1,000,000: 12s. Last read position: chr8:143,858,238
INFO 2026-05-28 00:26:05 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 8s. Last read position: chr8:144,517,621
INFO 2026-05-28 00:26:20 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:20:25s. Time for last 1,000,000: 14s. Last read position: chr9:19,379,501
INFO 2026-05-28 00:26:28 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:20:33s. Time for last 1,000,000: 8s. Last read position: chr9:36,191,157
INFO 2026-05-28 00:26:38 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:20:43s. Time for last 1,000,000: 9s. Last read position: chr9:91,724,834
INFO 2026-05-28 00:26:46 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:20:51s. Time for last 1,000,000: 8s. Last read position: chr9:113,178,677
INFO 2026-05-28 00:26:57 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:21:02s. Time for last 1,000,000: 10s. Last read position: chr9:126,614,487
INFO 2026-05-28 00:27:08 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:21:14s. Time for last 1,000,000: 11s. Last read position: chr9:130,356,242
INFO 2026-05-28 00:27:17 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:21:22s. Time for last 1,000,000: 8s. Last read position: chr9:135,822,156
INFO 2026-05-28 00:27:29 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:21:35s. Time for last 1,000,000: 12s. Last read position: chr9:137,552,408
INFO 2026-05-28 00:27:39 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:21:44s. Time for last 1,000,000: 9s. Last read position: chr10:13,344,816
INFO 2026-05-28 00:27:50 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:21:55s. Time for last 1,000,000: 10s. Last read position: chr10:32,017,279
INFO 2026-05-28 00:27:59 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 9s. Last read position: chr10:48,047,112
INFO 2026-05-28 00:28:08 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:22:13s. Time for last 1,000,000: 9s. Last read position: chr10:73,799,957
INFO 2026-05-28 00:28:20 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:22:25s. Time for last 1,000,000: 12s. Last read position: chr10:94,254,895
INFO 2026-05-28 00:28:33 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:22:38s. Time for last 1,000,000: 12s. Last read position: chr10:113,908,322
INFO 2026-05-28 00:28:40 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:22:46s. Time for last 1,000,000: 7s. Last read position: chr11:563,186
INFO 2026-05-28 00:28:50 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:22:55s. Time for last 1,000,000: 9s. Last read position: chr11:2,403,473
INFO 2026-05-28 00:29:02 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:23:07s. Time for last 1,000,000: 12s. Last read position: chr11:17,496,704
INFO 2026-05-28 00:29:12 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:23:17s. Time for last 1,000,000: 10s. Last read position: chr11:47,178,403
INFO 2026-05-28 00:29:27 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:23:33s. Time for last 1,000,000: 15s. Last read position: chr11:61,393,322
INFO 2026-05-28 00:29:32 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:23:37s. Time for last 1,000,000: 4s. Last read position: chr11:62,533,890
INFO 2026-05-28 00:29:41 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:23:46s. Time for last 1,000,000: 9s. Last read position: chr11:65,097,064
INFO 2026-05-28 00:29:52 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:23:57s. Time for last 1,000,000: 10s. Last read position: chr11:66,616,742
INFO 2026-05-28 00:30:05 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:24:10s. Time for last 1,000,000: 13s. Last read position: chr11:72,192,168
INFO 2026-05-28 00:30:18 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:24:23s. Time for last 1,000,000: 12s. Last read position: chr11:93,750,359
INFO 2026-05-28 00:30:28 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:24:33s. Time for last 1,000,000: 10s. Last read position: chr11:118,389,833
INFO 2026-05-28 00:30:38 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:24:43s. Time for last 1,000,000: 10s. Last read position: chr11:128,768,257
INFO 2026-05-28 00:30:50 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:24:55s. Time for last 1,000,000: 12s. Last read position: chr12:6,527,793
INFO 2026-05-28 00:31:04 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:25:09s. Time for last 1,000,000: 13s. Last read position: chr12:10,715,694
INFO 2026-05-28 00:31:11 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:25:17s. Time for last 1,000,000: 7s. Last read position: chr12:29,604,180
INFO 2026-05-28 00:31:22 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:25:27s. Time for last 1,000,000: 10s. Last read position: chr12:49,128,389
INFO 2026-05-28 00:31:30 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 8s. Last read position: chr12:52,451,985
INFO 2026-05-28 00:31:42 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:25:47s. Time for last 1,000,000: 12s. Last read position: chr12:56,160,074
INFO 2026-05-28 00:31:56 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:26:01s. Time for last 1,000,000: 13s. Last read position: chr12:57,696,309
INFO 2026-05-28 00:32:05 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:26:10s. Time for last 1,000,000: 9s. Last read position: chr12:93,410,513
INFO 2026-05-28 00:32:16 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:26:21s. Time for last 1,000,000: 10s. Last read position: chr12:110,436,596
INFO 2026-05-28 00:32:28 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:26:33s. Time for last 1,000,000: 11s. Last read position: chr12:122,127,309
INFO 2026-05-28 00:32:38 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 10s. Last read position: chr13:19,646,924
INFO 2026-05-28 00:32:46 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:26:52s. Time for last 1,000,000: 8s. Last read position: chr13:45,480,161
INFO 2026-05-28 00:32:58 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:27:03s. Time for last 1,000,000: 11s. Last read position: chr13:109,782,618
INFO 2026-05-28 00:33:12 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:27:17s. Time for last 1,000,000: 14s. Last read position: chr14:22,539,076
INFO 2026-05-28 00:33:24 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:27:29s. Time for last 1,000,000: 11s. Last read position: chr14:49,585,972
INFO 2026-05-28 00:33:43 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:27:48s. Time for last 1,000,000: 19s. Last read position: chr14:68,789,579
INFO 2026-05-28 00:33:52 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:27:57s. Time for last 1,000,000: 9s. Last read position: chr14:81,526,954
INFO 2026-05-28 00:34:26 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:28:32s. Time for last 1,000,000: 34s. Last read position: chr14:102,034,357
INFO 2026-05-28 00:34:55 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:29:00s. Time for last 1,000,000: 28s. Last read position: chr14:105,479,196
INFO 2026-05-28 00:34:57 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:29:03s. Time for last 1,000,000: 2s. Last read position: chr15:22,933,884
INFO 2026-05-28 00:35:14 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:29:19s. Time for last 1,000,000: 16s. Last read position: chr15:40,931,724
INFO 2026-05-28 00:35:23 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:29:28s. Time for last 1,000,000: 9s. Last read position: chr15:49,145,052
INFO 2026-05-28 00:35:37 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:29:42s. Time for last 1,000,000: 13s. Last read position: chr15:66,497,593
INFO 2026-05-28 00:35:47 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:29:52s. Time for last 1,000,000: 9s. Last read position: chr15:77,181,321
INFO 2026-05-28 00:35:56 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:30:01s. Time for last 1,000,000: 9s. Last read position: chr15:90,206,784
INFO 2026-05-28 00:36:05 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:30:10s. Time for last 1,000,000: 8s. Last read position: chr16:1,351,524
INFO 2026-05-28 00:36:21 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:30:26s. Time for last 1,000,000: 15s. Last read position: chr16:2,772,048
INFO 2026-05-28 00:36:30 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:30:35s. Time for last 1,000,000: 9s. Last read position: chr16:11,761,979
INFO 2026-05-28 00:36:38 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:30:43s. Time for last 1,000,000: 8s. Last read position: chr16:16,361,364
INFO 2026-05-28 00:36:43 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:30:48s. Time for last 1,000,000: 5s. Last read position: chr16:21,837,169
INFO 2026-05-28 00:36:50 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:30:56s. Time for last 1,000,000: 7s. Last read position: chr16:29,383,617
INFO 2026-05-28 00:36:56 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:31:01s. Time for last 1,000,000: 5s. Last read position: chr16:30,979,707
INFO 2026-05-28 00:37:06 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:31:11s. Time for last 1,000,000: 9s. Last read position: chr16:53,825,916
INFO 2026-05-28 00:37:16 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:31:22s. Time for last 1,000,000: 10s. Last read position: chr16:67,865,133
INFO 2026-05-28 00:37:27 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:31:32s. Time for last 1,000,000: 10s. Last read position: chr16:74,886,312
INFO 2026-05-28 00:37:33 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:31:38s. Time for last 1,000,000: 5s. Last read position: chr16:88,697,477
INFO 2026-05-28 00:37:47 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:31:52s. Time for last 1,000,000: 13s. Last read position: chr17:1,468,292
INFO 2026-05-28 00:37:56 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:32:01s. Time for last 1,000,000: 9s. Last read position: chr17:7,012,668
INFO 2026-05-28 00:38:06 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:32:11s. Time for last 1,000,000: 9s. Last read position: chr17:16,101,433
INFO 2026-05-28 00:38:16 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:32:21s. Time for last 1,000,000: 9s. Last read position: chr17:30,274,129
INFO 2026-05-28 00:38:26 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:32:31s. Time for last 1,000,000: 9s. Last read position: chr17:39,069,961
INFO 2026-05-28 00:38:37 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:32:42s. Time for last 1,000,000: 10s. Last read position: chr17:41,817,111
INFO 2026-05-28 00:38:49 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:32:55s. Time for last 1,000,000: 12s. Last read position: chr17:45,468,196
INFO 2026-05-28 00:38:57 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:33:02s. Time for last 1,000,000: 7s. Last read position: chr17:50,186,911
INFO 2026-05-28 00:39:03 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:33:08s. Time for last 1,000,000: 6s. Last read position: chr17:50,189,380
INFO 2026-05-28 00:39:10 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:33:15s. Time for last 1,000,000: 7s. Last read position: chr17:50,191,866
INFO 2026-05-28 00:39:19 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:33:24s. Time for last 1,000,000: 8s. Last read position: chr17:50,194,732
INFO 2026-05-28 00:39:28 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:33:33s. Time for last 1,000,000: 9s. Last read position: chr17:50,197,017
INFO 2026-05-28 00:39:40 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:33:45s. Time for last 1,000,000: 11s. Last read position: chr17:50,995,067
INFO 2026-05-28 00:39:51 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:33:56s. Time for last 1,000,000: 10s. Last read position: chr17:63,818,205
INFO 2026-05-28 00:40:01 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:34:06s. Time for last 1,000,000: 10s. Last read position: chr17:75,268,092
INFO 2026-05-28 00:40:14 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:34:19s. Time for last 1,000,000: 12s. Last read position: chr17:79,046,631
INFO 2026-05-28 00:40:32 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:34:38s. Time for last 1,000,000: 18s. Last read position: chr17:81,983,620
INFO 2026-05-28 00:40:43 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:34:48s. Time for last 1,000,000: 10s. Last read position: chr18:24,156,785
INFO 2026-05-28 00:40:51 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:34:57s. Time for last 1,000,000: 8s. Last read position: chr18:54,365,760
INFO 2026-05-28 00:41:04 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:35:09s. Time for last 1,000,000: 12s. Last read position: chr19:1,421,162
INFO 2026-05-28 00:41:11 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:35:16s. Time for last 1,000,000: 6s. Last read position: chr19:5,211,619
INFO 2026-05-28 00:41:19 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:35:25s. Time for last 1,000,000: 8s. Last read position: chr19:8,400,035
INFO 2026-05-28 00:41:40 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:35:45s. Time for last 1,000,000: 20s. Last read position: chr19:11,061,803
INFO 2026-05-28 00:41:48 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:35:53s. Time for last 1,000,000: 8s. Last read position: chr19:13,115,678
INFO 2026-05-28 00:41:56 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:36:01s. Time for last 1,000,000: 7s. Last read position: chr19:15,264,562
INFO 2026-05-28 00:42:06 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:36:11s. Time for last 1,000,000: 10s. Last read position: chr19:17,862,099
INFO 2026-05-28 00:42:13 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:36:18s. Time for last 1,000,000: 6s. Last read position: chr19:19,655,344
INFO 2026-05-28 00:42:21 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:36:26s. Time for last 1,000,000: 8s. Last read position: chr19:36,143,082
INFO 2026-05-28 00:42:29 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:36:35s. Time for last 1,000,000: 8s. Last read position: chr19:40,322,080
INFO 2026-05-28 00:42:39 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:36:44s. Time for last 1,000,000: 9s. Last read position: chr19:44,907,919
INFO 2026-05-28 00:42:45 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:36:50s. Time for last 1,000,000: 6s. Last read position: chr19:48,813,488
INFO 2026-05-28 00:42:53 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:36:58s. Time for last 1,000,000: 7s. Last read position: chr19:52,221,043
INFO 2026-05-28 00:42:59 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:37:04s. Time for last 1,000,000: 6s. Last read position: chr19:58,549,341
INFO 2026-05-28 00:43:07 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:37:12s. Time for last 1,000,000: 7s. Last read position: chr20:23,394,973
INFO 2026-05-28 00:43:17 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:37:22s. Time for last 1,000,000: 10s. Last read position: chr20:38,011,903
INFO 2026-05-28 00:43:28 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:37:33s. Time for last 1,000,000: 10s. Last read position: chr20:50,096,794
INFO 2026-05-28 00:43:41 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:37:46s. Time for last 1,000,000: 13s. Last read position: chr20:63,521,512
INFO 2026-05-28 00:43:46 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:37:51s. Time for last 1,000,000: 4s. Last read position: chr21:26,089,997
INFO 2026-05-28 00:44:02 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:38:07s. Time for last 1,000,000: 16s. Last read position: chr21:41,480,513
INFO 2026-05-28 00:44:10 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:38:16s. Time for last 1,000,000: 8s. Last read position: chr21:46,114,037
INFO 2026-05-28 00:44:21 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:38:26s. Time for last 1,000,000: 10s. Last read position: chr22:22,901,154
INFO 2026-05-28 00:44:30 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:38:35s. Time for last 1,000,000: 8s. Last read position: chr22:30,338,912
INFO 2026-05-28 00:44:38 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:38:43s. Time for last 1,000,000: 8s. Last read position: chr22:37,568,360
INFO 2026-05-28 00:44:46 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:38:51s. Time for last 1,000,000: 7s. Last read position: chr22:41,436,815
INFO 2026-05-28 00:44:54 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:38:59s. Time for last 1,000,000: 8s. Last read position: chr22:50,289,941
INFO 2026-05-28 00:45:00 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:39:05s. Time for last 1,000,000: 6s. Last read position: chrX:24,534,020
INFO 2026-05-28 00:45:16 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:39:21s. Time for last 1,000,000: 16s. Last read position: chrX:49,038,220
INFO 2026-05-28 00:45:28 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:39:33s. Time for last 1,000,000: 11s. Last read position: chrX:71,137,849
INFO 2026-05-28 00:45:38 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:39:43s. Time for last 1,000,000: 10s. Last read position: chrX:108,152,978
INFO 2026-05-28 00:45:47 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:39:52s. Time for last 1,000,000: 9s. Last read position: chrX:153,495,082
INFO 2026-05-28 00:46:00 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:40:05s. Time for last 1,000,000: 13s. Last read position: chrX:155,524,615
INFO 2026-05-28 00:46:01 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:40:06s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:46:03 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 40.18 minutes.
Runtime.totalMemory()=2953838592