/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 12:08:03 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 00:08:04 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_c95-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 00:08:04 GMT 2026] Executing as ?@nf-6ff02867e24358791fa5aa5501cc8600-857ee-ncm2b 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.XXXXR4cGtY/659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXR4cGtY/659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:08:06 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:08:17 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:8,015,519
INFO 2026-05-28 00:08:29 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 11s. Last read position: chr1:16,393,349
INFO 2026-05-28 00:08:40 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 11s. Last read position: chr1:22,639,071
INFO 2026-05-28 00:08:47 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 6s. Last read position: chr1:28,010,965
INFO 2026-05-28 00:08:56 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 9s. Last read position: chr1:36,303,889
INFO 2026-05-28 00:09:22 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 25s. Last read position: chr1:43,689,054
INFO 2026-05-28 00:09:32 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 10s. Last read position: chr1:54,043,388
INFO 2026-05-28 00:09:43 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 11s. Last read position: chr1:92,304,050
INFO 2026-05-28 00:09:53 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 9s. Last read position: chr1:113,594,518
INFO 2026-05-28 00:10:02 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 9s. Last read position: chr1:120,830,413
INFO 2026-05-28 00:10:11 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 9s. Last read position: chr1:149,487,342
INFO 2026-05-28 00:10:20 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 9s. Last read position: chr1:153,930,989
INFO 2026-05-28 00:10:40 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 19s. Last read position: chr1:155,717,098
INFO 2026-05-28 00:10:52 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 12s. Last read position: chr1:161,176,811
INFO 2026-05-28 00:11:03 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 10s. Last read position: chr1:180,492,328
INFO 2026-05-28 00:11:14 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 10s. Last read position: chr1:202,942,079
INFO 2026-05-28 00:11:24 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 10s. Last read position: chr1:220,102,505
INFO 2026-05-28 00:11:37 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 13s. Last read position: chr1:231,907,428
INFO 2026-05-28 00:11:53 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 16s. Last read position: chr2:8,877,072
INFO 2026-05-28 00:12:04 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 10s. Last read position: chr2:30,234,470
INFO 2026-05-28 00:12:11 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 6s. Last read position: chr2:32,916,406
INFO 2026-05-28 00:12:26 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 14s. Last read position: chr2:55,558,789
INFO 2026-05-28 00:12:48 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 22s. Last read position: chr2:74,366,844
INFO 2026-05-28 00:13:00 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 12s. Last read position: chr2:96,265,195
INFO 2026-05-28 00:13:10 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 9s. Last read position: chr2:109,836,542
INFO 2026-05-28 00:13:18 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 8s. Last read position: chr2:136,115,247
INFO 2026-05-28 00:13:35 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 17s. Last read position: chr2:178,574,048
INFO 2026-05-28 00:14:16 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 40s. Last read position: chr2:196,639,753
INFO 2026-05-28 00:14:31 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 14s. Last read position: chr2:215,365,553
INFO 2026-05-28 00:15:07 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 36s. Last read position: chr2:215,393,009
INFO 2026-05-28 00:16:23 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 76s. Last read position: chr2:215,433,377
INFO 2026-05-28 00:16:48 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 24s. Last read position: chr2:229,859,436
INFO 2026-05-28 00:17:12 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 24s. Last read position: chr2:240,375,131
INFO 2026-05-28 00:17:33 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 20s. Last read position: chr3:13,360,402
INFO 2026-05-28 00:17:47 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 13s. Last read position: chr3:40,458,661
INFO 2026-05-28 00:18:03 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 16s. Last read position: chr3:48,479,234
INFO 2026-05-28 00:18:15 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 12s. Last read position: chr3:52,291,042
INFO 2026-05-28 00:18:33 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 17s. Last read position: chr3:101,849,537
INFO 2026-05-28 00:18:43 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 10s. Last read position: chr3:124,873,481
INFO 2026-05-28 00:18:54 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 11s. Last read position: chr3:139,362,506
INFO 2026-05-28 00:19:06 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 11s. Last read position: chr3:179,576,884
INFO 2026-05-28 00:19:22 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 16s. Last read position: chr3:195,579,348
INFO 2026-05-28 00:19:40 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 18s. Last read position: chr4:4,240,344
INFO 2026-05-28 00:19:50 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 10s. Last read position: chr4:42,060,205
INFO 2026-05-28 00:20:01 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 10s. Last read position: chr4:76,895,800
INFO 2026-05-28 00:20:16 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 15s. Last read position: chr4:108,667,256
INFO 2026-05-28 00:20:34 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 17s. Last read position: chr4:153,788,547
INFO 2026-05-28 00:20:44 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 10s. Last read position: chr5:10,761,096
INFO 2026-05-28 00:21:02 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 18s. Last read position: chr5:52,800,465
INFO 2026-05-28 00:21:14 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 11s. Last read position: chr5:76,654,243
INFO 2026-05-28 00:21:32 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 18s. Last read position: chr5:103,133,572
INFO 2026-05-28 00:21:43 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 10s. Last read position: chr5:134,371,599
INFO 2026-05-28 00:21:54 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 11s. Last read position: chr5:141,183,923
INFO 2026-05-28 00:22:04 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 9s. Last read position: chr5:150,402,158
INFO 2026-05-28 00:22:12 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 7s. Last read position: chr5:150,533,017
INFO 2026-05-28 00:22:24 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 12s. Last read position: chr5:171,400,851
INFO 2026-05-28 00:22:33 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 9s. Last read position: chr5:177,608,553
INFO 2026-05-28 00:22:54 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 20s. Last read position: chr5:179,833,723
INFO 2026-05-28 00:23:04 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 9s. Last read position: chr6:7,580,484
INFO 2026-05-28 00:23:09 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 5s. Last read position: chr6:29,723,460
INFO 2026-05-28 00:23:18 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 8s. Last read position: chr6:31,702,045
INFO 2026-05-28 00:23:24 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 5s. Last read position: chr6:32,934,873
INFO 2026-05-28 00:23:31 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 7s. Last read position: chr6:36,596,783
INFO 2026-05-28 00:23:39 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 8s. Last read position: chr6:53,065,659
INFO 2026-05-28 00:24:03 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 23s. Last read position: chr6:100,785,660
INFO 2026-05-28 00:24:14 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 11s. Last read position: chr6:138,255,743
INFO 2026-05-28 00:24:28 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 13s. Last read position: chr6:163,562,007
INFO 2026-05-28 00:24:38 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 10s. Last read position: chr7:5,528,535
INFO 2026-05-28 00:24:51 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:16:45s. Time for last 1,000,000: 12s. Last read position: chr7:36,576,611
INFO 2026-05-28 00:25:00 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 8s. Last read position: chr7:70,784,967
INFO 2026-05-28 00:25:07 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 6s. Last read position: chr7:77,749,804
INFO 2026-05-28 00:25:33 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 26s. Last read position: chr7:98,386,017
INFO 2026-05-28 00:25:43 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 10s. Last read position: chr7:102,355,881
INFO 2026-05-28 00:25:56 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:17:50s. Time for last 1,000,000: 12s. Last read position: chr7:128,609,533
INFO 2026-05-28 00:26:03 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:17:57s. Time for last 1,000,000: 6s. Last read position: chr7:143,267,685
INFO 2026-05-28 00:26:17 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 14s. Last read position: chr7:155,680,742
INFO 2026-05-28 00:26:33 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:18:27s. Time for last 1,000,000: 16s. Last read position: chr8:26,624,273
INFO 2026-05-28 00:26:47 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 13s. Last read position: chr8:47,737,476
INFO 2026-05-28 00:27:01 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:18:55s. Time for last 1,000,000: 14s. Last read position: chr8:70,127,011
INFO 2026-05-28 00:27:09 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:19:03s. Time for last 1,000,000: 8s. Last read position: chr8:98,950,675
INFO 2026-05-28 00:27:32 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 22s. Last read position: chr8:115,619,207
INFO 2026-05-28 00:27:43 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 11s. Last read position: chr8:143,310,175
INFO 2026-05-28 00:27:51 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 7s. Last read position: chr8:143,858,900
INFO 2026-05-28 00:27:52 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:19:46s. Time for last 1,000,000: 0s. Last read position: chr8:143,861,127
INFO 2026-05-28 00:27:53 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 0s. Last read position: chr8:143,862,977
INFO 2026-05-28 00:27:54 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:19:48s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,987
INFO 2026-05-28 00:27:55 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:19:49s. Time for last 1,000,000: 0s. Last read position: chr8:143,871,024
INFO 2026-05-28 00:28:06 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:19:59s. Time for last 1,000,000: 10s. Last read position: chr8:144,243,586
INFO 2026-05-28 00:28:17 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:20:11s. Time for last 1,000,000: 11s. Last read position: chr9:6,434,030
INFO 2026-05-28 00:28:27 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:20:21s. Time for last 1,000,000: 10s. Last read position: chr9:37,819,254
INFO 2026-05-28 00:28:37 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 9s. Last read position: chr9:98,201,592
INFO 2026-05-28 00:28:48 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:20:42s. Time for last 1,000,000: 11s. Last read position: chr9:121,331,403
INFO 2026-05-28 00:29:01 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:20:54s. Time for last 1,000,000: 12s. Last read position: chr9:128,993,260
INFO 2026-05-28 00:29:10 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:21:04s. Time for last 1,000,000: 9s. Last read position: chr9:134,756,765
INFO 2026-05-28 00:29:22 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:21:16s. Time for last 1,000,000: 11s. Last read position: chr9:137,716,630
INFO 2026-05-28 00:29:32 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 10s. Last read position: chr10:24,543,822
INFO 2026-05-28 00:29:45 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:21:39s. Time for last 1,000,000: 12s. Last read position: chr10:46,009,455
INFO 2026-05-28 00:29:54 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:21:47s. Time for last 1,000,000: 8s. Last read position: chr10:73,072,034
INFO 2026-05-28 00:30:17 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 23s. Last read position: chr10:89,339,821
INFO 2026-05-28 00:30:28 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:22:22s. Time for last 1,000,000: 11s. Last read position: chr10:102,362,637
INFO 2026-05-28 00:30:40 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:22:34s. Time for last 1,000,000: 11s. Last read position: chr11:209,814
INFO 2026-05-28 00:30:50 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:22:43s. Time for last 1,000,000: 9s. Last read position: chr11:1,761,405
INFO 2026-05-28 00:31:03 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:22:57s. Time for last 1,000,000: 13s. Last read position: chr11:12,208,029
INFO 2026-05-28 00:31:13 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:23:07s. Time for last 1,000,000: 10s. Last read position: chr11:46,681,306
INFO 2026-05-28 00:31:25 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:23:19s. Time for last 1,000,000: 12s. Last read position: chr11:60,919,889
INFO 2026-05-28 00:31:34 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:23:28s. Time for last 1,000,000: 8s. Last read position: chr11:62,572,584
INFO 2026-05-28 00:31:44 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:23:38s. Time for last 1,000,000: 10s. Last read position: chr11:65,121,555
INFO 2026-05-28 00:31:55 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:23:49s. Time for last 1,000,000: 10s. Last read position: chr11:67,352,691
INFO 2026-05-28 00:32:09 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:24:03s. Time for last 1,000,000: 14s. Last read position: chr11:72,843,303
INFO 2026-05-28 00:32:20 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:24:14s. Time for last 1,000,000: 11s. Last read position: chr11:102,402,051
INFO 2026-05-28 00:32:32 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:24:25s. Time for last 1,000,000: 11s. Last read position: chr11:119,049,179
INFO 2026-05-28 00:32:43 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:24:36s. Time for last 1,000,000: 10s. Last read position: chr11:134,371,106
INFO 2026-05-28 00:33:01 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:24:55s. Time for last 1,000,000: 18s. Last read position: chr12:7,065,138
INFO 2026-05-28 00:33:09 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:25:02s. Time for last 1,000,000: 7s. Last read position: chr12:26,979,802
INFO 2026-05-28 00:33:19 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:25:13s. Time for last 1,000,000: 10s. Last read position: chr12:49,128,858
INFO 2026-05-28 00:33:29 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:25:22s. Time for last 1,000,000: 9s. Last read position: chr12:53,454,790
INFO 2026-05-28 00:33:38 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:25:32s. Time for last 1,000,000: 9s. Last read position: chr12:56,109,856
INFO 2026-05-28 00:33:52 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:25:46s. Time for last 1,000,000: 13s. Last read position: chr12:57,498,476
INFO 2026-05-28 00:34:04 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:25:58s. Time for last 1,000,000: 12s. Last read position: chr12:91,108,397
INFO 2026-05-28 00:34:17 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:26:11s. Time for last 1,000,000: 12s. Last read position: chr12:109,460,636
INFO 2026-05-28 00:34:32 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:26:26s. Time for last 1,000,000: 14s. Last read position: chr12:120,161,572
INFO 2026-05-28 00:34:43 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:26:37s. Time for last 1,000,000: 11s. Last read position: chr12:131,941,861
INFO 2026-05-28 00:34:52 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:26:45s. Time for last 1,000,000: 8s. Last read position: chr13:32,536,639
INFO 2026-05-28 00:35:01 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:26:55s. Time for last 1,000,000: 9s. Last read position: chr13:76,885,604
INFO 2026-05-28 00:35:14 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:27:08s. Time for last 1,000,000: 13s. Last read position: chr13:113,820,859
INFO 2026-05-28 00:35:26 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:27:20s. Time for last 1,000,000: 12s. Last read position: chr14:24,233,289
INFO 2026-05-28 00:35:39 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:27:32s. Time for last 1,000,000: 12s. Last read position: chr14:53,063,013
INFO 2026-05-28 00:36:05 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:27:58s. Time for last 1,000,000: 25s. Last read position: chr14:69,769,527
INFO 2026-05-28 00:36:14 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:28:08s. Time for last 1,000,000: 9s. Last read position: chr14:91,870,248
INFO 2026-05-28 00:37:05 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:28:59s. Time for last 1,000,000: 50s. Last read position: chr14:102,983,575
INFO 2026-05-28 00:37:15 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:29:09s. Time for last 1,000,000: 9s. Last read position: chr14:105,668,195
INFO 2026-05-28 00:37:17 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:29:10s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,147
INFO 2026-05-28 00:37:18 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:29:12s. Time for last 1,000,000: 1s. Last read position: chr14:105,855,091
INFO 2026-05-28 00:37:29 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:29:23s. Time for last 1,000,000: 11s. Last read position: chr15:39,600,863
INFO 2026-05-28 00:37:39 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:29:33s. Time for last 1,000,000: 10s. Last read position: chr15:44,715,466
INFO 2026-05-28 00:37:54 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:29:48s. Time for last 1,000,000: 14s. Last read position: chr15:61,983,981
INFO 2026-05-28 00:38:06 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:30:00s. Time for last 1,000,000: 11s. Last read position: chr15:72,570,298
INFO 2026-05-28 00:38:18 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:30:11s. Time for last 1,000,000: 11s. Last read position: chr15:83,164,060
INFO 2026-05-28 00:38:29 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:30:23s. Time for last 1,000,000: 11s. Last read position: chr15:100,892,515
INFO 2026-05-28 00:38:45 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:30:38s. Time for last 1,000,000: 15s. Last read position: chr16:2,099,959
INFO 2026-05-28 00:38:57 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:30:51s. Time for last 1,000,000: 12s. Last read position: chr16:3,777,613
INFO 2026-05-28 00:39:07 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:31:01s. Time for last 1,000,000: 10s. Last read position: chr16:15,133,901
INFO 2026-05-28 00:39:14 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:31:07s. Time for last 1,000,000: 6s. Last read position: chr16:18,868,201
INFO 2026-05-28 00:39:18 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:31:12s. Time for last 1,000,000: 4s. Last read position: chr16:21,916,002
INFO 2026-05-28 00:39:27 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:31:21s. Time for last 1,000,000: 8s. Last read position: chr16:28,652,295
INFO 2026-05-28 00:39:34 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:31:28s. Time for last 1,000,000: 6s. Last read position: chr16:30,112,131
INFO 2026-05-28 00:39:40 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:31:34s. Time for last 1,000,000: 6s. Last read position: chr16:31,458,217
INFO 2026-05-28 00:39:51 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:31:45s. Time for last 1,000,000: 11s. Last read position: chr16:57,456,575
INFO 2026-05-28 00:40:03 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:31:56s. Time for last 1,000,000: 11s. Last read position: chr16:70,251,040
INFO 2026-05-28 00:40:13 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:32:06s. Time for last 1,000,000: 9s. Last read position: chr16:87,383,563
INFO 2026-05-28 00:40:26 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:32:20s. Time for last 1,000,000: 13s. Last read position: chr17:1,480,545
INFO 2026-05-28 00:40:37 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:32:31s. Time for last 1,000,000: 11s. Last read position: chr17:5,004,906
INFO 2026-05-28 00:40:47 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:32:41s. Time for last 1,000,000: 9s. Last read position: chr17:13,002,478
INFO 2026-05-28 00:40:59 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:32:53s. Time for last 1,000,000: 12s. Last read position: chr17:29,093,425
INFO 2026-05-28 00:41:10 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:33:04s. Time for last 1,000,000: 10s. Last read position: chr17:39,200,339
INFO 2026-05-28 00:41:21 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:33:15s. Time for last 1,000,000: 10s. Last read position: chr17:39,707,026
INFO 2026-05-28 00:41:35 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:33:29s. Time for last 1,000,000: 13s. Last read position: chr17:39,709,872
INFO 2026-05-28 00:41:52 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:33:46s. Time for last 1,000,000: 17s. Last read position: chr17:39,712,396
INFO 2026-05-28 00:42:15 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:34:08s. Time for last 1,000,000: 22s. Last read position: chr17:39,716,408
INFO 2026-05-28 00:42:42 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:34:36s. Time for last 1,000,000: 27s. Last read position: chr17:39,723,589
INFO 2026-05-28 00:43:15 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:35:09s. Time for last 1,000,000: 33s. Last read position: chr17:39,726,581
INFO 2026-05-28 00:43:48 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:35:42s. Time for last 1,000,000: 33s. Last read position: chr17:39,746,095
INFO 2026-05-28 00:44:00 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:35:53s. Time for last 1,000,000: 11s. Last read position: chr17:44,351,037
INFO 2026-05-28 00:44:10 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:36:03s. Time for last 1,000,000: 9s. Last read position: chr17:50,185,778
INFO 2026-05-28 00:44:15 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:36:09s. Time for last 1,000,000: 5s. Last read position: chr17:50,190,348
INFO 2026-05-28 00:44:24 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:36:18s. Time for last 1,000,000: 8s. Last read position: chr17:50,195,593
INFO 2026-05-28 00:44:35 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:36:29s. Time for last 1,000,000: 10s. Last read position: chr17:50,392,875
INFO 2026-05-28 00:44:45 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:36:39s. Time for last 1,000,000: 10s. Last read position: chr17:51,285,288
INFO 2026-05-28 00:44:56 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:36:50s. Time for last 1,000,000: 10s. Last read position: chr17:59,685,216
INFO 2026-05-28 00:45:07 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:37:01s. Time for last 1,000,000: 11s. Last read position: chr17:64,500,549
INFO 2026-05-28 00:45:21 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:37:15s. Time for last 1,000,000: 13s. Last read position: chr17:75,182,815
INFO 2026-05-28 00:45:34 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:37:28s. Time for last 1,000,000: 13s. Last read position: chr17:80,040,146
INFO 2026-05-28 00:45:52 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:37:45s. Time for last 1,000,000: 17s. Last read position: chr17:80,430,046
INFO 2026-05-28 00:46:15 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:38:08s. Time for last 1,000,000: 22s. Last read position: chr17:81,846,441
INFO 2026-05-28 00:46:43 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:38:37s. Time for last 1,000,000: 28s. Last read position: chr17:82,057,292
INFO 2026-05-28 00:46:50 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:38:43s. Time for last 1,000,000: 6s. Last read position: chr17:82,083,778
INFO 2026-05-28 00:46:58 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:38:52s. Time for last 1,000,000: 8s. Last read position: chr17:82,087,462
INFO 2026-05-28 00:47:12 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:39:06s. Time for last 1,000,000: 13s. Last read position: chr17:82,093,308
INFO 2026-05-28 00:47:26 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:39:20s. Time for last 1,000,000: 13s. Last read position: chr18:8,379,271
INFO 2026-05-28 00:47:37 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:39:30s. Time for last 1,000,000: 10s. Last read position: chr18:51,176,484
INFO 2026-05-28 00:47:51 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:39:45s. Time for last 1,000,000: 14s. Last read position: chr19:1,081,663
INFO 2026-05-28 00:47:59 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:39:53s. Time for last 1,000,000: 8s. Last read position: chr19:3,150,214
INFO 2026-05-28 00:48:08 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:40:02s. Time for last 1,000,000: 8s. Last read position: chr19:6,707,193
INFO 2026-05-28 00:48:20 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:40:14s. Time for last 1,000,000: 12s. Last read position: chr19:10,718,302
INFO 2026-05-28 00:48:35 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:40:29s. Time for last 1,000,000: 15s. Last read position: chr19:14,433,503
INFO 2026-05-28 00:48:46 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:40:39s. Time for last 1,000,000: 10s. Last read position: chr19:17,838,054
INFO 2026-05-28 00:48:52 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:40:46s. Time for last 1,000,000: 6s. Last read position: chr19:34,172,660
INFO 2026-05-28 00:49:02 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:40:55s. Time for last 1,000,000: 9s. Last read position: chr19:39,329,568
INFO 2026-05-28 00:49:13 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:41:07s. Time for last 1,000,000: 11s. Last read position: chr19:42,294,031
INFO 2026-05-28 00:49:19 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:41:13s. Time for last 1,000,000: 6s. Last read position: chr19:46,777,002
INFO 2026-05-28 00:49:27 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:41:21s. Time for last 1,000,000: 7s. Last read position: chr19:49,653,528
INFO 2026-05-28 00:49:35 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:41:29s. Time for last 1,000,000: 8s. Last read position: chr19:55,014,776
INFO 2026-05-28 00:49:42 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:41:36s. Time for last 1,000,000: 6s. Last read position: chr20:1,392,838
INFO 2026-05-28 00:49:50 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:41:43s. Time for last 1,000,000: 7s. Last read position: chr20:25,048,086
INFO 2026-05-28 00:50:01 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:41:55s. Time for last 1,000,000: 11s. Last read position: chr20:38,509,071
INFO 2026-05-28 00:50:12 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:42:06s. Time for last 1,000,000: 11s. Last read position: chr20:50,893,508
INFO 2026-05-28 00:50:34 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:42:27s. Time for last 1,000,000: 21s. Last read position: chr20:62,804,929
INFO 2026-05-28 00:50:37 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:42:31s. Time for last 1,000,000: 3s. Last read position: chr21:8,444,601
INFO 2026-05-28 00:50:48 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:42:41s. Time for last 1,000,000: 10s. Last read position: chr21:37,153,099
INFO 2026-05-28 00:51:07 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:43:00s. Time for last 1,000,000: 19s. Last read position: chr21:46,003,476
INFO 2026-05-28 00:51:19 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:43:12s. Time for last 1,000,000: 12s. Last read position: chr22:21,962,865
INFO 2026-05-28 00:51:26 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:43:20s. Time for last 1,000,000: 7s. Last read position: chr22:29,282,486
INFO 2026-05-28 00:51:38 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:43:32s. Time for last 1,000,000: 12s. Last read position: chr22:36,319,618
INFO 2026-05-28 00:51:46 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:43:40s. Time for last 1,000,000: 7s. Last read position: chr22:41,149,087
INFO 2026-05-28 00:51:54 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:43:48s. Time for last 1,000,000: 8s. Last read position: chr22:46,762,794
INFO 2026-05-28 00:52:03 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:43:56s. Time for last 1,000,000: 8s. Last read position: chrX:2,740,808
INFO 2026-05-28 00:52:10 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:44:03s. Time for last 1,000,000: 6s. Last read position: chrX:24,073,124
INFO 2026-05-28 00:52:29 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:44:22s. Time for last 1,000,000: 18s. Last read position: chrX:48,976,322
INFO 2026-05-28 00:52:40 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:44:34s. Time for last 1,000,000: 11s. Last read position: chrX:67,711,445
INFO 2026-05-28 00:52:51 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:44:44s. Time for last 1,000,000: 10s. Last read position: chrX:118,398,391
INFO 2026-05-28 00:53:01 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:44:55s. Time for last 1,000,000: 10s. Last read position: chrX:154,358,554
INFO 2026-05-28 00:53:11 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:45:05s. Time for last 1,000,000: 9s. Last read position: KI270734.1:138,489
INFO 2026-05-28 00:53:11 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:45:05s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:53:12 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 45.15 minutes.
Runtime.totalMemory()=3376939008