/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 12:06:54 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 00:06:54 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bua-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 00:06:54 GMT 2026] Executing as ?@nf-08b244e78451ce955283de608bd2be20-c17f3-5jz86 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.XXXXYr9l2M/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXYr9l2M/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:06:56 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:07:08 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:2,229,585
INFO 2026-05-28 00:07:18 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 9s. Last read position: chr1:11,091,080
INFO 2026-05-28 00:07:27 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 9s. Last read position: chr1:19,141,673
INFO 2026-05-28 00:07:40 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 12s. Last read position: chr1:22,910,532
INFO 2026-05-28 00:07:47 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 7s. Last read position: chr1:28,594,057
INFO 2026-05-28 00:08:00 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 13s. Last read position: chr1:35,190,817
INFO 2026-05-28 00:08:24 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 24s. Last read position: chr1:40,408,650
INFO 2026-05-28 00:08:34 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 10s. Last read position: chr1:51,271,166
INFO 2026-05-28 00:08:47 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 12s. Last read position: chr1:77,949,154
INFO 2026-05-28 00:08:59 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 12s. Last read position: chr1:100,287,153
INFO 2026-05-28 00:09:13 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 13s. Last read position: chr1:113,981,199
INFO 2026-05-28 00:09:21 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 7s. Last read position: chr1:120,557,743
INFO 2026-05-28 00:09:27 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 6s. Last read position: chr1:148,749,308
INFO 2026-05-28 00:09:34 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 6s. Last read position: chr1:150,968,476
INFO 2026-05-28 00:09:43 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 9s. Last read position: chr1:154,260,957
INFO 2026-05-28 00:10:01 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 17s. Last read position: chr1:156,134,452
INFO 2026-05-28 00:10:16 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 15s. Last read position: chr1:156,986,109
INFO 2026-05-28 00:10:29 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 12s. Last read position: chr1:165,680,658
INFO 2026-05-28 00:10:38 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 8s. Last read position: chr1:182,603,244
INFO 2026-05-28 00:10:44 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 6s. Last read position: chr1:186,313,986
INFO 2026-05-28 00:10:53 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 9s. Last read position: chr1:203,347,768
INFO 2026-05-28 00:11:01 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 7s. Last read position: chr1:222,659,785
INFO 2026-05-28 00:11:13 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 11s. Last read position: chr1:234,607,387
INFO 2026-05-28 00:11:26 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 13s. Last read position: chr2:1,663,626
INFO 2026-05-28 00:11:35 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 9s. Last read position: chr2:27,083,458
INFO 2026-05-28 00:11:46 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 10s. Last read position: chr2:32,916,374
INFO 2026-05-28 00:11:55 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 9s. Last read position: chr2:47,839,641
INFO 2026-05-28 00:12:23 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 27s. Last read position: chr2:70,214,350
INFO 2026-05-28 00:12:35 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 12s. Last read position: chr2:97,167,596
INFO 2026-05-28 00:12:49 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 13s. Last read position: chr2:110,534,559
INFO 2026-05-28 00:13:01 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 12s. Last read position: chr2:136,114,885
INFO 2026-05-28 00:13:20 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 18s. Last read position: chr2:176,093,040
INFO 2026-05-28 00:13:37 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 16s. Last read position: chr2:188,997,176
INFO 2026-05-28 00:13:53 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 16s. Last read position: chr2:189,081,034
INFO 2026-05-28 00:14:27 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 33s. Last read position: chr2:203,416,928
INFO 2026-05-28 00:14:48 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 21s. Last read position: chr2:215,372,037
INFO 2026-05-28 00:15:20 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 31s. Last read position: chr2:215,381,070
INFO 2026-05-28 00:16:08 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 47s. Last read position: chr2:215,404,548
INFO 2026-05-28 00:17:17 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 69s. Last read position: chr2:215,423,457
INFO 2026-05-28 00:18:25 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 68s. Last read position: chr2:216,663,982
INFO 2026-05-28 00:18:34 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 9s. Last read position: chr2:219,570,770
INFO 2026-05-28 00:18:50 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 15s. Last read position: chr2:237,340,559
INFO 2026-05-28 00:19:13 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 23s. Last read position: chr2:237,371,861
INFO 2026-05-28 00:19:47 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 33s. Last read position: chr2:241,229,659
INFO 2026-05-28 00:20:07 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 20s. Last read position: chr3:15,256,292
INFO 2026-05-28 00:20:24 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 17s. Last read position: chr3:42,638,246
INFO 2026-05-28 00:20:36 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 11s. Last read position: chr3:49,300,495
INFO 2026-05-28 00:20:47 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 11s. Last read position: chr3:53,288,231
INFO 2026-05-28 00:21:01 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 14s. Last read position: chr3:98,901,185
INFO 2026-05-28 00:21:14 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 13s. Last read position: chr3:122,437,181
INFO 2026-05-28 00:21:23 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 8s. Last read position: chr3:129,586,655
INFO 2026-05-28 00:21:35 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 11s. Last read position: chr3:154,305,123
INFO 2026-05-28 00:21:48 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 12s. Last read position: chr3:184,316,147
INFO 2026-05-28 00:22:08 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 20s. Last read position: chr4:1,171,073
INFO 2026-05-28 00:22:21 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 12s. Last read position: chr4:41,935,519
INFO 2026-05-28 00:22:33 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 12s. Last read position: chr4:84,735,071
INFO 2026-05-28 00:22:49 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 15s. Last read position: chr4:122,224,554
INFO 2026-05-28 00:22:59 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 10s. Last read position: chr4:182,755,041
INFO 2026-05-28 00:23:11 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 11s. Last read position: chr5:14,461,281
INFO 2026-05-28 00:23:27 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 16s. Last read position: chr5:52,929,673
INFO 2026-05-28 00:23:36 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 9s. Last read position: chr5:80,040,183
INFO 2026-05-28 00:23:50 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 13s. Last read position: chr5:102,990,270
INFO 2026-05-28 00:24:02 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 11s. Last read position: chr5:138,431,533
INFO 2026-05-28 00:24:10 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 7s. Last read position: chr5:142,315,001
INFO 2026-05-28 00:24:18 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 8s. Last read position: chr5:150,132,814
INFO 2026-05-28 00:24:27 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:17:31s. Time for last 1,000,000: 9s. Last read position: chr5:151,799,991
INFO 2026-05-28 00:24:40 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:17:43s. Time for last 1,000,000: 12s. Last read position: chr5:177,458,253
INFO 2026-05-28 00:24:56 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 16s. Last read position: chr6:3,153,965
INFO 2026-05-28 00:25:01 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:18:04s. Time for last 1,000,000: 5s. Last read position: chr6:26,451,676
INFO 2026-05-28 00:25:06 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 5s. Last read position: chr6:31,354,124
INFO 2026-05-28 00:25:13 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:18:17s. Time for last 1,000,000: 7s. Last read position: chr6:31,828,250
INFO 2026-05-28 00:25:20 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 6s. Last read position: chr6:33,320,735
INFO 2026-05-28 00:25:29 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:18:32s. Time for last 1,000,000: 9s. Last read position: chr6:43,224,250
INFO 2026-05-28 00:25:50 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 21s. Last read position: chr6:75,102,689
INFO 2026-05-28 00:26:09 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 18s. Last read position: chr6:107,635,231
INFO 2026-05-28 00:26:20 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 11s. Last read position: chr6:132,297,109
INFO 2026-05-28 00:26:36 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:19:39s. Time for last 1,000,000: 16s. Last read position: chr6:156,778,516
INFO 2026-05-28 00:26:49 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:19:52s. Time for last 1,000,000: 12s. Last read position: chr7:259,759
INFO 2026-05-28 00:26:57 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:20:01s. Time for last 1,000,000: 8s. Last read position: chr7:5,527,674
INFO 2026-05-28 00:27:06 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:20:09s. Time for last 1,000,000: 8s. Last read position: chr7:16,406,063
INFO 2026-05-28 00:27:22 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:20:25s. Time for last 1,000,000: 15s. Last read position: chr7:39,951,810
INFO 2026-05-28 00:27:30 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:20:33s. Time for last 1,000,000: 8s. Last read position: chr7:54,755,805
INFO 2026-05-28 00:27:38 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:20:41s. Time for last 1,000,000: 7s. Last read position: chr7:76,048,213
INFO 2026-05-28 00:27:53 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:20:56s. Time for last 1,000,000: 15s. Last read position: chr7:94,409,764
INFO 2026-05-28 00:28:11 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:21:15s. Time for last 1,000,000: 18s. Last read position: chr7:98,990,478
INFO 2026-05-28 00:28:19 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:21:23s. Time for last 1,000,000: 8s. Last read position: chr7:102,653,459
INFO 2026-05-28 00:28:45 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:21:48s. Time for last 1,000,000: 25s. Last read position: chr7:128,609,540
INFO 2026-05-28 00:28:54 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 9s. Last read position: chr7:149,019,120
INFO 2026-05-28 00:29:14 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:22:17s. Time for last 1,000,000: 19s. Last read position: chr8:13,499,808
INFO 2026-05-28 00:29:24 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:22:27s. Time for last 1,000,000: 10s. Last read position: chr8:26,655,646
INFO 2026-05-28 00:29:45 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:22:48s. Time for last 1,000,000: 20s. Last read position: chr8:41,620,972
INFO 2026-05-28 00:29:57 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:23:00s. Time for last 1,000,000: 12s. Last read position: chr8:73,292,241
INFO 2026-05-28 00:30:11 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:23:14s. Time for last 1,000,000: 13s. Last read position: chr8:103,375,766
INFO 2026-05-28 00:30:25 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:23:28s. Time for last 1,000,000: 13s. Last read position: chr8:143,559,430
INFO 2026-05-28 00:30:38 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:23:41s. Time for last 1,000,000: 13s. Last read position: chr8:144,443,994
INFO 2026-05-28 00:30:51 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:23:54s. Time for last 1,000,000: 12s. Last read position: chr9:35,548,192
INFO 2026-05-28 00:31:00 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:24:03s. Time for last 1,000,000: 8s. Last read position: chr9:96,937,069
INFO 2026-05-28 00:31:13 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:24:17s. Time for last 1,000,000: 13s. Last read position: chr9:121,135,874
INFO 2026-05-28 00:31:27 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:24:30s. Time for last 1,000,000: 13s. Last read position: chr9:128,591,559
INFO 2026-05-28 00:31:37 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:24:41s. Time for last 1,000,000: 10s. Last read position: chr9:134,754,310
INFO 2026-05-28 00:31:54 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:24:57s. Time for last 1,000,000: 16s. Last read position: chr10:472,488
INFO 2026-05-28 00:32:04 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:25:07s. Time for last 1,000,000: 10s. Last read position: chr10:32,910,348
INFO 2026-05-28 00:32:16 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:25:19s. Time for last 1,000,000: 12s. Last read position: chr10:72,275,020
INFO 2026-05-28 00:32:27 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:25:30s. Time for last 1,000,000: 10s. Last read position: chr10:97,441,198
INFO 2026-05-28 00:32:38 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:25:41s. Time for last 1,000,000: 11s. Last read position: chr10:126,996,801
INFO 2026-05-28 00:32:47 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:25:50s. Time for last 1,000,000: 9s. Last read position: chr11:1,753,629
INFO 2026-05-28 00:32:54 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:25:57s. Time for last 1,000,000: 6s. Last read position: chr11:2,971,458
INFO 2026-05-28 00:33:09 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:26:12s. Time for last 1,000,000: 15s. Last read position: chr11:16,974,713
INFO 2026-05-28 00:33:21 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:26:24s. Time for last 1,000,000: 11s. Last read position: chr11:47,157,063
INFO 2026-05-28 00:33:35 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:26:38s. Time for last 1,000,000: 14s. Last read position: chr11:62,374,839
INFO 2026-05-28 00:33:44 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:26:47s. Time for last 1,000,000: 8s. Last read position: chr11:64,860,021
INFO 2026-05-28 00:33:55 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:26:58s. Time for last 1,000,000: 10s. Last read position: chr11:66,315,688
INFO 2026-05-28 00:34:08 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:27:11s. Time for last 1,000,000: 12s. Last read position: chr11:72,015,894
INFO 2026-05-28 00:34:21 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:27:24s. Time for last 1,000,000: 13s. Last read position: chr11:86,022,404
INFO 2026-05-28 00:34:32 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:27:36s. Time for last 1,000,000: 11s. Last read position: chr11:117,394,950
INFO 2026-05-28 00:34:44 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:27:47s. Time for last 1,000,000: 11s. Last read position: chr11:128,694,184
INFO 2026-05-28 00:35:01 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:28:04s. Time for last 1,000,000: 16s. Last read position: chr12:6,514,780
INFO 2026-05-28 00:35:21 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:28:24s. Time for last 1,000,000: 19s. Last read position: chr12:9,069,768
INFO 2026-05-28 00:35:29 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:28:33s. Time for last 1,000,000: 8s. Last read position: chr12:22,625,465
INFO 2026-05-28 00:35:41 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:28:44s. Time for last 1,000,000: 11s. Last read position: chr12:49,040,804
INFO 2026-05-28 00:35:50 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:28:53s. Time for last 1,000,000: 8s. Last read position: chr12:52,014,707
INFO 2026-05-28 00:36:04 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:29:07s. Time for last 1,000,000: 14s. Last read position: chr12:54,283,036
INFO 2026-05-28 00:36:17 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:29:20s. Time for last 1,000,000: 13s. Last read position: chr12:56,688,022
INFO 2026-05-28 00:36:30 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:29:33s. Time for last 1,000,000: 12s. Last read position: chr12:57,206,531
INFO 2026-05-28 00:36:44 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:29:47s. Time for last 1,000,000: 13s. Last read position: chr12:67,657,219
INFO 2026-05-28 00:36:55 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:29:59s. Time for last 1,000,000: 11s. Last read position: chr12:93,378,173
INFO 2026-05-28 00:37:12 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:30:15s. Time for last 1,000,000: 16s. Last read position: chr12:109,852,684
INFO 2026-05-28 00:37:29 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:30:32s. Time for last 1,000,000: 17s. Last read position: chr12:118,411,082
INFO 2026-05-28 00:37:41 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:30:44s. Time for last 1,000,000: 12s. Last read position: chr12:124,343,101
INFO 2026-05-28 00:37:55 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:30:58s. Time for last 1,000,000: 13s. Last read position: chr13:20,064,515
INFO 2026-05-28 00:38:04 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:31:07s. Time for last 1,000,000: 9s. Last read position: chr13:37,579,033
INFO 2026-05-28 00:38:15 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:31:18s. Time for last 1,000,000: 10s. Last read position: chr13:51,395,300
INFO 2026-05-28 00:38:28 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:31:31s. Time for last 1,000,000: 13s. Last read position: chr13:102,865,796
INFO 2026-05-28 00:38:42 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:31:45s. Time for last 1,000,000: 14s. Last read position: chr13:110,492,113
INFO 2026-05-28 00:38:54 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:31:57s. Time for last 1,000,000: 11s. Last read position: chr14:22,924,109
INFO 2026-05-28 00:39:06 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:32:09s. Time for last 1,000,000: 12s. Last read position: chr14:52,014,389
INFO 2026-05-28 00:39:19 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:32:22s. Time for last 1,000,000: 12s. Last read position: chr14:74,611,559
INFO 2026-05-28 00:39:31 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:32:35s. Time for last 1,000,000: 12s. Last read position: chr14:102,002,543
INFO 2026-05-28 00:40:15 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:33:18s. Time for last 1,000,000: 43s. Last read position: chr15:32,602,572
INFO 2026-05-28 00:40:24 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:33:27s. Time for last 1,000,000: 9s. Last read position: chr15:43,765,925
INFO 2026-05-28 00:40:35 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:33:38s. Time for last 1,000,000: 11s. Last read position: chr15:58,717,622
INFO 2026-05-28 00:40:47 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:33:51s. Time for last 1,000,000: 12s. Last read position: chr15:70,096,848
INFO 2026-05-28 00:40:58 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:34:01s. Time for last 1,000,000: 10s. Last read position: chr15:75,356,169
INFO 2026-05-28 00:41:08 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:34:11s. Time for last 1,000,000: 10s. Last read position: chr15:85,723,300
INFO 2026-05-28 00:41:19 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:34:22s. Time for last 1,000,000: 10s. Last read position: chr16:367,605
INFO 2026-05-28 00:41:39 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:34:42s. Time for last 1,000,000: 19s. Last read position: chr16:2,528,365
INFO 2026-05-28 00:41:52 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:34:55s. Time for last 1,000,000: 13s. Last read position: chr16:11,440,964
INFO 2026-05-28 00:41:59 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:35:02s. Time for last 1,000,000: 6s. Last read position: chr16:16,369,047
INFO 2026-05-28 00:42:03 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:35:07s. Time for last 1,000,000: 4s. Last read position: chr16:21,857,319
INFO 2026-05-28 00:42:11 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:35:15s. Time for last 1,000,000: 8s. Last read position: chr16:29,485,456
INFO 2026-05-28 00:42:19 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:35:23s. Time for last 1,000,000: 8s. Last read position: chr16:31,064,428
INFO 2026-05-28 00:42:31 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:35:34s. Time for last 1,000,000: 11s. Last read position: chr16:58,543,854
INFO 2026-05-28 00:42:43 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:35:47s. Time for last 1,000,000: 12s. Last read position: chr16:71,449,647
INFO 2026-05-28 00:42:51 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:35:55s. Time for last 1,000,000: 7s. Last read position: chr16:88,586,621
INFO 2026-05-28 00:43:06 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:36:09s. Time for last 1,000,000: 14s. Last read position: chr17:1,777,294
INFO 2026-05-28 00:43:17 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:36:20s. Time for last 1,000,000: 11s. Last read position: chr17:7,316,218
INFO 2026-05-28 00:43:27 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:36:31s. Time for last 1,000,000: 10s. Last read position: chr17:15,704,559
INFO 2026-05-28 00:43:38 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:36:42s. Time for last 1,000,000: 10s. Last read position: chr17:28,674,390
INFO 2026-05-28 00:43:51 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:36:54s. Time for last 1,000,000: 12s. Last read position: chr17:38,257,049
INFO 2026-05-28 00:44:00 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:37:03s. Time for last 1,000,000: 9s. Last read position: chr17:42,022,375
INFO 2026-05-28 00:44:16 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:37:19s. Time for last 1,000,000: 15s. Last read position: chr17:45,514,923
INFO 2026-05-28 00:44:25 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:37:28s. Time for last 1,000,000: 8s. Last read position: chr17:50,186,324
INFO 2026-05-28 00:44:31 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:37:34s. Time for last 1,000,000: 6s. Last read position: chr17:50,188,547
INFO 2026-05-28 00:44:37 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:37:41s. Time for last 1,000,000: 6s. Last read position: chr17:50,189,862
INFO 2026-05-28 00:44:45 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:37:48s. Time for last 1,000,000: 7s. Last read position: chr17:50,191,979
INFO 2026-05-28 00:44:54 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:37:57s. Time for last 1,000,000: 8s. Last read position: chr17:50,194,376
INFO 2026-05-28 00:45:04 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:38:07s. Time for last 1,000,000: 10s. Last read position: chr17:50,195,927
INFO 2026-05-28 00:45:16 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:38:19s. Time for last 1,000,000: 11s. Last read position: chr17:50,197,745
INFO 2026-05-28 00:45:30 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:38:33s. Time for last 1,000,000: 13s. Last read position: chr17:50,966,207
INFO 2026-05-28 00:45:40 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:38:43s. Time for last 1,000,000: 10s. Last read position: chr17:62,680,288
INFO 2026-05-28 00:45:53 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:38:56s. Time for last 1,000,000: 13s. Last read position: chr17:73,235,614
INFO 2026-05-28 00:46:05 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:39:08s. Time for last 1,000,000: 11s. Last read position: chr17:79,796,298
INFO 2026-05-28 00:46:27 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:39:30s. Time for last 1,000,000: 22s. Last read position: chr17:82,010,856
INFO 2026-05-28 00:46:39 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:39:43s. Time for last 1,000,000: 12s. Last read position: chr18:23,136,529
INFO 2026-05-28 00:47:03 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:40:06s. Time for last 1,000,000: 23s. Last read position: chr18:62,157,780
INFO 2026-05-28 00:47:12 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:40:15s. Time for last 1,000,000: 9s. Last read position: chr19:1,440,232
INFO 2026-05-28 00:47:19 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:40:22s. Time for last 1,000,000: 7s. Last read position: chr19:4,659,994
INFO 2026-05-28 00:47:29 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:40:32s. Time for last 1,000,000: 9s. Last read position: chr19:10,115,064
INFO 2026-05-28 00:47:48 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:40:52s. Time for last 1,000,000: 19s. Last read position: chr19:12,628,079
INFO 2026-05-28 00:47:58 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:41:01s. Time for last 1,000,000: 9s. Last read position: chr19:15,113,851
INFO 2026-05-28 00:48:08 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:41:11s. Time for last 1,000,000: 10s. Last read position: chr19:17,423,790
INFO 2026-05-28 00:48:15 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:41:18s. Time for last 1,000,000: 6s. Last read position: chr19:21,033,571
INFO 2026-05-28 00:48:24 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:41:27s. Time for last 1,000,000: 9s. Last read position: chr19:39,389,647
INFO 2026-05-28 00:48:36 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:41:39s. Time for last 1,000,000: 12s. Last read position: chr19:42,250,500
INFO 2026-05-28 00:48:45 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:41:48s. Time for last 1,000,000: 9s. Last read position: chr19:45,785,822
INFO 2026-05-28 00:48:52 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:41:56s. Time for last 1,000,000: 7s. Last read position: chr19:49,336,928
INFO 2026-05-28 00:49:01 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 8s. Last read position: chr19:53,576,793
INFO 2026-05-28 00:49:07 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:42:10s. Time for last 1,000,000: 6s. Last read position: chr19:58,129,053
INFO 2026-05-28 00:49:15 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:42:18s. Time for last 1,000,000: 8s. Last read position: chr20:17,635,599
INFO 2026-05-28 00:49:26 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:42:29s. Time for last 1,000,000: 10s. Last read position: chr20:35,632,681
INFO 2026-05-28 00:49:39 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:42:42s. Time for last 1,000,000: 12s. Last read position: chr20:46,011,577
INFO 2026-05-28 00:49:44 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:42:48s. Time for last 1,000,000: 5s. Last read position: chr20:57,709,851
INFO 2026-05-28 00:50:07 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:43:10s. Time for last 1,000,000: 22s. Last read position: chr20:62,956,806
INFO 2026-05-28 00:50:11 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:43:14s. Time for last 1,000,000: 4s. Last read position: chr21:8,444,612
INFO 2026-05-28 00:50:24 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:43:28s. Time for last 1,000,000: 13s. Last read position: chr21:43,959,838
INFO 2026-05-28 00:50:32 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:43:36s. Time for last 1,000,000: 7s. Last read position: chr21:45,997,472
INFO 2026-05-28 00:50:42 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:43:45s. Time for last 1,000,000: 9s. Last read position: chr21:46,118,620
INFO 2026-05-28 00:50:55 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:43:58s. Time for last 1,000,000: 13s. Last read position: chr22:20,117,596
INFO 2026-05-28 00:51:07 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:44:10s. Time for last 1,000,000: 11s. Last read position: chr22:31,715,122
INFO 2026-05-28 00:51:15 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:44:18s. Time for last 1,000,000: 8s. Last read position: chr22:41,252,894
INFO 2026-05-28 00:51:23 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:44:26s. Time for last 1,000,000: 8s. Last read position: chrX:2,723,324
INFO 2026-05-28 00:51:30 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:44:33s. Time for last 1,000,000: 6s. Last read position: chrX:40,071,019
INFO 2026-05-28 00:51:47 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:44:50s. Time for last 1,000,000: 17s. Last read position: chrX:49,039,188
INFO 2026-05-28 00:52:00 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:45:03s. Time for last 1,000,000: 12s. Last read position: chrX:55,452,971
INFO 2026-05-28 00:52:12 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:45:15s. Time for last 1,000,000: 12s. Last read position: chrX:78,125,994
INFO 2026-05-28 00:52:19 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:45:22s. Time for last 1,000,000: 6s. Last read position: chrX:119,873,357
INFO 2026-05-28 00:52:30 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:45:33s. Time for last 1,000,000: 10s. Last read position: chrX:153,956,358
INFO 2026-05-28 00:52:43 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:45:47s. Time for last 1,000,000: 13s. Last read position: KI270727.1:22,198
INFO 2026-05-28 00:52:44 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:45:47s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:52:46 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 45.86 minutes.
Runtime.totalMemory()=3358588928