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/13/94aaa7a0a9d3719391b76813d36420/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/94aaa7a0a9d3719391b76813d36420/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/a10cb2628baf3ec8d9b42f14d99014/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/fe053422129edd295606c1eb6a2617/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
==> 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 12:08:17 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 00:08:17 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bTo-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 00:08:17 GMT 2026] Executing as ?@nf-1394aaa7a0a9d3719391b76813d36420-61433-9bh6p 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.XXXXB5snrr/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXB5snrr/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:08:19 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:08:35 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:1,702,944
INFO 2026-05-28 00:08:44 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 9s. Last read position: chr1:9,755,304
INFO 2026-05-28 00:09:00 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 15s. Last read position: chr1:17,027,748
INFO 2026-05-28 00:09:18 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 18s. Last read position: chr1:21,854,745
INFO 2026-05-28 00:09:28 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 10s. Last read position: chr1:23,975,007
INFO 2026-05-28 00:09:41 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 12s. Last read position: chr1:30,877,117
INFO 2026-05-28 00:09:56 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 14s. Last read position: chr1:36,156,402
INFO 2026-05-28 00:10:24 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 27s. Last read position: chr1:42,929,751
INFO 2026-05-28 00:10:37 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 13s. Last read position: chr1:52,353,179
INFO 2026-05-28 00:10:48 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 10s. Last read position: chr1:87,104,600
INFO 2026-05-28 00:11:00 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 12s. Last read position: chr1:114,730,546
INFO 2026-05-28 00:11:13 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 12s. Last read position: chr1:148,953,383
INFO 2026-05-28 00:11:19 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 6s. Last read position: chr1:153,561,419
INFO 2026-05-28 00:11:33 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 13s. Last read position: chr1:155,327,089
INFO 2026-05-28 00:11:55 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 22s. Last read position: chr1:159,054,834
INFO 2026-05-28 00:12:06 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 11s. Last read position: chr1:169,733,623
INFO 2026-05-28 00:12:13 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 6s. Last read position: chr1:183,232,230
INFO 2026-05-28 00:12:21 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 7s. Last read position: chr1:201,782,546
INFO 2026-05-28 00:12:31 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 10s. Last read position: chr1:209,623,979
INFO 2026-05-28 00:12:38 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 7s. Last read position: chr1:226,363,941
INFO 2026-05-28 00:12:56 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 17s. Last read position: chr2:45,906
INFO 2026-05-28 00:13:08 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 12s. Last read position: chr2:24,303,808
INFO 2026-05-28 00:13:19 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 10s. Last read position: chr2:32,916,256
INFO 2026-05-28 00:13:25 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 5s. Last read position: chr2:33,275,047
INFO 2026-05-28 00:13:36 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 11s. Last read position: chr2:54,630,935
INFO 2026-05-28 00:13:56 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 20s. Last read position: chr2:71,349,561
INFO 2026-05-28 00:14:10 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 13s. Last read position: chr2:95,855,806
INFO 2026-05-28 00:14:18 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 8s. Last read position: chr2:110,534,738
INFO 2026-05-28 00:14:27 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 8s. Last read position: chr2:144,388,795
INFO 2026-05-28 00:14:39 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 12s. Last read position: chr2:174,568,000
INFO 2026-05-28 00:15:13 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 33s. Last read position: chr2:188,996,398
INFO 2026-05-28 00:15:27 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 14s. Last read position: chr2:194,328,140
INFO 2026-05-28 00:15:41 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 13s. Last read position: chr2:215,365,564
INFO 2026-05-28 00:16:05 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 24s. Last read position: chr2:215,378,175
INFO 2026-05-28 00:16:45 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 39s. Last read position: chr2:215,397,703
INFO 2026-05-28 00:17:34 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 49s. Last read position: chr2:215,420,709
INFO 2026-05-28 00:18:37 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 62s. Last read position: chr2:217,978,784
INFO 2026-05-28 00:18:49 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 11s. Last read position: chr2:231,282,059
INFO 2026-05-28 00:19:05 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 16s. Last read position: chr2:240,593,888
INFO 2026-05-28 00:19:19 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 13s. Last read position: chr3:31,623,783
INFO 2026-05-28 00:19:34 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 14s. Last read position: chr3:48,566,509
INFO 2026-05-28 00:20:02 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 28s. Last read position: chr3:49,129,055
INFO 2026-05-28 00:20:12 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 9s. Last read position: chr3:56,745,389
INFO 2026-05-28 00:20:26 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 14s. Last read position: chr3:105,550,191
INFO 2026-05-28 00:20:35 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 8s. Last read position: chr3:126,727,142
INFO 2026-05-28 00:20:45 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 9s. Last read position: chr3:136,151,223
INFO 2026-05-28 00:20:56 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 11s. Last read position: chr3:161,238,812
INFO 2026-05-28 00:21:11 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 14s. Last read position: chr3:184,325,616
INFO 2026-05-28 00:21:29 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 18s. Last read position: chr4:508,874
INFO 2026-05-28 00:21:42 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 13s. Last read position: chr4:7,043,694
INFO 2026-05-28 00:21:50 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 8s. Last read position: chr4:39,890,308
INFO 2026-05-28 00:22:00 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 9s. Last read position: chr4:78,844,980
INFO 2026-05-28 00:22:16 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 16s. Last read position: chr4:119,300,357
INFO 2026-05-28 00:22:26 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 10s. Last read position: chr4:185,399,586
INFO 2026-05-28 00:22:42 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 15s. Last read position: chr5:16,670,694
INFO 2026-05-28 00:22:52 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 10s. Last read position: chr5:65,809,568
INFO 2026-05-28 00:23:06 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 13s. Last read position: chr5:103,028,931
INFO 2026-05-28 00:23:16 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 9s. Last read position: chr5:138,947,317
INFO 2026-05-28 00:23:25 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 8s. Last read position: chr5:150,402,578
INFO 2026-05-28 00:23:33 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:14s. Time for last 1,000,000: 8s. Last read position: chr5:154,875,317
INFO 2026-05-28 00:23:43 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 9s. Last read position: chr5:179,125,037
INFO 2026-05-28 00:23:54 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 11s. Last read position: chr6:7,565,358
INFO 2026-05-28 00:24:00 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 5s. Last read position: chr6:27,810,173
INFO 2026-05-28 00:24:09 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 8s. Last read position: chr6:31,354,633
INFO 2026-05-28 00:24:14 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 5s. Last read position: chr6:31,829,299
INFO 2026-05-28 00:24:21 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 7s. Last read position: chr6:33,412,297
INFO 2026-05-28 00:24:28 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 7s. Last read position: chr6:43,143,416
INFO 2026-05-28 00:25:06 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 37s. Last read position: chr6:56,639,275
INFO 2026-05-28 00:25:25 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 19s. Last read position: chr6:106,555,816
INFO 2026-05-28 00:25:35 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 10s. Last read position: chr6:137,878,949
INFO 2026-05-28 00:25:44 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 8s. Last read position: chr6:158,776,407
INFO 2026-05-28 00:25:57 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 12s. Last read position: chr7:852,822
INFO 2026-05-28 00:26:05 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:17:45s. Time for last 1,000,000: 8s. Last read position: chr7:5,528,306
INFO 2026-05-28 00:26:13 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 8s. Last read position: chr7:22,818,008
INFO 2026-05-28 00:26:27 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 13s. Last read position: chr7:44,112,670
INFO 2026-05-28 00:26:36 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:18:16s. Time for last 1,000,000: 8s. Last read position: chr7:55,157,670
INFO 2026-05-28 00:26:47 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:18:27s. Time for last 1,000,000: 10s. Last read position: chr7:73,690,955
INFO 2026-05-28 00:27:00 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 13s. Last read position: chr7:92,307,646
INFO 2026-05-28 00:27:13 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:18:53s. Time for last 1,000,000: 13s. Last read position: chr7:98,625,006
INFO 2026-05-28 00:27:22 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 9s. Last read position: chr7:102,567,058
INFO 2026-05-28 00:27:39 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 17s. Last read position: chr7:128,089,630
INFO 2026-05-28 00:27:47 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 7s. Last read position: chr7:144,371,279
INFO 2026-05-28 00:28:05 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 17s. Last read position: chr8:11,853,328
INFO 2026-05-28 00:28:17 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:19:57s. Time for last 1,000,000: 11s. Last read position: chr8:38,831,136
INFO 2026-05-28 00:28:31 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:20:11s. Time for last 1,000,000: 13s. Last read position: chr8:69,603,225
INFO 2026-05-28 00:28:47 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:20:27s. Time for last 1,000,000: 16s. Last read position: chr8:100,920,541
INFO 2026-05-28 00:28:57 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:20:37s. Time for last 1,000,000: 9s. Last read position: chr8:129,750,464
INFO 2026-05-28 00:29:18 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:20:58s. Time for last 1,000,000: 20s. Last read position: chr8:143,727,377
INFO 2026-05-28 00:29:23 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:21:03s. Time for last 1,000,000: 5s. Last read position: chr8:143,922,351
INFO 2026-05-28 00:29:39 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:21:20s. Time for last 1,000,000: 16s. Last read position: chr8:144,398,043
INFO 2026-05-28 00:29:48 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:21:28s. Time for last 1,000,000: 8s. Last read position: chr9:35,059,576
INFO 2026-05-28 00:29:56 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:21:37s. Time for last 1,000,000: 8s. Last read position: chr9:36,594,657
INFO 2026-05-28 00:30:06 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:21:46s. Time for last 1,000,000: 9s. Last read position: chr9:92,729,194
INFO 2026-05-28 00:30:15 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:21:55s. Time for last 1,000,000: 8s. Last read position: chr9:113,373,832
INFO 2026-05-28 00:30:31 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 16s. Last read position: chr9:121,327,387
INFO 2026-05-28 00:30:42 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:22:22s. Time for last 1,000,000: 11s. Last read position: chr9:130,500,973
INFO 2026-05-28 00:30:52 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:22:32s. Time for last 1,000,000: 9s. Last read position: chr9:136,410,718
INFO 2026-05-28 00:31:04 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:22:44s. Time for last 1,000,000: 12s. Last read position: chr10:7,799,792
INFO 2026-05-28 00:31:13 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:22:53s. Time for last 1,000,000: 8s. Last read position: chr10:32,901,563
INFO 2026-05-28 00:31:29 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:23:09s. Time for last 1,000,000: 15s. Last read position: chr10:62,091,461
INFO 2026-05-28 00:31:38 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:23:18s. Time for last 1,000,000: 8s. Last read position: chr10:76,887,296
INFO 2026-05-28 00:31:49 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:23:29s. Time for last 1,000,000: 10s. Last read position: chr10:97,430,501
INFO 2026-05-28 00:32:01 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:23:41s. Time for last 1,000,000: 11s. Last read position: chr10:104,038,516
INFO 2026-05-28 00:32:13 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:23:53s. Time for last 1,000,000: 12s. Last read position: chr10:122,248,718
INFO 2026-05-28 00:32:20 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:24:00s. Time for last 1,000,000: 7s. Last read position: chr11:460,204
INFO 2026-05-28 00:32:31 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:24:11s. Time for last 1,000,000: 10s. Last read position: chr11:6,614,563
INFO 2026-05-28 00:32:45 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:24:25s. Time for last 1,000,000: 13s. Last read position: chr11:18,396,823
INFO 2026-05-28 00:32:58 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:24:38s. Time for last 1,000,000: 13s. Last read position: chr11:46,383,467
INFO 2026-05-28 00:33:09 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:24:50s. Time for last 1,000,000: 11s. Last read position: chr11:60,927,638
INFO 2026-05-28 00:33:18 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:24:59s. Time for last 1,000,000: 9s. Last read position: chr11:62,525,718
INFO 2026-05-28 00:33:26 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:25:07s. Time for last 1,000,000: 7s. Last read position: chr11:62,888,576
INFO 2026-05-28 00:33:35 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:25:16s. Time for last 1,000,000: 8s. Last read position: chr11:65,208,253
INFO 2026-05-28 00:33:45 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:25:25s. Time for last 1,000,000: 9s. Last read position: chr11:66,275,903
INFO 2026-05-28 00:33:55 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 9s. Last read position: chr11:69,643,074
INFO 2026-05-28 00:34:09 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:25:50s. Time for last 1,000,000: 14s. Last read position: chr11:75,404,756
INFO 2026-05-28 00:34:20 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:26:00s. Time for last 1,000,000: 10s. Last read position: chr11:102,162,501
INFO 2026-05-28 00:34:29 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:26:09s. Time for last 1,000,000: 9s. Last read position: chr11:118,902,553
INFO 2026-05-28 00:34:40 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:26:20s. Time for last 1,000,000: 10s. Last read position: chr11:130,140,445
INFO 2026-05-28 00:34:55 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:26:36s. Time for last 1,000,000: 15s. Last read position: chr12:6,602,020
INFO 2026-05-28 00:35:04 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:26:44s. Time for last 1,000,000: 8s. Last read position: chr12:10,126,573
INFO 2026-05-28 00:35:13 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:26:54s. Time for last 1,000,000: 9s. Last read position: chr12:46,362,492
INFO 2026-05-28 00:35:22 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:27:03s. Time for last 1,000,000: 8s. Last read position: chr12:50,192,469
INFO 2026-05-28 00:35:26 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:27:07s. Time for last 1,000,000: 4s. Last read position: chr12:52,492,852
INFO 2026-05-28 00:35:33 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:27:13s. Time for last 1,000,000: 6s. Last read position: chr12:53,443,598
INFO 2026-05-28 00:35:47 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:27:27s. Time for last 1,000,000: 13s. Last read position: chr12:56,164,303
INFO 2026-05-28 00:36:00 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:27:41s. Time for last 1,000,000: 13s. Last read position: chr12:57,490,291
INFO 2026-05-28 00:36:12 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:27:52s. Time for last 1,000,000: 11s. Last read position: chr12:91,146,124
INFO 2026-05-28 00:36:24 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:28:04s. Time for last 1,000,000: 12s. Last read position: chr12:108,792,527
INFO 2026-05-28 00:36:37 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:28:17s. Time for last 1,000,000: 12s. Last read position: chr12:120,222,894
INFO 2026-05-28 00:36:48 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:28:28s. Time for last 1,000,000: 10s. Last read position: chr12:131,941,902
INFO 2026-05-28 00:36:55 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:28:35s. Time for last 1,000,000: 6s. Last read position: chr13:37,582,381
INFO 2026-05-28 00:37:05 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:28:45s. Time for last 1,000,000: 10s. Last read position: chr13:99,295,660
INFO 2026-05-28 00:37:18 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:28:59s. Time for last 1,000,000: 13s. Last read position: chr13:110,879,636
INFO 2026-05-28 00:37:28 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:29:08s. Time for last 1,000,000: 9s. Last read position: chr14:23,321,574
INFO 2026-05-28 00:37:39 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:29:19s. Time for last 1,000,000: 11s. Last read position: chr14:50,748,031
INFO 2026-05-28 00:38:00 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:29:40s. Time for last 1,000,000: 20s. Last read position: chr14:67,347,433
INFO 2026-05-28 00:38:11 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:29:51s. Time for last 1,000,000: 11s. Last read position: chr14:75,280,654
INFO 2026-05-28 00:38:22 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:30:03s. Time for last 1,000,000: 11s. Last read position: chr14:101,995,071
INFO 2026-05-28 00:39:08 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:30:48s. Time for last 1,000,000: 45s. Last read position: chr14:104,944,019
INFO 2026-05-28 00:39:11 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:30:52s. Time for last 1,000,000: 3s. Last read position: chr14:105,643,368
INFO 2026-05-28 00:39:20 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:31:00s. Time for last 1,000,000: 8s. Last read position: chr15:39,593,204
INFO 2026-05-28 00:39:29 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:31:10s. Time for last 1,000,000: 9s. Last read position: chr15:52,319,214
INFO 2026-05-28 00:39:43 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:31:24s. Time for last 1,000,000: 13s. Last read position: chr15:72,351,132
INFO 2026-05-28 00:39:52 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:31:33s. Time for last 1,000,000: 9s. Last read position: chr15:89,116,324
INFO 2026-05-28 00:40:03 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:31:43s. Time for last 1,000,000: 10s. Last read position: chr16:1,352,136
INFO 2026-05-28 00:40:18 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:31:58s. Time for last 1,000,000: 15s. Last read position: chr16:3,069,092
INFO 2026-05-28 00:40:30 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:32:10s. Time for last 1,000,000: 11s. Last read position: chr16:15,988,078
INFO 2026-05-28 00:40:36 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:32:16s. Time for last 1,000,000: 5s. Last read position: chr16:22,454,703
INFO 2026-05-28 00:40:43 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:32:23s. Time for last 1,000,000: 7s. Last read position: chr16:29,996,589
INFO 2026-05-28 00:40:51 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:32:32s. Time for last 1,000,000: 8s. Last read position: chr16:47,083,483
INFO 2026-05-28 00:41:01 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:32:41s. Time for last 1,000,000: 9s. Last read position: chr16:57,663,521
INFO 2026-05-28 00:41:11 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:32:51s. Time for last 1,000,000: 10s. Last read position: chr16:69,710,987
INFO 2026-05-28 00:41:21 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:33:01s. Time for last 1,000,000: 9s. Last read position: chr16:87,392,457
INFO 2026-05-28 00:41:32 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:33:12s. Time for last 1,000,000: 10s. Last read position: chr17:1,361,961
INFO 2026-05-28 00:41:42 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:33:23s. Time for last 1,000,000: 10s. Last read position: chr17:7,393,758
INFO 2026-05-28 00:41:52 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:33:32s. Time for last 1,000,000: 9s. Last read position: chr17:17,522,380
INFO 2026-05-28 00:42:04 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:33:44s. Time for last 1,000,000: 11s. Last read position: chr17:29,577,206
INFO 2026-05-28 00:42:14 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:33:54s. Time for last 1,000,000: 9s. Last read position: chr17:39,707,122
INFO 2026-05-28 00:42:20 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:34:00s. Time for last 1,000,000: 6s. Last read position: chr17:41,586,333
INFO 2026-05-28 00:42:26 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:34:06s. Time for last 1,000,000: 5s. Last read position: chr17:42,315,574
INFO 2026-05-28 00:42:40 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:34:20s. Time for last 1,000,000: 13s. Last read position: chr17:48,530,674
INFO 2026-05-28 00:42:47 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:34:27s. Time for last 1,000,000: 7s. Last read position: chr17:50,187,014
INFO 2026-05-28 00:42:53 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:34:34s. Time for last 1,000,000: 6s. Last read position: chr17:50,188,926
INFO 2026-05-28 00:43:01 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:34:41s. Time for last 1,000,000: 7s. Last read position: chr17:50,190,355
INFO 2026-05-28 00:43:09 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:34:49s. Time for last 1,000,000: 8s. Last read position: chr17:50,192,830
INFO 2026-05-28 00:43:18 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:34:58s. Time for last 1,000,000: 8s. Last read position: chr17:50,194,792
INFO 2026-05-28 00:43:28 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:35:08s. Time for last 1,000,000: 9s. Last read position: chr17:50,196,487
INFO 2026-05-28 00:43:39 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:35:20s. Time for last 1,000,000: 11s. Last read position: chr17:50,199,312
INFO 2026-05-28 00:43:51 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:35:32s. Time for last 1,000,000: 11s. Last read position: chr17:59,683,727
INFO 2026-05-28 00:44:03 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:35:43s. Time for last 1,000,000: 11s. Last read position: chr17:74,230,951
INFO 2026-05-28 00:44:17 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:35:57s. Time for last 1,000,000: 14s. Last read position: chr17:76,472,947
INFO 2026-05-28 00:44:29 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:36:09s. Time for last 1,000,000: 11s. Last read position: chr17:81,510,818
INFO 2026-05-28 00:44:50 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:36:30s. Time for last 1,000,000: 20s. Last read position: chr18:669,094
INFO 2026-05-28 00:45:01 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:36:41s. Time for last 1,000,000: 11s. Last read position: chr18:23,894,956
INFO 2026-05-28 00:45:20 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:37:01s. Time for last 1,000,000: 19s. Last read position: chr18:49,490,877
INFO 2026-05-28 00:45:32 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:37:12s. Time for last 1,000,000: 11s. Last read position: chr19:1,104,832
INFO 2026-05-28 00:45:40 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:37:20s. Time for last 1,000,000: 7s. Last read position: chr19:3,118,937
INFO 2026-05-28 00:45:48 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:37:28s. Time for last 1,000,000: 7s. Last read position: chr19:6,697,435
INFO 2026-05-28 00:45:58 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:37:38s. Time for last 1,000,000: 9s. Last read position: chr19:10,361,950
INFO 2026-05-28 00:46:13 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:37:53s. Time for last 1,000,000: 14s. Last read position: chr19:13,112,955
INFO 2026-05-28 00:46:22 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:38:02s. Time for last 1,000,000: 9s. Last read position: chr19:15,427,434
INFO 2026-05-28 00:46:30 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:38:10s. Time for last 1,000,000: 8s. Last read position: chr19:18,573,715
INFO 2026-05-28 00:46:39 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:38:19s. Time for last 1,000,000: 8s. Last read position: chr19:35,654,618
INFO 2026-05-28 00:46:47 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:38:27s. Time for last 1,000,000: 8s. Last read position: chr19:39,972,227
INFO 2026-05-28 00:46:58 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:38:38s. Time for last 1,000,000: 11s. Last read position: chr19:42,412,552
INFO 2026-05-28 00:47:05 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:38:45s. Time for last 1,000,000: 6s. Last read position: chr19:47,741,062
INFO 2026-05-28 00:47:13 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:38:53s. Time for last 1,000,000: 7s. Last read position: chr19:49,969,869
INFO 2026-05-28 00:47:19 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:38:59s. Time for last 1,000,000: 6s. Last read position: chr19:57,747,014
INFO 2026-05-28 00:47:26 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:39:06s. Time for last 1,000,000: 6s. Last read position: chr20:14,326,089
INFO 2026-05-28 00:47:34 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:39:15s. Time for last 1,000,000: 8s. Last read position: chr20:35,556,104
INFO 2026-05-28 00:47:46 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:39:26s. Time for last 1,000,000: 11s. Last read position: chr20:45,899,832
INFO 2026-05-28 00:47:56 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:39:36s. Time for last 1,000,000: 10s. Last read position: chr20:58,909,738
INFO 2026-05-28 00:48:05 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:39:45s. Time for last 1,000,000: 9s. Last read position: chr21:6,117,142
INFO 2026-05-28 00:48:11 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:39:52s. Time for last 1,000,000: 6s. Last read position: chr21:33,345,360
INFO 2026-05-28 00:48:24 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:40:04s. Time for last 1,000,000: 12s. Last read position: chr21:44,806,761
INFO 2026-05-28 00:48:34 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:40:15s. Time for last 1,000,000: 10s. Last read position: chr21:46,286,941
INFO 2026-05-28 00:48:44 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:40:24s. Time for last 1,000,000: 9s. Last read position: chr22:24,168,503
INFO 2026-05-28 00:48:54 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:40:34s. Time for last 1,000,000: 10s. Last read position: chr22:35,423,308
INFO 2026-05-28 00:49:01 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:40:41s. Time for last 1,000,000: 7s. Last read position: chr22:37,947,240
INFO 2026-05-28 00:49:09 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:40:49s. Time for last 1,000,000: 7s. Last read position: chr22:42,834,240
INFO 2026-05-28 00:49:18 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:40:59s. Time for last 1,000,000: 9s. Last read position: chr22:50,504,427
INFO 2026-05-28 00:49:24 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:41:04s. Time for last 1,000,000: 5s. Last read position: chrX:24,527,593
INFO 2026-05-28 00:49:39 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:41:19s. Time for last 1,000,000: 14s. Last read position: chrX:49,030,334
INFO 2026-05-28 00:49:50 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:41:30s. Time for last 1,000,000: 11s. Last read position: chrX:77,522,354
INFO 2026-05-28 00:49:59 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:41:39s. Time for last 1,000,000: 9s. Last read position: chrX:136,231,606
INFO 2026-05-28 00:50:15 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:41:55s. Time for last 1,000,000: 15s. Last read position: chrX:154,365,198
INFO 2026-05-28 00:50:24 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 8s. Last read position: */*
[Thu May 28 00:50:25 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 42.14 minutes.
Runtime.totalMemory()=3059744768