/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 12:09:13 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 00:09:13 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bUW-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 00:09:13 GMT 2026] Executing as ?@nf-01ac0faa583e07f63b6e2cd85cfa4576-70fa1-jmj2h 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.XXXXzyE2zl/659_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXzyE2zl/659_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:09:15 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:09:27 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:8,541,262
INFO 2026-05-28 00:09:38 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 11s. Last read position: chr1:16,993,700
INFO 2026-05-28 00:09:49 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 11s. Last read position: chr1:22,639,097
INFO 2026-05-28 00:09:56 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 6s. Last read position: chr1:27,773,364
INFO 2026-05-28 00:10:05 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 8s. Last read position: chr1:35,192,749
INFO 2026-05-28 00:10:25 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 19s. Last read position: chr1:43,588,928
INFO 2026-05-28 00:10:34 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 9s. Last read position: chr1:52,237,834
INFO 2026-05-28 00:10:46 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 11s. Last read position: chr1:84,658,318
INFO 2026-05-28 00:10:54 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 8s. Last read position: chr1:110,012,901
INFO 2026-05-28 00:11:04 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 9s. Last read position: chr1:117,878,005
INFO 2026-05-28 00:11:11 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 6s. Last read position: chr1:148,108,537
INFO 2026-05-28 00:11:17 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 6s. Last read position: chr1:151,369,136
INFO 2026-05-28 00:11:30 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 12s. Last read position: chr1:155,169,846
INFO 2026-05-28 00:11:47 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 17s. Last read position: chr1:156,745,316
INFO 2026-05-28 00:11:58 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 10s. Last read position: chr1:169,124,886
INFO 2026-05-28 00:12:04 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 6s. Last read position: chr1:182,842,614
INFO 2026-05-28 00:12:14 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 9s. Last read position: chr1:203,797,513
INFO 2026-05-28 00:12:19 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 5s. Last read position: chr1:206,934,434
INFO 2026-05-28 00:12:23 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 3s. Last read position: chr1:206,939,212
INFO 2026-05-28 00:12:33 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 10s. Last read position: chr1:224,389,836
INFO 2026-05-28 00:12:42 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 8s. Last read position: chr1:236,537,498
INFO 2026-05-28 00:12:54 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 12s. Last read position: chr2:20,202,174
INFO 2026-05-28 00:13:03 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 8s. Last read position: chr2:32,468,495
INFO 2026-05-28 00:13:08 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,411
INFO 2026-05-28 00:13:16 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 8s. Last read position: chr2:47,379,923
INFO 2026-05-28 00:13:31 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 14s. Last read position: chr2:65,239,851
INFO 2026-05-28 00:13:45 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 13s. Last read position: chr2:85,350,088
INFO 2026-05-28 00:13:54 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 9s. Last read position: chr2:100,995,406
INFO 2026-05-28 00:14:00 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 6s. Last read position: chr2:113,193,051
INFO 2026-05-28 00:14:10 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 9s. Last read position: chr2:158,625,026
INFO 2026-05-28 00:14:26 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 15s. Last read position: chr2:181,915,230
INFO 2026-05-28 00:14:40 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 14s. Last read position: chr2:202,467,579
INFO 2026-05-28 00:14:53 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 13s. Last read position: chr2:218,745,106
INFO 2026-05-28 00:15:09 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 15s. Last read position: chr2:232,735,180
INFO 2026-05-28 00:15:26 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 17s. Last read position: chr3:9,791,362
INFO 2026-05-28 00:15:37 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 10s. Last read position: chr3:37,326,011
INFO 2026-05-28 00:15:54 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 17s. Last read position: chr3:47,007,568
INFO 2026-05-28 00:16:13 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 18s. Last read position: chr3:49,676,122
INFO 2026-05-28 00:16:23 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 10s. Last read position: chr3:56,633,614
INFO 2026-05-28 00:16:40 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 16s. Last read position: chr3:100,744,872
INFO 2026-05-28 00:16:49 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 9s. Last read position: chr3:127,022,318
INFO 2026-05-28 00:17:01 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 11s. Last read position: chr3:143,043,187
INFO 2026-05-28 00:17:11 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 10s. Last read position: chr3:183,663,499
INFO 2026-05-28 00:17:28 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 17s. Last read position: chr3:195,726,542
INFO 2026-05-28 00:17:56 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 28s. Last read position: chr3:197,623,220
INFO 2026-05-28 00:18:08 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 11s. Last read position: chr4:13,599,262
INFO 2026-05-28 00:18:19 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 11s. Last read position: chr4:55,396,166
INFO 2026-05-28 00:18:27 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 8s. Last read position: chr4:78,911,629
INFO 2026-05-28 00:18:42 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 14s. Last read position: chr4:118,281,944
INFO 2026-05-28 00:18:59 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 17s. Last read position: chr4:153,295,460
INFO 2026-05-28 00:19:10 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 11s. Last read position: chr5:1,581,682
INFO 2026-05-28 00:19:23 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 12s. Last read position: chr5:43,295,751
INFO 2026-05-28 00:19:33 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 9s. Last read position: chr5:75,350,089
INFO 2026-05-28 00:19:53 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 20s. Last read position: chr5:112,878,682
INFO 2026-05-28 00:20:03 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 10s. Last read position: chr5:135,571,300
INFO 2026-05-28 00:20:15 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 12s. Last read position: chr5:141,865,101
INFO 2026-05-28 00:20:28 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 13s. Last read position: chr5:154,053,401
INFO 2026-05-28 00:20:42 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 13s. Last read position: chr5:175,961,343
INFO 2026-05-28 00:21:01 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 18s. Last read position: chr5:179,963,538
INFO 2026-05-28 00:21:13 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 11s. Last read position: chr6:7,910,548
INFO 2026-05-28 00:21:17 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 4s. Last read position: chr6:27,146,533
INFO 2026-05-28 00:21:24 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 7s. Last read position: chr6:31,270,267
INFO 2026-05-28 00:21:33 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 8s. Last read position: chr6:31,954,721
INFO 2026-05-28 00:21:41 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 8s. Last read position: chr6:35,287,623
INFO 2026-05-28 00:21:48 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 7s. Last read position: chr6:44,256,778
INFO 2026-05-28 00:22:09 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 20s. Last read position: chr6:85,489,494
INFO 2026-05-28 00:22:21 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 11s. Last read position: chr6:116,511,622
INFO 2026-05-28 00:22:36 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 15s. Last read position: chr6:144,548,753
INFO 2026-05-28 00:22:46 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 10s. Last read position: chr6:166,956,159
INFO 2026-05-28 00:22:56 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 9s. Last read position: chr7:5,528,467
INFO 2026-05-28 00:23:07 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 10s. Last read position: chr7:26,184,977
INFO 2026-05-28 00:23:20 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 13s. Last read position: chr7:55,978,242
INFO 2026-05-28 00:23:27 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 7s. Last read position: chr7:76,060,385
INFO 2026-05-28 00:23:45 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 17s. Last read position: chr7:99,531,683
INFO 2026-05-28 00:23:51 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 5s. Last read position: chr7:100,992,618
INFO 2026-05-28 00:23:53 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,507
INFO 2026-05-28 00:23:53 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,049
INFO 2026-05-28 00:23:55 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,897
INFO 2026-05-28 00:23:57 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 2s. Last read position: chr7:100,998,028
INFO 2026-05-28 00:23:58 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,278
INFO 2026-05-28 00:24:00 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 2s. Last read position: chr7:101,000,411
INFO 2026-05-28 00:24:03 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 2s. Last read position: chr7:101,001,312
INFO 2026-05-28 00:24:04 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr7:101,002,881
INFO 2026-05-28 00:24:06 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 2s. Last read position: chr7:101,032,992
INFO 2026-05-28 00:24:18 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 11s. Last read position: chr7:117,480,072
INFO 2026-05-28 00:24:26 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 8s. Last read position: chr7:139,596,926
INFO 2026-05-28 00:24:34 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:15:18s. Time for last 1,000,000: 7s. Last read position: chr7:152,077,855
INFO 2026-05-28 00:24:49 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 15s. Last read position: chr8:29,110,027
INFO 2026-05-28 00:25:01 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 12s. Last read position: chr8:54,135,367
INFO 2026-05-28 00:25:10 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 9s. Last read position: chr8:85,480,670
INFO 2026-05-28 00:25:26 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:16:11s. Time for last 1,000,000: 16s. Last read position: chr8:100,718,160
INFO 2026-05-28 00:25:40 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 13s. Last read position: chr8:127,738,652
INFO 2026-05-28 00:25:52 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 11s. Last read position: chr8:143,858,317
INFO 2026-05-28 00:25:53 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:16:37s. Time for last 1,000,000: 0s. Last read position: chr8:143,861,771
INFO 2026-05-28 00:25:54 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,373
INFO 2026-05-28 00:25:57 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 3s. Last read position: chr8:143,925,209
INFO 2026-05-28 00:26:09 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 12s. Last read position: chr9:2,077,740
INFO 2026-05-28 00:26:19 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 10s. Last read position: chr9:35,162,165
INFO 2026-05-28 00:26:30 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 10s. Last read position: chr9:83,970,746
INFO 2026-05-28 00:26:38 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 8s. Last read position: chr9:104,800,524
INFO 2026-05-28 00:26:49 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:17:33s. Time for last 1,000,000: 10s. Last read position: chr9:123,089,792
INFO 2026-05-28 00:26:59 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:17:44s. Time for last 1,000,000: 10s. Last read position: chr9:128,617,676
INFO 2026-05-28 00:27:09 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 9s. Last read position: chr9:133,554,457
INFO 2026-05-28 00:27:18 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:18:02s. Time for last 1,000,000: 8s. Last read position: chr9:137,614,646
INFO 2026-05-28 00:27:31 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 12s. Last read position: chr10:28,610,803
INFO 2026-05-28 00:27:40 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:18:24s. Time for last 1,000,000: 9s. Last read position: chr10:59,812,679
INFO 2026-05-28 00:27:50 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:18:35s. Time for last 1,000,000: 10s. Last read position: chr10:78,037,219
INFO 2026-05-28 00:27:59 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:18:43s. Time for last 1,000,000: 8s. Last read position: chr10:99,880,038
INFO 2026-05-28 00:28:12 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 12s. Last read position: chr10:114,300,322
INFO 2026-05-28 00:28:29 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 17s. Last read position: chr10:122,598,905
INFO 2026-05-28 00:28:53 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 23s. Last read position: chr11:319,979
INFO 2026-05-28 00:29:01 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 7s. Last read position: chr11:1,164,178
INFO 2026-05-28 00:29:05 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:19:49s. Time for last 1,000,000: 4s. Last read position: chr11:1,184,144
INFO 2026-05-28 00:29:09 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:19:53s. Time for last 1,000,000: 4s. Last read position: chr11:1,190,136
INFO 2026-05-28 00:29:14 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:19:58s. Time for last 1,000,000: 5s. Last read position: chr11:1,226,782
INFO 2026-05-28 00:29:19 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:20:04s. Time for last 1,000,000: 5s. Last read position: chr11:1,244,051
INFO 2026-05-28 00:29:23 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:20:08s. Time for last 1,000,000: 3s. Last read position: chr11:1,247,847
INFO 2026-05-28 00:29:29 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 6s. Last read position: chr11:1,257,675
INFO 2026-05-28 00:29:40 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:20:24s. Time for last 1,000,000: 10s. Last read position: chr11:9,968,532
INFO 2026-05-28 00:29:50 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:20:34s. Time for last 1,000,000: 10s. Last read position: chr11:32,933,523
INFO 2026-05-28 00:30:00 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:20:45s. Time for last 1,000,000: 10s. Last read position: chr11:47,577,425
INFO 2026-05-28 00:30:15 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:21:00s. Time for last 1,000,000: 15s. Last read position: chr11:62,517,559
INFO 2026-05-28 00:30:19 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:21:04s. Time for last 1,000,000: 3s. Last read position: chr11:62,595,812
INFO 2026-05-28 00:30:28 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:21:13s. Time for last 1,000,000: 8s. Last read position: chr11:65,183,188
INFO 2026-05-28 00:30:39 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:21:23s. Time for last 1,000,000: 10s. Last read position: chr11:67,399,612
INFO 2026-05-28 00:30:50 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:21:35s. Time for last 1,000,000: 11s. Last read position: chr11:72,781,003
INFO 2026-05-28 00:31:02 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:21:46s. Time for last 1,000,000: 11s. Last read position: chr11:104,942,918
INFO 2026-05-28 00:31:12 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:21:56s. Time for last 1,000,000: 10s. Last read position: chr11:121,588,108
INFO 2026-05-28 00:31:21 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:22:05s. Time for last 1,000,000: 8s. Last read position: chr12:545,392
INFO 2026-05-28 00:31:36 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:22:21s. Time for last 1,000,000: 15s. Last read position: chr12:7,108,358
INFO 2026-05-28 00:31:44 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:22:28s. Time for last 1,000,000: 7s. Last read position: chr12:30,713,805
INFO 2026-05-28 00:31:53 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:22:38s. Time for last 1,000,000: 9s. Last read position: chr12:49,741,592
INFO 2026-05-28 00:32:03 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:22:48s. Time for last 1,000,000: 9s. Last read position: chr12:53,443,516
INFO 2026-05-28 00:32:18 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:23:02s. Time for last 1,000,000: 14s. Last read position: chr12:56,311,206
INFO 2026-05-28 00:32:32 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:23:16s. Time for last 1,000,000: 13s. Last read position: chr12:57,718,355
INFO 2026-05-28 00:32:40 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:23:24s. Time for last 1,000,000: 7s. Last read position: chr12:76,030,919
INFO 2026-05-28 00:32:54 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:23:39s. Time for last 1,000,000: 14s. Last read position: chr12:105,208,010
INFO 2026-05-28 00:33:05 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:23:49s. Time for last 1,000,000: 10s. Last read position: chr12:117,186,471
INFO 2026-05-28 00:33:14 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:23:59s. Time for last 1,000,000: 9s. Last read position: chr12:124,325,378
INFO 2026-05-28 00:33:23 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:24:08s. Time for last 1,000,000: 8s. Last read position: chr13:27,434,890
INFO 2026-05-28 00:33:32 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:24:16s. Time for last 1,000,000: 8s. Last read position: chr13:53,028,831
INFO 2026-05-28 00:33:34 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:24:18s. Time for last 1,000,000: 1s. Last read position: chr13:53,050,513
INFO 2026-05-28 00:33:43 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:24:28s. Time for last 1,000,000: 9s. Last read position: chr13:110,210,174
INFO 2026-05-28 00:33:55 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:24:39s. Time for last 1,000,000: 11s. Last read position: chr14:23,071,476
INFO 2026-05-28 00:34:07 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:24:52s. Time for last 1,000,000: 12s. Last read position: chr14:49,585,957
INFO 2026-05-28 00:34:25 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:25:09s. Time for last 1,000,000: 17s. Last read position: chr14:64,208,838
INFO 2026-05-28 00:34:38 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:25:23s. Time for last 1,000,000: 13s. Last read position: chr14:76,155,001
INFO 2026-05-28 00:34:50 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:25:34s. Time for last 1,000,000: 11s. Last read position: chr14:101,991,568
INFO 2026-05-28 00:35:36 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:26:20s. Time for last 1,000,000: 46s. Last read position: chr14:104,948,418
INFO 2026-05-28 00:35:39 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:26:23s. Time for last 1,000,000: 2s. Last read position: chr15:20,466,220
INFO 2026-05-28 00:35:52 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:26:36s. Time for last 1,000,000: 13s. Last read position: chr15:41,333,008
INFO 2026-05-28 00:36:00 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:26:44s. Time for last 1,000,000: 8s. Last read position: chr15:45,103,985
INFO 2026-05-28 00:36:10 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:26:55s. Time for last 1,000,000: 10s. Last read position: chr15:59,618,797
INFO 2026-05-28 00:36:27 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:27:11s. Time for last 1,000,000: 16s. Last read position: chr15:67,066,332
INFO 2026-05-28 00:36:37 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:27:21s. Time for last 1,000,000: 10s. Last read position: chr15:77,054,268
INFO 2026-05-28 00:36:47 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:27:32s. Time for last 1,000,000: 10s. Last read position: chr15:89,806,303
INFO 2026-05-28 00:36:57 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:27:42s. Time for last 1,000,000: 10s. Last read position: chr16:683,536
INFO 2026-05-28 00:37:11 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:27:56s. Time for last 1,000,000: 14s. Last read position: chr16:2,767,228
INFO 2026-05-28 00:37:22 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:28:06s. Time for last 1,000,000: 10s. Last read position: chr16:14,833,918
INFO 2026-05-28 00:37:31 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:28:15s. Time for last 1,000,000: 9s. Last read position: chr16:19,487,092
INFO 2026-05-28 00:37:37 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:28:22s. Time for last 1,000,000: 6s. Last read position: chr16:28,388,130
INFO 2026-05-28 00:37:47 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:28:31s. Time for last 1,000,000: 9s. Last read position: chr16:30,069,974
INFO 2026-05-28 00:37:54 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:28:38s. Time for last 1,000,000: 7s. Last read position: chr16:50,078,766
INFO 2026-05-28 00:38:06 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:28:50s. Time for last 1,000,000: 11s. Last read position: chr16:67,611,269
INFO 2026-05-28 00:38:15 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:29:00s. Time for last 1,000,000: 9s. Last read position: chr16:74,471,232
INFO 2026-05-28 00:38:23 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:29:07s. Time for last 1,000,000: 7s. Last read position: chr16:89,280,353
INFO 2026-05-28 00:38:37 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:29:21s. Time for last 1,000,000: 13s. Last read position: chr17:2,670,226
INFO 2026-05-28 00:38:47 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:29:31s. Time for last 1,000,000: 9s. Last read position: chr17:7,260,439
INFO 2026-05-28 00:38:58 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:29:42s. Time for last 1,000,000: 11s. Last read position: chr17:16,101,339
INFO 2026-05-28 00:39:09 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:29:53s. Time for last 1,000,000: 11s. Last read position: chr17:28,697,702
INFO 2026-05-28 00:39:21 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:30:05s. Time for last 1,000,000: 11s. Last read position: chr17:37,323,227
INFO 2026-05-28 00:39:34 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:30:18s. Time for last 1,000,000: 13s. Last read position: chr17:39,727,951
INFO 2026-05-28 00:39:45 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:30:29s. Time for last 1,000,000: 10s. Last read position: chr17:42,719,187
INFO 2026-05-28 00:39:56 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:30:40s. Time for last 1,000,000: 10s. Last read position: chr17:47,813,739
INFO 2026-05-28 00:40:04 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:30:48s. Time for last 1,000,000: 8s. Last read position: chr17:50,657,169
INFO 2026-05-28 00:40:15 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:30:59s. Time for last 1,000,000: 10s. Last read position: chr17:60,000,110
INFO 2026-05-28 00:40:25 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:31:10s. Time for last 1,000,000: 10s. Last read position: chr17:74,762,092
INFO 2026-05-28 00:40:39 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:31:23s. Time for last 1,000,000: 13s. Last read position: chr17:76,391,137
INFO 2026-05-28 00:40:50 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:31:34s. Time for last 1,000,000: 11s. Last read position: chr17:81,511,200
INFO 2026-05-28 00:41:10 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:31:54s. Time for last 1,000,000: 20s. Last read position: chr18:203,178
INFO 2026-05-28 00:41:18 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:32:03s. Time for last 1,000,000: 8s. Last read position: chr18:36,146,316
INFO 2026-05-28 00:41:31 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:32:15s. Time for last 1,000,000: 12s. Last read position: chr18:63,487,054
INFO 2026-05-28 00:41:40 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:32:24s. Time for last 1,000,000: 9s. Last read position: chr19:1,300,358
INFO 2026-05-28 00:41:47 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:32:31s. Time for last 1,000,000: 6s. Last read position: chr19:4,099,218
INFO 2026-05-28 00:41:54 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:32:39s. Time for last 1,000,000: 7s. Last read position: chr19:8,321,520
INFO 2026-05-28 00:42:11 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:32:55s. Time for last 1,000,000: 16s. Last read position: chr19:11,666,346
INFO 2026-05-28 00:42:19 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:33:04s. Time for last 1,000,000: 8s. Last read position: chr19:15,265,296
INFO 2026-05-28 00:42:28 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:33:12s. Time for last 1,000,000: 8s. Last read position: chr19:19,386,119
INFO 2026-05-28 00:42:37 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:33:22s. Time for last 1,000,000: 9s. Last read position: chr19:36,236,510
INFO 2026-05-28 00:42:45 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:33:29s. Time for last 1,000,000: 7s. Last read position: chr19:39,474,514
INFO 2026-05-28 00:42:47 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:33:32s. Time for last 1,000,000: 2s. Last read position: chr19:39,877,190
INFO 2026-05-28 00:42:50 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:33:34s. Time for last 1,000,000: 2s. Last read position: chr19:39,886,475
INFO 2026-05-28 00:42:53 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:33:38s. Time for last 1,000,000: 3s. Last read position: chr19:39,893,339
INFO 2026-05-28 00:42:57 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:33:41s. Time for last 1,000,000: 3s. Last read position: chr19:39,913,819
INFO 2026-05-28 00:43:04 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:33:48s. Time for last 1,000,000: 6s. Last read position: chr19:40,601,390
INFO 2026-05-28 00:43:11 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:33:56s. Time for last 1,000,000: 7s. Last read position: chr19:41,860,825
INFO 2026-05-28 00:43:19 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:34:03s. Time for last 1,000,000: 7s. Last read position: chr19:46,608,222
INFO 2026-05-28 00:43:27 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:34:12s. Time for last 1,000,000: 8s. Last read position: chr19:49,513,257
INFO 2026-05-28 00:43:38 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:34:22s. Time for last 1,000,000: 10s. Last read position: chr19:54,201,536
INFO 2026-05-28 00:43:45 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:34:29s. Time for last 1,000,000: 6s. Last read position: chr20:1,319,608
INFO 2026-05-28 00:43:53 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:34:38s. Time for last 1,000,000: 8s. Last read position: chr20:23,633,881
INFO 2026-05-28 00:44:03 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:34:47s. Time for last 1,000,000: 9s. Last read position: chr20:35,725,058
INFO 2026-05-28 00:44:14 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:34:59s. Time for last 1,000,000: 11s. Last read position: chr20:48,998,209
INFO 2026-05-28 00:44:25 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:35:10s. Time for last 1,000,000: 11s. Last read position: chr20:63,521,541
INFO 2026-05-28 00:44:32 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:35:16s. Time for last 1,000,000: 6s. Last read position: chr21:32,384,359
INFO 2026-05-28 00:44:46 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:35:30s. Time for last 1,000,000: 14s. Last read position: chr21:42,518,481
INFO 2026-05-28 00:44:55 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:35:40s. Time for last 1,000,000: 9s. Last read position: chr22:20,859,093
INFO 2026-05-28 00:45:05 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:35:49s. Time for last 1,000,000: 9s. Last read position: chr22:29,528,130
INFO 2026-05-28 00:45:13 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:35:58s. Time for last 1,000,000: 8s. Last read position: chr22:37,231,275
INFO 2026-05-28 00:45:22 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:36:07s. Time for last 1,000,000: 8s. Last read position: chr22:41,680,311
INFO 2026-05-28 00:45:30 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:36:15s. Time for last 1,000,000: 8s. Last read position: chr22:50,467,614
INFO 2026-05-28 00:45:38 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:36:22s. Time for last 1,000,000: 7s. Last read position: chrX:40,074,611
INFO 2026-05-28 00:45:53 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:36:37s. Time for last 1,000,000: 15s. Last read position: chrX:53,238,150
INFO 2026-05-28 00:46:06 SinglePassSamProgram Processed 214,000,000 records. Elapsed time: 00:36:50s. Time for last 1,000,000: 13s. Last read position: chrX:77,853,942
INFO 2026-05-28 00:46:14 SinglePassSamProgram Processed 215,000,000 records. Elapsed time: 00:36:58s. Time for last 1,000,000: 7s. Last read position: chrX:132,072,358
INFO 2026-05-28 00:46:23 SinglePassSamProgram Processed 216,000,000 records. Elapsed time: 00:37:07s. Time for last 1,000,000: 9s. Last read position: GL000220.1:116,593
INFO 2026-05-28 00:46:23 SinglePassSamProgram Processed 217,000,000 records. Elapsed time: 00:37:08s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:46:25 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 37.19 minutes.
Runtime.totalMemory()=2918187008