/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 27, 2026 11:53:53 PM 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
[Wed May 27 23:53:53 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bCu-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
[Wed May 27 23:53:53 GMT 2026] Executing as ?@nf-3858505d6356f0acc51f0d9276e11c4f-009f8-hm2pm 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.XXXXdvQ8vK/659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXdvQ8vK/659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-27 23:53:55 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-27 23:54:05 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 9s. Last read position: chr1:16,587,205
INFO 2026-05-27 23:54:15 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 10s. Last read position: chr1:27,109,721
INFO 2026-05-27 23:54:36 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 20s. Last read position: chr1:41,513,525
INFO 2026-05-27 23:54:45 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 8s. Last read position: chr1:110,041,494
INFO 2026-05-27 23:54:50 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 5s. Last read position: chr1:145,394,977
INFO 2026-05-27 23:54:56 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 5s. Last read position: chr1:148,563,807
INFO 2026-05-27 23:55:01 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 4s. Last read position: chr1:150,511,107
INFO 2026-05-27 23:55:08 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 7s. Last read position: chr1:153,811,755
INFO 2026-05-27 23:55:20 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 12s. Last read position: chr1:155,765,148
INFO 2026-05-27 23:55:35 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 14s. Last read position: chr1:156,671,583
INFO 2026-05-27 23:55:42 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 7s. Last read position: chr1:171,557,634
INFO 2026-05-27 23:55:48 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 5s. Last read position: chr1:201,200,337
INFO 2026-05-27 23:55:55 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 7s. Last read position: chr1:201,712,816
INFO 2026-05-27 23:56:02 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 6s. Last read position: chr1:212,619,513
INFO 2026-05-27 23:56:09 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 7s. Last read position: chr1:234,608,764
INFO 2026-05-27 23:56:17 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 8s. Last read position: chr2:28,776,853
INFO 2026-05-27 23:56:22 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,264
INFO 2026-05-27 23:56:28 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 6s. Last read position: chr2:33,398,363
INFO 2026-05-27 23:56:39 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 10s. Last read position: chr2:61,348,174
INFO 2026-05-27 23:56:53 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 14s. Last read position: chr2:74,880,502
INFO 2026-05-27 23:57:01 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 7s. Last read position: chr2:110,535,666
INFO 2026-05-27 23:57:12 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 11s. Last read position: chr2:188,999,476
INFO 2026-05-27 23:57:25 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 13s. Last read position: chr2:205,716,245
INFO 2026-05-27 23:57:45 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 19s. Last read position: chr2:215,406,351
INFO 2026-05-27 23:58:19 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 34s. Last read position: chr2:217,897,942
INFO 2026-05-27 23:58:33 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 13s. Last read position: chr2:238,194,735
INFO 2026-05-27 23:58:43 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 10s. Last read position: chr3:33,114,416
INFO 2026-05-27 23:58:51 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 8s. Last read position: chr3:48,469,123
INFO 2026-05-27 23:59:05 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 13s. Last read position: chr3:51,386,237
INFO 2026-05-27 23:59:16 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 11s. Last read position: chr3:72,378,616
INFO 2026-05-27 23:59:25 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 8s. Last read position: chr3:123,700,553
INFO 2026-05-27 23:59:33 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 8s. Last read position: chr3:143,985,631
INFO 2026-05-27 23:59:44 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 10s. Last read position: chr3:194,441,399
INFO 2026-05-27 23:59:54 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 10s. Last read position: chr4:7,043,629
INFO 2026-05-28 00:00:07 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 12s. Last read position: chr4:67,681,562
INFO 2026-05-28 00:00:31 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 24s. Last read position: chr4:139,698,176
INFO 2026-05-28 00:00:55 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 23s. Last read position: chr5:17,275,360
INFO 2026-05-28 00:01:09 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 14s. Last read position: chr5:83,512,102
INFO 2026-05-28 00:01:37 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 28s. Last read position: chr5:134,826,947
INFO 2026-05-28 00:01:48 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 10s. Last read position: chr5:141,491,380
INFO 2026-05-28 00:02:01 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 12s. Last read position: chr5:151,042,658
INFO 2026-05-28 00:02:19 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 17s. Last read position: chr5:177,483,681
INFO 2026-05-28 00:02:39 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 20s. Last read position: chr6:7,231,811
INFO 2026-05-28 00:02:49 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 10s. Last read position: chr6:31,540,358
INFO 2026-05-28 00:03:04 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 14s. Last read position: chr6:32,079,110
INFO 2026-05-28 00:03:21 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 17s. Last read position: chr6:35,245,230
INFO 2026-05-28 00:03:32 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 11s. Last read position: chr6:56,482,833
INFO 2026-05-28 00:04:07 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 34s. Last read position: chr6:113,896,782
INFO 2026-05-28 00:04:20 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 12s. Last read position: chr6:151,944,410
INFO 2026-05-28 00:04:51 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 31s. Last read position: chr7:1,444,998
INFO 2026-05-28 00:05:06 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 14s. Last read position: chr7:44,756,925
INFO 2026-05-28 00:05:18 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 11s. Last read position: chr7:76,304,058
INFO 2026-05-28 00:05:42 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 24s. Last read position: chr7:99,908,761
INFO 2026-05-28 00:05:52 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 10s. Last read position: chr7:102,567,010
INFO 2026-05-28 00:06:02 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 9s. Last read position: chr7:128,854,672
INFO 2026-05-28 00:06:12 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 10s. Last read position: chr7:149,266,515
INFO 2026-05-28 00:06:34 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 21s. Last read position: chr8:18,872,057
INFO 2026-05-28 00:06:45 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 11s. Last read position: chr8:38,331,501
INFO 2026-05-28 00:07:14 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 28s. Last read position: chr8:69,658,530
INFO 2026-05-28 00:07:33 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 19s. Last read position: chr8:133,238,788
INFO 2026-05-28 00:07:54 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 20s. Last read position: chr8:143,922,940
INFO 2026-05-28 00:08:15 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 21s. Last read position: chr9:4,719,195
INFO 2026-05-28 00:08:27 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 11s. Last read position: chr9:76,399,489
INFO 2026-05-28 00:08:39 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 12s. Last read position: chr9:111,484,061
INFO 2026-05-28 00:09:01 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 21s. Last read position: chr9:122,984,569
INFO 2026-05-28 00:09:20 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 19s. Last read position: chr9:129,831,034
INFO 2026-05-28 00:09:32 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 11s. Last read position: chr9:136,451,254
INFO 2026-05-28 00:09:46 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:15:51s. Time for last 1,000,000: 14s. Last read position: chr10:17,229,421
INFO 2026-05-28 00:10:00 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 13s. Last read position: chr10:45,757,029
INFO 2026-05-28 00:10:13 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 12s. Last read position: chr10:73,794,538
INFO 2026-05-28 00:10:35 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 21s. Last read position: chr10:96,158,406
INFO 2026-05-28 00:10:48 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 13s. Last read position: chr10:119,042,706
INFO 2026-05-28 00:10:59 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 10s. Last read position: chr11:2,133,101
INFO 2026-05-28 00:11:12 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:17:17s. Time for last 1,000,000: 13s. Last read position: chr11:6,640,539
INFO 2026-05-28 00:11:30 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:17:34s. Time for last 1,000,000: 17s. Last read position: chr11:19,934,066
INFO 2026-05-28 00:11:51 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 21s. Last read position: chr11:57,310,064
INFO 2026-05-28 00:12:03 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:18:08s. Time for last 1,000,000: 12s. Last read position: chr11:62,529,723
INFO 2026-05-28 00:12:15 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 11s. Last read position: chr11:65,532,768
INFO 2026-05-28 00:12:31 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:18:36s. Time for last 1,000,000: 16s. Last read position: chr11:67,398,579
INFO 2026-05-28 00:12:54 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 23s. Last read position: chr11:74,085,756
INFO 2026-05-28 00:13:10 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:19:14s. Time for last 1,000,000: 15s. Last read position: chr11:117,315,603
INFO 2026-05-28 00:13:27 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:19:32s. Time for last 1,000,000: 17s. Last read position: chr12:753,536
INFO 2026-05-28 00:13:42 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 15s. Last read position: chr12:8,655,415
INFO 2026-05-28 00:13:57 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:20:02s. Time for last 1,000,000: 14s. Last read position: chr12:48,837,989
INFO 2026-05-28 00:14:10 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 12s. Last read position: chr12:53,465,942
INFO 2026-05-28 00:14:27 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:20:32s. Time for last 1,000,000: 17s. Last read position: chr12:57,092,913
INFO 2026-05-28 00:14:40 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:20:44s. Time for last 1,000,000: 12s. Last read position: chr12:57,516,870
INFO 2026-05-28 00:14:49 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:20:54s. Time for last 1,000,000: 9s. Last read position: chr12:104,265,766
INFO 2026-05-28 00:15:00 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:21:05s. Time for last 1,000,000: 10s. Last read position: chr12:121,810,602
INFO 2026-05-28 00:15:16 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:21:20s. Time for last 1,000,000: 15s. Last read position: chr12:132,711,025
INFO 2026-05-28 00:15:24 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:21:29s. Time for last 1,000,000: 8s. Last read position: chr13:110,201,491
INFO 2026-05-28 00:15:35 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:21:39s. Time for last 1,000,000: 10s. Last read position: chr14:23,321,784
INFO 2026-05-28 00:15:49 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:21:53s. Time for last 1,000,000: 14s. Last read position: chr14:64,427,315
INFO 2026-05-28 00:16:00 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:22:05s. Time for last 1,000,000: 11s. Last read position: chr14:74,949,382
INFO 2026-05-28 00:16:29 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:22:33s. Time for last 1,000,000: 28s. Last read position: chr14:103,657,608
INFO 2026-05-28 00:16:42 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:22:46s. Time for last 1,000,000: 13s. Last read position: chr15:25,781,081
INFO 2026-05-28 00:16:50 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:22:54s. Time for last 1,000,000: 7s. Last read position: chr15:43,523,163
INFO 2026-05-28 00:17:01 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:23:05s. Time for last 1,000,000: 11s. Last read position: chr15:64,156,841
INFO 2026-05-28 00:17:10 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:23:14s. Time for last 1,000,000: 9s. Last read position: chr15:75,206,589
INFO 2026-05-28 00:17:19 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:23:23s. Time for last 1,000,000: 9s. Last read position: chr15:89,632,861
INFO 2026-05-28 00:17:27 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:23:32s. Time for last 1,000,000: 8s. Last read position: chr16:1,764,176
INFO 2026-05-28 00:17:45 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:23:50s. Time for last 1,000,000: 17s. Last read position: chr16:2,930,609
INFO 2026-05-28 00:17:53 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:23:57s. Time for last 1,000,000: 7s. Last read position: chr16:15,129,977
INFO 2026-05-28 00:17:57 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:24:02s. Time for last 1,000,000: 4s. Last read position: chr16:18,390,686
INFO 2026-05-28 00:18:01 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:24:06s. Time for last 1,000,000: 4s. Last read position: chr16:27,363,228
INFO 2026-05-28 00:18:09 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:24:13s. Time for last 1,000,000: 7s. Last read position: chr16:30,224,649
INFO 2026-05-28 00:18:15 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:24:19s. Time for last 1,000,000: 5s. Last read position: chr16:55,479,555
INFO 2026-05-28 00:18:24 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:24:29s. Time for last 1,000,000: 9s. Last read position: chr16:70,146,132
INFO 2026-05-28 00:18:32 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:24:36s. Time for last 1,000,000: 7s. Last read position: chr16:88,738,059
INFO 2026-05-28 00:18:43 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:24:47s. Time for last 1,000,000: 10s. Last read position: chr17:4,891,638
INFO 2026-05-28 00:18:52 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:24:56s. Time for last 1,000,000: 8s. Last read position: chr17:8,444,339
INFO 2026-05-28 00:19:01 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:25:05s. Time for last 1,000,000: 9s. Last read position: chr17:28,689,364
INFO 2026-05-28 00:19:10 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:25:14s. Time for last 1,000,000: 8s. Last read position: chr17:38,890,462
INFO 2026-05-28 00:19:19 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:25:24s. Time for last 1,000,000: 9s. Last read position: chr17:44,212,826
INFO 2026-05-28 00:19:27 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:25:31s. Time for last 1,000,000: 7s. Last read position: chr17:50,187,528
INFO 2026-05-28 00:19:33 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:25:37s. Time for last 1,000,000: 5s. Last read position: chr17:50,192,640
INFO 2026-05-28 00:19:41 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:25:45s. Time for last 1,000,000: 8s. Last read position: chr17:50,196,646
INFO 2026-05-28 00:19:50 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:25:55s. Time for last 1,000,000: 9s. Last read position: chr17:63,496,864
INFO 2026-05-28 00:20:03 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:26:07s. Time for last 1,000,000: 12s. Last read position: chr17:76,685,129
INFO 2026-05-28 00:20:15 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:26:19s. Time for last 1,000,000: 12s. Last read position: chr18:8,796,368
INFO 2026-05-28 00:20:24 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:26:28s. Time for last 1,000,000: 9s. Last read position: chr18:76,441,738
INFO 2026-05-28 00:20:32 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:26:36s. Time for last 1,000,000: 7s. Last read position: chr19:2,726,589
INFO 2026-05-28 00:20:39 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 7s. Last read position: chr19:7,629,825
INFO 2026-05-28 00:20:52 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:26:56s. Time for last 1,000,000: 13s. Last read position: chr19:12,792,683
INFO 2026-05-28 00:21:04 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:27:09s. Time for last 1,000,000: 12s. Last read position: chr19:16,086,480
INFO 2026-05-28 00:21:12 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:27:17s. Time for last 1,000,000: 7s. Last read position: chr19:33,205,675
INFO 2026-05-28 00:21:19 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:27:24s. Time for last 1,000,000: 7s. Last read position: chr19:39,485,699
INFO 2026-05-28 00:21:28 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:27:33s. Time for last 1,000,000: 9s. Last read position: chr19:42,274,560
INFO 2026-05-28 00:21:35 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:27:40s. Time for last 1,000,000: 6s. Last read position: chr19:47,271,455
INFO 2026-05-28 00:21:41 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:27:46s. Time for last 1,000,000: 6s. Last read position: chr19:49,862,257
INFO 2026-05-28 00:21:48 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:27:52s. Time for last 1,000,000: 6s. Last read position: chr19:55,661,057
INFO 2026-05-28 00:21:54 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:27:59s. Time for last 1,000,000: 6s. Last read position: chr20:17,659,158
INFO 2026-05-28 00:22:02 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:28:07s. Time for last 1,000,000: 7s. Last read position: chr20:41,098,244
INFO 2026-05-28 00:22:10 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:28:14s. Time for last 1,000,000: 7s. Last read position: chr20:58,895,650
INFO 2026-05-28 00:22:15 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:28:20s. Time for last 1,000,000: 5s. Last read position: chr21:8,217,348
INFO 2026-05-28 00:22:17 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:28:21s. Time for last 1,000,000: 1s. Last read position: chr21:25,976,014
INFO 2026-05-28 00:22:26 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:28:30s. Time for last 1,000,000: 9s. Last read position: chr21:45,866,644
INFO 2026-05-28 00:22:33 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:28:37s. Time for last 1,000,000: 7s. Last read position: chr21:46,122,147
INFO 2026-05-28 00:22:44 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:28:48s. Time for last 1,000,000: 10s. Last read position: chr22:30,344,960
INFO 2026-05-28 00:22:52 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:28:56s. Time for last 1,000,000: 7s. Last read position: chr22:37,877,991
INFO 2026-05-28 00:22:59 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:29:04s. Time for last 1,000,000: 7s. Last read position: chr22:41,273,592
INFO 2026-05-28 00:23:06 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:29:11s. Time for last 1,000,000: 6s. Last read position: chr22:50,244,082
INFO 2026-05-28 00:23:14 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:29:19s. Time for last 1,000,000: 8s. Last read position: chrX:12,976,837
INFO 2026-05-28 00:23:26 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:29:30s. Time for last 1,000,000: 11s. Last read position: chrX:53,250,495
INFO 2026-05-28 00:23:35 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:29:39s. Time for last 1,000,000: 9s. Last read position: chrX:107,714,476
INFO 2026-05-28 00:23:47 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:29:52s. Time for last 1,000,000: 12s. Last read position: chrX:154,364,670
INFO 2026-05-28 00:23:55 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:29:59s. Time for last 1,000,000: 7s. Last read position: GL000220.1:160,636
INFO 2026-05-28 00:23:56 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:30:00s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:23:58 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 30.08 minutes.
Runtime.totalMemory()=2952265728