Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ctat_ref_annot.interval_list
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/53a695275ecc63738686f29c2419f5/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/fcd38962fda4458dbd8f7135f6eb99/659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/02bbba86886b5c435d9b413719b0b9/659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/53a695275ecc63738686f29c2419f5/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
==> STAGING COMPLETE (6 inputs)
/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 12:02:33 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 00:02:33 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bNS-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 00:02:33 GMT 2026] Executing as ?@nf-ca53a695275ecc63738686f29c2419f5-b5d13-lr6tv 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.XXXXefH5Li/659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXefH5Li/659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:02:36 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:02:49 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: chr1:6,233,629
INFO 2026-05-28 00:03:02 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 12s. Last read position: chr1:16,205,569
INFO 2026-05-28 00:03:18 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 15s. Last read position: chr1:21,874,933
INFO 2026-05-28 00:03:29 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 11s. Last read position: chr1:27,113,933
INFO 2026-05-28 00:03:44 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 15s. Last read position: chr1:33,329,092
INFO 2026-05-28 00:04:33 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 48s. Last read position: chr1:40,304,836
INFO 2026-05-28 00:04:49 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 16s. Last read position: chr1:52,032,682
INFO 2026-05-28 00:05:03 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 13s. Last read position: chr1:89,054,752
INFO 2026-05-28 00:05:18 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 15s. Last read position: chr1:113,659,137
INFO 2026-05-28 00:05:29 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 10s. Last read position: chr1:145,994,607
INFO 2026-05-28 00:05:38 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 9s. Last read position: chr1:150,579,034
INFO 2026-05-28 00:05:50 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 12s. Last read position: chr1:154,170,419
INFO 2026-05-28 00:06:09 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 18s. Last read position: chr1:155,189,696
INFO 2026-05-28 00:06:30 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 20s. Last read position: chr1:156,138,640
INFO 2026-05-28 00:06:44 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 13s. Last read position: chr1:161,542,804
INFO 2026-05-28 00:06:51 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 7s. Last read position: chr1:180,824,915
INFO 2026-05-28 00:07:02 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 10s. Last read position: chr1:201,484,583
INFO 2026-05-28 00:07:11 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 9s. Last read position: chr1:207,021,933
INFO 2026-05-28 00:07:18 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 7s. Last read position: chr1:223,712,785
INFO 2026-05-28 00:07:35 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 17s. Last read position: chr1:229,495,536
INFO 2026-05-28 00:07:47 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 11s. Last read position: chr2:3,354,550
INFO 2026-05-28 00:07:56 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 8s. Last read position: chr2:28,776,861
INFO 2026-05-28 00:08:01 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 5s. Last read position: chr2:32,916,406
INFO 2026-05-28 00:08:09 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 7s. Last read position: chr2:47,162,617
INFO 2026-05-28 00:08:28 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 19s. Last read position: chr2:70,835,503
INFO 2026-05-28 00:08:38 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 10s. Last read position: chr2:85,663,371
INFO 2026-05-28 00:08:46 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 7s. Last read position: chr2:88,788,441
INFO 2026-05-28 00:08:54 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 8s. Last read position: chr2:110,547,166
INFO 2026-05-28 00:09:04 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 9s. Last read position: chr2:156,568,914
INFO 2026-05-28 00:09:25 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 20s. Last read position: chr2:188,985,238
INFO 2026-05-28 00:09:39 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 14s. Last read position: chr2:197,497,262
INFO 2026-05-28 00:09:56 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 16s. Last read position: chr2:215,372,159
INFO 2026-05-28 00:10:36 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 40s. Last read position: chr2:215,404,552
INFO 2026-05-28 00:12:03 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 86s. Last read position: chr2:216,190,301
INFO 2026-05-28 00:12:19 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 15s. Last read position: chr2:230,417,610
INFO 2026-05-28 00:12:44 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 25s. Last read position: chr2:240,568,922
INFO 2026-05-28 00:13:01 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 16s. Last read position: chr3:14,135,747
INFO 2026-05-28 00:13:14 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 13s. Last read position: chr3:41,199,650
INFO 2026-05-28 00:13:35 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 21s. Last read position: chr3:49,016,499
INFO 2026-05-28 00:13:53 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 17s. Last read position: chr3:52,229,376
INFO 2026-05-28 00:14:19 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 26s. Last read position: chr3:93,874,366
INFO 2026-05-28 00:14:34 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 15s. Last read position: chr3:123,657,186
INFO 2026-05-28 00:14:49 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 14s. Last read position: chr3:136,002,349
INFO 2026-05-28 00:15:02 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 13s. Last read position: chr3:170,163,924
INFO 2026-05-28 00:15:24 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 22s. Last read position: chr3:188,609,794
INFO 2026-05-28 00:15:41 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 16s. Last read position: chr4:1,366,364
INFO 2026-05-28 00:15:56 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 14s. Last read position: chr4:22,515,491
INFO 2026-05-28 00:16:02 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 6s. Last read position: chr4:25,670,784
INFO 2026-05-28 00:16:12 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 10s. Last read position: chr4:25,676,548
INFO 2026-05-28 00:16:28 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 15s. Last read position: chr4:56,911,415
INFO 2026-05-28 00:16:43 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 15s. Last read position: chr4:87,480,495
INFO 2026-05-28 00:16:59 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 16s. Last read position: chr4:122,258,757
INFO 2026-05-28 00:17:14 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 15s. Last read position: chr4:168,877,870
INFO 2026-05-28 00:17:24 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 9s. Last read position: chr5:9,066,531
INFO 2026-05-28 00:17:41 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 17s. Last read position: chr5:40,680,996
INFO 2026-05-28 00:17:52 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:15:16s. Time for last 1,000,000: 10s. Last read position: chr5:70,475,545
INFO 2026-05-28 00:18:02 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 10s. Last read position: chr5:90,399,379
INFO 2026-05-28 00:18:22 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 19s. Last read position: chr5:132,557,300
INFO 2026-05-28 00:18:33 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 11s. Last read position: chr5:139,481,563
INFO 2026-05-28 00:18:45 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 11s. Last read position: chr5:147,405,667
INFO 2026-05-28 00:18:56 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 11s. Last read position: chr5:150,404,691
INFO 2026-05-28 00:19:08 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 11s. Last read position: chr5:150,648,937
INFO 2026-05-28 00:19:19 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 11s. Last read position: chr5:170,383,732
INFO 2026-05-28 00:19:36 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 17s. Last read position: chr5:177,332,202
INFO 2026-05-28 00:19:54 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 18s. Last read position: chr5:179,836,554
INFO 2026-05-28 00:20:04 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 9s. Last read position: chr6:7,246,635
INFO 2026-05-28 00:20:10 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:17:34s. Time for last 1,000,000: 6s. Last read position: chr6:29,889,392
INFO 2026-05-28 00:20:18 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 7s. Last read position: chr6:31,636,254
INFO 2026-05-28 00:20:29 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 10s. Last read position: chr6:32,068,498
INFO 2026-05-28 00:20:38 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:18:02s. Time for last 1,000,000: 9s. Last read position: chr6:33,205,692
INFO 2026-05-28 00:20:45 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 7s. Last read position: chr6:41,789,269
INFO 2026-05-28 00:21:06 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:18:30s. Time for last 1,000,000: 21s. Last read position: chr6:71,288,907
INFO 2026-05-28 00:21:23 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:18:47s. Time for last 1,000,000: 16s. Last read position: chr6:117,383,315
INFO 2026-05-28 00:21:34 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:18:58s. Time for last 1,000,000: 11s. Last read position: chr6:151,807,926
INFO 2026-05-28 00:21:56 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 22s. Last read position: chr7:1,470,939
INFO 2026-05-28 00:22:06 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 9s. Last read position: chr7:5,529,390
INFO 2026-05-28 00:22:19 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 12s. Last read position: chr7:40,133,100
INFO 2026-05-28 00:22:29 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:19:52s. Time for last 1,000,000: 9s. Last read position: chr7:56,104,281
INFO 2026-05-28 00:22:42 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:20:06s. Time for last 1,000,000: 13s. Last read position: chr7:76,302,950
INFO 2026-05-28 00:23:05 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:20:28s. Time for last 1,000,000: 22s. Last read position: chr7:94,424,424
INFO 2026-05-28 00:23:19 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:20:42s. Time for last 1,000,000: 14s. Last read position: chr7:100,873,275
INFO 2026-05-28 00:23:34 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:20:58s. Time for last 1,000,000: 15s. Last read position: chr7:121,351,201
INFO 2026-05-28 00:23:45 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:21:09s. Time for last 1,000,000: 11s. Last read position: chr7:142,546,364
INFO 2026-05-28 00:23:57 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:21:21s. Time for last 1,000,000: 12s. Last read position: chr7:158,945,720
INFO 2026-05-28 00:24:17 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:21:41s. Time for last 1,000,000: 19s. Last read position: chr8:22,164,025
INFO 2026-05-28 00:24:27 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:21:51s. Time for last 1,000,000: 9s. Last read position: chr8:37,844,658
INFO 2026-05-28 00:24:46 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:22:10s. Time for last 1,000,000: 19s. Last read position: chr8:55,950,712
INFO 2026-05-28 00:24:57 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:22:21s. Time for last 1,000,000: 11s. Last read position: chr8:97,825,134
INFO 2026-05-28 00:25:18 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:22:42s. Time for last 1,000,000: 21s. Last read position: chr8:125,267,567
INFO 2026-05-28 00:25:32 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:22:56s. Time for last 1,000,000: 14s. Last read position: chr8:143,859,105
INFO 2026-05-28 00:25:42 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:23:06s. Time for last 1,000,000: 9s. Last read position: chr8:144,106,372
INFO 2026-05-28 00:25:55 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:23:19s. Time for last 1,000,000: 13s. Last read position: chr9:32,544,108
INFO 2026-05-28 00:26:05 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:23:29s. Time for last 1,000,000: 9s. Last read position: chr9:72,355,979
INFO 2026-05-28 00:26:14 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:23:38s. Time for last 1,000,000: 9s. Last read position: chr9:101,540,898
INFO 2026-05-28 00:26:29 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:23:53s. Time for last 1,000,000: 14s. Last read position: chr9:121,096,477
INFO 2026-05-28 00:26:41 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:24:05s. Time for last 1,000,000: 11s. Last read position: chr9:128,582,723
INFO 2026-05-28 00:26:53 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:24:17s. Time for last 1,000,000: 12s. Last read position: chr9:133,561,268
INFO 2026-05-28 00:27:07 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:24:31s. Time for last 1,000,000: 14s. Last read position: chr9:137,180,199
INFO 2026-05-28 00:27:18 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:24:41s. Time for last 1,000,000: 10s. Last read position: chr10:24,533,112
INFO 2026-05-28 00:27:30 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:24:54s. Time for last 1,000,000: 12s. Last read position: chr10:49,458,940
INFO 2026-05-28 00:27:41 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:25:05s. Time for last 1,000,000: 10s. Last read position: chr10:73,792,808
INFO 2026-05-28 00:27:50 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:25:14s. Time for last 1,000,000: 9s. Last read position: chr10:79,559,434
INFO 2026-05-28 00:27:56 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:25:20s. Time for last 1,000,000: 5s. Last read position: chr10:93,347,754
INFO 2026-05-28 00:28:11 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:25:34s. Time for last 1,000,000: 14s. Last read position: chr10:104,314,982
INFO 2026-05-28 00:28:34 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:25:58s. Time for last 1,000,000: 23s. Last read position: chr10:122,643,183
INFO 2026-05-28 00:28:44 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:26:08s. Time for last 1,000,000: 9s. Last read position: chr11:500,641
INFO 2026-05-28 00:28:54 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:26:18s. Time for last 1,000,000: 10s. Last read position: chr11:1,242,193
INFO 2026-05-28 00:29:00 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:26:24s. Time for last 1,000,000: 5s. Last read position: chr11:1,246,858
INFO 2026-05-28 00:29:07 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:26:31s. Time for last 1,000,000: 7s. Last read position: chr11:1,252,417
INFO 2026-05-28 00:29:19 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 12s. Last read position: chr11:2,928,516
INFO 2026-05-28 00:29:35 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:26:58s. Time for last 1,000,000: 15s. Last read position: chr11:12,221,616
INFO 2026-05-28 00:29:46 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:27:09s. Time for last 1,000,000: 10s. Last read position: chr11:44,605,108
INFO 2026-05-28 00:29:57 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:27:20s. Time for last 1,000,000: 11s. Last read position: chr11:57,795,663
INFO 2026-05-28 00:30:10 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:27:34s. Time for last 1,000,000: 13s. Last read position: chr11:62,527,850
INFO 2026-05-28 00:30:18 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:27:42s. Time for last 1,000,000: 8s. Last read position: chr11:64,261,496
INFO 2026-05-28 00:30:29 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:27:53s. Time for last 1,000,000: 11s. Last read position: chr11:65,647,408
INFO 2026-05-28 00:30:40 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:28:04s. Time for last 1,000,000: 11s. Last read position: chr11:67,585,173
INFO 2026-05-28 00:30:56 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:28:20s. Time for last 1,000,000: 15s. Last read position: chr11:72,781,097
INFO 2026-05-28 00:31:08 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:28:31s. Time for last 1,000,000: 11s. Last read position: chr11:95,838,142
INFO 2026-05-28 00:31:17 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:28:41s. Time for last 1,000,000: 9s. Last read position: chr11:118,407,039
INFO 2026-05-28 00:31:29 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:28:53s. Time for last 1,000,000: 11s. Last read position: chr11:126,266,193
INFO 2026-05-28 00:31:42 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:29:06s. Time for last 1,000,000: 13s. Last read position: chr12:6,018,740
INFO 2026-05-28 00:32:01 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:29:24s. Time for last 1,000,000: 18s. Last read position: chr12:7,086,400
INFO 2026-05-28 00:32:09 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:29:32s. Time for last 1,000,000: 7s. Last read position: chr12:14,882,126
INFO 2026-05-28 00:32:27 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:29:51s. Time for last 1,000,000: 18s. Last read position: chr12:47,785,783
INFO 2026-05-28 00:32:38 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:30:02s. Time for last 1,000,000: 11s. Last read position: chr12:51,975,329
INFO 2026-05-28 00:32:52 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:30:16s. Time for last 1,000,000: 13s. Last read position: chr12:54,281,918
INFO 2026-05-28 00:33:07 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:30:31s. Time for last 1,000,000: 14s. Last read position: chr12:56,712,448
INFO 2026-05-28 00:33:23 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:30:47s. Time for last 1,000,000: 16s. Last read position: chr12:57,546,057
INFO 2026-05-28 00:33:36 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:31:00s. Time for last 1,000,000: 12s. Last read position: chr12:91,108,305
INFO 2026-05-28 00:33:47 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:31:11s. Time for last 1,000,000: 11s. Last read position: chr12:109,179,283
INFO 2026-05-28 00:34:01 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:31:25s. Time for last 1,000,000: 13s. Last read position: chr12:119,712,228
INFO 2026-05-28 00:34:14 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:31:38s. Time for last 1,000,000: 12s. Last read position: chr12:124,346,593
INFO 2026-05-28 00:34:26 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:31:49s. Time for last 1,000,000: 11s. Last read position: chr13:28,177,921
INFO 2026-05-28 00:34:35 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:31:59s. Time for last 1,000,000: 9s. Last read position: chr13:75,530,193
INFO 2026-05-28 00:34:52 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:32:16s. Time for last 1,000,000: 16s. Last read position: chr13:110,512,086
INFO 2026-05-28 00:35:05 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:32:29s. Time for last 1,000,000: 13s. Last read position: chr14:23,063,549
INFO 2026-05-28 00:35:19 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:32:42s. Time for last 1,000,000: 13s. Last read position: chr14:49,583,642
INFO 2026-05-28 00:35:39 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:33:02s. Time for last 1,000,000: 19s. Last read position: chr14:67,279,436
INFO 2026-05-28 00:35:51 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:33:15s. Time for last 1,000,000: 12s. Last read position: chr14:74,809,530
INFO 2026-05-28 00:35:59 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:33:23s. Time for last 1,000,000: 8s. Last read position: chr14:94,768,440
INFO 2026-05-28 00:36:49 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:34:13s. Time for last 1,000,000: 49s. Last read position: chr14:104,940,716
INFO 2026-05-28 00:37:00 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:34:24s. Time for last 1,000,000: 11s. Last read position: chr15:29,708,812
INFO 2026-05-28 00:37:10 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:34:34s. Time for last 1,000,000: 9s. Last read position: chr15:43,456,482
INFO 2026-05-28 00:37:22 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:34:46s. Time for last 1,000,000: 12s. Last read position: chr15:60,355,939
INFO 2026-05-28 00:37:36 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:35:00s. Time for last 1,000,000: 14s. Last read position: chr15:72,375,760
INFO 2026-05-28 00:37:50 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:35:14s. Time for last 1,000,000: 13s. Last read position: chr15:82,372,352
INFO 2026-05-28 00:38:02 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:35:26s. Time for last 1,000,000: 11s. Last read position: chr15:92,942,842
INFO 2026-05-28 00:38:12 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:35:36s. Time for last 1,000,000: 10s. Last read position: chr16:1,778,164
INFO 2026-05-28 00:38:32 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:35:56s. Time for last 1,000,000: 19s. Last read position: chr16:4,114,743
INFO 2026-05-28 00:38:44 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:36:08s. Time for last 1,000,000: 11s. Last read position: chr16:15,708,805
INFO 2026-05-28 00:38:54 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:36:18s. Time for last 1,000,000: 9s. Last read position: chr16:21,423,936
INFO 2026-05-28 00:39:02 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:36:26s. Time for last 1,000,000: 8s. Last read position: chr16:28,905,709
INFO 2026-05-28 00:39:10 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:36:34s. Time for last 1,000,000: 8s. Last read position: chr16:30,738,009
INFO 2026-05-28 00:39:19 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:36:43s. Time for last 1,000,000: 8s. Last read position: chr16:56,609,287
INFO 2026-05-28 00:39:32 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:36:56s. Time for last 1,000,000: 13s. Last read position: chr16:68,230,394
INFO 2026-05-28 00:39:44 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:37:08s. Time for last 1,000,000: 11s. Last read position: chr16:75,640,332
INFO 2026-05-28 00:39:54 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:37:18s. Time for last 1,000,000: 10s. Last read position: chr17:247,181
INFO 2026-05-28 00:40:08 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:37:32s. Time for last 1,000,000: 13s. Last read position: chr17:4,739,438
INFO 2026-05-28 00:40:18 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:37:42s. Time for last 1,000,000: 10s. Last read position: chr17:7,845,659
INFO 2026-05-28 00:40:31 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:37:54s. Time for last 1,000,000: 12s. Last read position: chr17:17,796,602
INFO 2026-05-28 00:40:43 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:38:07s. Time for last 1,000,000: 12s. Last read position: chr17:30,379,667
INFO 2026-05-28 00:40:53 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:38:17s. Time for last 1,000,000: 10s. Last read position: chr17:39,201,221
INFO 2026-05-28 00:41:11 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:38:35s. Time for last 1,000,000: 17s. Last read position: chr17:42,405,207
INFO 2026-05-28 00:41:22 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:38:46s. Time for last 1,000,000: 10s. Last read position: chr17:47,838,290
INFO 2026-05-28 00:41:28 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:38:52s. Time for last 1,000,000: 6s. Last read position: chr17:50,187,945
INFO 2026-05-28 00:41:35 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:38:59s. Time for last 1,000,000: 6s. Last read position: chr17:50,190,096
INFO 2026-05-28 00:41:43 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:39:07s. Time for last 1,000,000: 8s. Last read position: chr17:50,194,021
INFO 2026-05-28 00:41:56 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:39:20s. Time for last 1,000,000: 12s. Last read position: chr17:50,196,178
INFO 2026-05-28 00:42:11 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:39:34s. Time for last 1,000,000: 14s. Last read position: chr17:50,201,414
INFO 2026-05-28 00:42:23 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:39:47s. Time for last 1,000,000: 12s. Last read position: chr17:62,650,378
INFO 2026-05-28 00:42:35 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:39:59s. Time for last 1,000,000: 12s. Last read position: chr17:75,100,336
INFO 2026-05-28 00:42:50 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:40:14s. Time for last 1,000,000: 15s. Last read position: chr17:78,971,963
INFO 2026-05-28 00:43:12 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:40:35s. Time for last 1,000,000: 21s. Last read position: chr17:81,869,173
INFO 2026-05-28 00:43:23 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:40:47s. Time for last 1,000,000: 11s. Last read position: chr18:20,951,318
INFO 2026-05-28 00:43:37 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:41:01s. Time for last 1,000,000: 13s. Last read position: chr18:75,286,915
INFO 2026-05-28 00:43:48 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:41:11s. Time for last 1,000,000: 10s. Last read position: chr19:1,417,514
INFO 2026-05-28 00:43:55 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:41:19s. Time for last 1,000,000: 7s. Last read position: chr19:4,327,324
INFO 2026-05-28 00:44:04 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:41:28s. Time for last 1,000,000: 9s. Last read position: chr19:6,743,513
INFO 2026-05-28 00:44:16 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:41:39s. Time for last 1,000,000: 11s. Last read position: chr19:10,467,252
INFO 2026-05-28 00:44:32 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:41:56s. Time for last 1,000,000: 16s. Last read position: chr19:12,949,389
INFO 2026-05-28 00:44:40 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 8s. Last read position: chr19:15,458,600
INFO 2026-05-28 00:44:48 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:42:12s. Time for last 1,000,000: 7s. Last read position: chr19:18,785,506
INFO 2026-05-28 00:44:57 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:42:21s. Time for last 1,000,000: 8s. Last read position: chr19:36,142,925
INFO 2026-05-28 00:45:04 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:42:28s. Time for last 1,000,000: 7s. Last read position: chr19:39,889,693
INFO 2026-05-28 00:45:17 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:42:41s. Time for last 1,000,000: 13s. Last read position: chr19:42,088,626
INFO 2026-05-28 00:45:24 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:42:48s. Time for last 1,000,000: 6s. Last read position: chr19:45,468,533
INFO 2026-05-28 00:45:31 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:42:55s. Time for last 1,000,000: 7s. Last read position: chr19:48,919,264
INFO 2026-05-28 00:45:42 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:43:05s. Time for last 1,000,000: 10s. Last read position: chr19:50,359,042
INFO 2026-05-28 00:45:50 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:43:14s. Time for last 1,000,000: 8s. Last read position: chr19:55,388,035
INFO 2026-05-28 00:45:56 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:43:20s. Time for last 1,000,000: 6s. Last read position: chr20:3,703,370
INFO 2026-05-28 00:46:04 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:43:28s. Time for last 1,000,000: 8s. Last read position: chr20:32,728,123
INFO 2026-05-28 00:46:15 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:43:39s. Time for last 1,000,000: 10s. Last read position: chr20:44,943,185
INFO 2026-05-28 00:46:25 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:43:49s. Time for last 1,000,000: 10s. Last read position: chr20:58,891,856
INFO 2026-05-28 00:46:37 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:44:01s. Time for last 1,000,000: 11s. Last read position: chr21:6,450,619
INFO 2026-05-28 00:46:42 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:44:05s. Time for last 1,000,000: 4s. Last read position: chr21:32,347,505
INFO 2026-05-28 00:46:56 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:44:20s. Time for last 1,000,000: 14s. Last read position: chr21:44,325,234
INFO 2026-05-28 00:47:09 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:44:32s. Time for last 1,000,000: 12s. Last read position: chr21:46,567,458
INFO 2026-05-28 00:47:18 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:44:42s. Time for last 1,000,000: 9s. Last read position: chr22:24,164,507
INFO 2026-05-28 00:47:30 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:44:54s. Time for last 1,000,000: 12s. Last read position: chr22:35,656,382
INFO 2026-05-28 00:47:38 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:45:02s. Time for last 1,000,000: 7s. Last read position: chr22:39,031,800
INFO 2026-05-28 00:47:47 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:45:10s. Time for last 1,000,000: 8s. Last read position: chr22:46,372,882
INFO 2026-05-28 00:47:57 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:45:21s. Time for last 1,000,000: 10s. Last read position: chrX:2,723,324
INFO 2026-05-28 00:48:09 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:45:33s. Time for last 1,000,000: 11s. Last read position: chrX:47,145,450
INFO 2026-05-28 00:48:21 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:45:45s. Time for last 1,000,000: 12s. Last read position: chrX:65,667,740
INFO 2026-05-28 00:48:33 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:45:57s. Time for last 1,000,000: 11s. Last read position: chrX:101,353,294
INFO 2026-05-28 00:48:42 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:46:05s. Time for last 1,000,000: 8s. Last read position: chrX:133,536,019
INFO 2026-05-28 00:48:53 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:46:17s. Time for last 1,000,000: 11s. Last read position: chrX:154,359,606
INFO 2026-05-28 00:49:14 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:46:38s. Time for last 1,000,000: 20s. Last read position: GL000220.1:116,864
INFO 2026-05-28 00:49:15 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:46:39s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 00:49:16 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 46.72 minutes.
Runtime.totalMemory()=2928148480