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/f8/22d3ee253fdb5cf994392d4957438c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e8e59ffccb205e8ca63548b7bc97ef/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/22d3ee253fdb5cf994392d4957438c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/f2a5f29f2cf05d1cc4af6ddfb691f7/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
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 8:30:29 PM 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 20:30:29 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BT-20_FFPE_RNA_0001_B23LG7FLT4_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 20:30:29 GMT 2026] Executing as ?@nf-f822d3ee253fdb5cf994392d4957438c-c15a3-qp4x9 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.XXXXxJGFYe/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXxJGFYe/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 20:30:32 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:30:48 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:8,016,337
INFO 2026-05-28 20:31:07 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 19s. Last read position: chr1:12,607,362
INFO 2026-05-28 20:31:22 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 14s. Last read position: chr1:21,349,813
INFO 2026-05-28 20:31:36 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 14s. Last read position: chr1:26,958,185
INFO 2026-05-28 20:31:50 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 13s. Last read position: chr1:35,184,500
INFO 2026-05-28 20:32:24 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 34s. Last read position: chr1:43,303,327
INFO 2026-05-28 20:32:39 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 14s. Last read position: chr1:56,444,867
INFO 2026-05-28 20:32:51 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 12s. Last read position: chr1:93,562,352
INFO 2026-05-28 20:33:05 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 14s. Last read position: chr1:119,618,834
INFO 2026-05-28 20:33:10 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 4s. Last read position: chr1:148,590,894
INFO 2026-05-28 20:33:19 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 8s. Last read position: chr1:153,689,805
INFO 2026-05-28 20:33:38 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 19s. Last read position: chr1:156,225,067
INFO 2026-05-28 20:33:47 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 9s. Last read position: chr1:171,557,318
INFO 2026-05-28 20:33:57 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 9s. Last read position: chr1:201,209,927
INFO 2026-05-28 20:34:11 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 14s. Last read position: chr1:206,447,141
INFO 2026-05-28 20:34:29 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 17s. Last read position: chr1:228,367,106
INFO 2026-05-28 20:34:45 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 15s. Last read position: chr2:3,580,157
INFO 2026-05-28 20:34:55 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 10s. Last read position: chr2:25,282,462
INFO 2026-05-28 20:35:08 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 13s. Last read position: chr2:32,916,264
INFO 2026-05-28 20:35:16 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 7s. Last read position: chr2:37,007,082
INFO 2026-05-28 20:35:30 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 14s. Last read position: chr2:55,322,600
INFO 2026-05-28 20:35:54 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 23s. Last read position: chr2:74,346,287
INFO 2026-05-28 20:36:04 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 10s. Last read position: chr2:97,647,346
INFO 2026-05-28 20:36:11 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 7s. Last read position: chr2:110,535,051
INFO 2026-05-28 20:36:23 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 11s. Last read position: chr2:135,778,965
INFO 2026-05-28 20:36:40 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 17s. Last read position: chr2:176,123,093
INFO 2026-05-28 20:37:10 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 29s. Last read position: chr2:189,010,818
INFO 2026-05-28 20:37:34 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 23s. Last read position: chr2:215,430,734
INFO 2026-05-28 20:37:56 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 22s. Last read position: chr2:219,556,084
INFO 2026-05-28 20:38:13 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 16s. Last read position: chr2:237,376,947
INFO 2026-05-28 20:38:36 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 23s. Last read position: chr3:9,757,110
INFO 2026-05-28 20:38:53 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 16s. Last read position: chr3:32,336,136
INFO 2026-05-28 20:39:12 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 19s. Last read position: chr3:47,123,962
INFO 2026-05-28 20:39:31 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 18s. Last read position: chr3:49,533,053
INFO 2026-05-28 20:39:51 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 20s. Last read position: chr3:58,081,638
INFO 2026-05-28 20:40:12 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 20s. Last read position: chr3:96,814,720
INFO 2026-05-28 20:40:30 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 18s. Last read position: chr3:123,647,321
INFO 2026-05-28 20:40:42 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 11s. Last read position: chr3:136,601,316
INFO 2026-05-28 20:40:54 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 12s. Last read position: chr3:170,178,818
INFO 2026-05-28 20:41:15 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 20s. Last read position: chr3:194,406,045
INFO 2026-05-28 20:41:36 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 21s. Last read position: chr4:2,950,016
INFO 2026-05-28 20:41:51 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 14s. Last read position: chr4:21,245,162
INFO 2026-05-28 20:42:02 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 11s. Last read position: chr4:54,281,570
INFO 2026-05-28 20:42:32 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 30s. Last read position: chr4:87,114,921
INFO 2026-05-28 20:42:59 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 26s. Last read position: chr4:119,271,522
INFO 2026-05-28 20:43:16 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 17s. Last read position: chr4:155,690,080
INFO 2026-05-28 20:43:30 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 13s. Last read position: chr5:1,625,712
INFO 2026-05-28 20:43:42 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 12s. Last read position: chr5:39,377,237
INFO 2026-05-28 20:43:53 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 10s. Last read position: chr5:71,509,711
INFO 2026-05-28 20:44:05 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 11s. Last read position: chr5:110,740,874
INFO 2026-05-28 20:44:16 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 10s. Last read position: chr5:138,467,088
INFO 2026-05-28 20:44:23 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 7s. Last read position: chr5:141,494,813
INFO 2026-05-28 20:44:35 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 11s. Last read position: chr5:150,649,849
INFO 2026-05-28 20:44:52 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 17s. Last read position: chr5:176,433,313
INFO 2026-05-28 20:45:09 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 17s. Last read position: chr6:2,348,869
INFO 2026-05-28 20:45:24 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 14s. Last read position: chr6:26,124,406
INFO 2026-05-28 20:45:38 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 14s. Last read position: chr6:31,828,010
INFO 2026-05-28 20:45:54 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 15s. Last read position: chr6:33,320,080
INFO 2026-05-28 20:46:03 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:30s. Time for last 1,000,000: 9s. Last read position: chr6:43,338,636
INFO 2026-05-28 20:46:22 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 18s. Last read position: chr6:75,156,387
INFO 2026-05-28 20:46:37 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:16:04s. Time for last 1,000,000: 15s. Last read position: chr6:111,314,055
INFO 2026-05-28 20:46:57 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 19s. Last read position: chr6:142,753,452
INFO 2026-05-28 20:47:08 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 10s. Last read position: chr6:151,961,198
INFO 2026-05-28 20:47:27 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 19s. Last read position: chr6:167,965,942
INFO 2026-05-28 20:47:36 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 8s. Last read position: chr7:5,527,722
INFO 2026-05-28 20:47:45 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 9s. Last read position: chr7:31,302,196
INFO 2026-05-28 20:47:53 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 7s. Last read position: chr7:45,083,440
INFO 2026-05-28 20:48:02 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 8s. Last read position: chr7:72,925,619
INFO 2026-05-28 20:48:07 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:17:34s. Time for last 1,000,000: 4s. Last read position: chr7:75,987,365
INFO 2026-05-28 20:48:24 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 16s. Last read position: chr7:97,966,851
INFO 2026-05-28 20:48:35 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 11s. Last read position: chr7:102,197,288
INFO 2026-05-28 20:48:47 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 12s. Last read position: chr7:111,794,689
INFO 2026-05-28 20:48:58 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 10s. Last read position: chr7:134,933,724
INFO 2026-05-28 20:49:11 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 13s. Last read position: chr7:143,604,605
INFO 2026-05-28 20:49:28 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 17s. Last read position: chr7:153,750,920
INFO 2026-05-28 20:49:39 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:19:06s. Time for last 1,000,000: 10s. Last read position: chr8:22,148,611
INFO 2026-05-28 20:49:48 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 8s. Last read position: chr8:38,278,281
INFO 2026-05-28 20:50:05 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:19:32s. Time for last 1,000,000: 17s. Last read position: chr8:67,064,487
INFO 2026-05-28 20:50:24 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 18s. Last read position: chr8:100,721,366
INFO 2026-05-28 20:50:42 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 18s. Last read position: chr8:142,664,630
INFO 2026-05-28 20:50:52 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:20:19s. Time for last 1,000,000: 9s. Last read position: chr8:144,792,016
INFO 2026-05-28 20:51:03 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 11s. Last read position: chr9:26,722,953
INFO 2026-05-28 20:51:12 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:20:39s. Time for last 1,000,000: 9s. Last read position: chr9:41,448,914
INFO 2026-05-28 20:51:22 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:20:49s. Time for last 1,000,000: 9s. Last read position: chr9:92,514,771
INFO 2026-05-28 20:51:38 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:21:05s. Time for last 1,000,000: 15s. Last read position: chr9:99,221,812
INFO 2026-05-28 20:51:50 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:21:18s. Time for last 1,000,000: 12s. Last read position: chr9:114,288,464
INFO 2026-05-28 20:52:06 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:21:33s. Time for last 1,000,000: 15s. Last read position: chr9:127,447,878
INFO 2026-05-28 20:52:22 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:21:49s. Time for last 1,000,000: 15s. Last read position: chr9:131,192,265
INFO 2026-05-28 20:52:31 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 9s. Last read position: chr9:136,377,984
INFO 2026-05-28 20:52:44 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 12s. Last read position: chr10:5,906,445
INFO 2026-05-28 20:53:02 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:22:29s. Time for last 1,000,000: 17s. Last read position: chr10:31,520,234
INFO 2026-05-28 20:53:11 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:22:38s. Time for last 1,000,000: 9s. Last read position: chr10:58,787,057
INFO 2026-05-28 20:53:32 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:22:59s. Time for last 1,000,000: 21s. Last read position: chr10:75,021,267
INFO 2026-05-28 20:53:57 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:23:24s. Time for last 1,000,000: 24s. Last read position: chr10:87,864,387
INFO 2026-05-28 20:54:09 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:23:37s. Time for last 1,000,000: 12s. Last read position: chr10:101,356,798
INFO 2026-05-28 20:54:30 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:23:57s. Time for last 1,000,000: 20s. Last read position: chr10:117,543,483
INFO 2026-05-28 20:54:44 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:24:11s. Time for last 1,000,000: 14s. Last read position: chr11:309,134
INFO 2026-05-28 20:54:58 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:24:25s. Time for last 1,000,000: 13s. Last read position: chr11:3,369,724
INFO 2026-05-28 20:55:22 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:24:50s. Time for last 1,000,000: 24s. Last read position: chr11:12,870,869
INFO 2026-05-28 20:55:37 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:25:05s. Time for last 1,000,000: 15s. Last read position: chr11:46,320,716
INFO 2026-05-28 20:55:56 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:25:23s. Time for last 1,000,000: 18s. Last read position: chr11:62,520,593
INFO 2026-05-28 20:56:08 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 11s. Last read position: chr11:64,911,263
INFO 2026-05-28 20:56:18 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:25:46s. Time for last 1,000,000: 10s. Last read position: chr11:65,865,943
INFO 2026-05-28 20:56:27 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:25:54s. Time for last 1,000,000: 8s. Last read position: chr11:68,892,436
INFO 2026-05-28 20:56:50 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:26:17s. Time for last 1,000,000: 23s. Last read position: chr11:75,400,783
INFO 2026-05-28 20:57:07 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:26:34s. Time for last 1,000,000: 16s. Last read position: chr11:101,127,977
INFO 2026-05-28 20:57:24 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:26:52s. Time for last 1,000,000: 17s. Last read position: chr11:117,345,873
INFO 2026-05-28 20:57:38 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:27:05s. Time for last 1,000,000: 13s. Last read position: chr11:128,810,808
INFO 2026-05-28 20:57:58 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:27:25s. Time for last 1,000,000: 20s. Last read position: chr12:6,935,552
INFO 2026-05-28 20:58:06 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:27:33s. Time for last 1,000,000: 8s. Last read position: chr12:23,950,912
INFO 2026-05-28 20:58:19 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:27:46s. Time for last 1,000,000: 12s. Last read position: chr12:49,041,050
INFO 2026-05-28 20:58:39 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:28:06s. Time for last 1,000,000: 19s. Last read position: chr12:53,463,849
INFO 2026-05-28 20:58:57 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:28:24s. Time for last 1,000,000: 18s. Last read position: chr12:57,093,454
INFO 2026-05-28 20:59:13 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:28:40s. Time for last 1,000,000: 15s. Last read position: chr12:62,690,276
INFO 2026-05-28 20:59:27 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:28:55s. Time for last 1,000,000: 14s. Last read position: chr12:100,072,692
INFO 2026-05-28 20:59:43 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:29:10s. Time for last 1,000,000: 15s. Last read position: chr12:112,405,979
INFO 2026-05-28 20:59:52 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:29:20s. Time for last 1,000,000: 9s. Last read position: chr12:122,354,492
INFO 2026-05-28 21:00:05 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:29:32s. Time for last 1,000,000: 12s. Last read position: chr12:132,563,150
INFO 2026-05-28 21:00:15 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:29:42s. Time for last 1,000,000: 9s. Last read position: chr13:35,236,386
INFO 2026-05-28 21:00:27 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:29:54s. Time for last 1,000,000: 12s. Last read position: chr13:75,621,794
INFO 2026-05-28 21:00:44 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:30:11s. Time for last 1,000,000: 16s. Last read position: chr13:113,811,799
INFO 2026-05-28 21:00:57 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:30:24s. Time for last 1,000,000: 13s. Last read position: chr14:24,376,034
INFO 2026-05-28 21:01:10 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:30:37s. Time for last 1,000,000: 12s. Last read position: chr14:49,586,764
INFO 2026-05-28 21:01:27 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:30:54s. Time for last 1,000,000: 17s. Last read position: chr14:65,095,747
INFO 2026-05-28 21:01:37 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:31:05s. Time for last 1,000,000: 10s. Last read position: chr14:75,281,278
INFO 2026-05-28 21:01:48 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:31:15s. Time for last 1,000,000: 10s. Last read position: chr14:101,925,122
INFO 2026-05-28 21:02:27 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:31:54s. Time for last 1,000,000: 38s. Last read position: chr15:28,229,497
INFO 2026-05-28 21:02:39 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:32:06s. Time for last 1,000,000: 11s. Last read position: chr15:41,770,864
INFO 2026-05-28 21:02:51 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:32:18s. Time for last 1,000,000: 12s. Last read position: chr15:57,232,757
INFO 2026-05-28 21:03:05 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:32:32s. Time for last 1,000,000: 13s. Last read position: chr15:66,499,431
INFO 2026-05-28 21:03:16 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:32:44s. Time for last 1,000,000: 11s. Last read position: chr15:75,609,936
INFO 2026-05-28 21:03:27 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:32:55s. Time for last 1,000,000: 11s. Last read position: chr15:87,977,773
INFO 2026-05-28 21:03:38 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:33:05s. Time for last 1,000,000: 10s. Last read position: chr16:488,940
INFO 2026-05-28 21:04:00 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:33:27s. Time for last 1,000,000: 22s. Last read position: chr16:2,253,921
INFO 2026-05-28 21:04:13 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:33:40s. Time for last 1,000,000: 12s. Last read position: chr16:4,336,986
INFO 2026-05-28 21:04:22 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:33:49s. Time for last 1,000,000: 8s. Last read position: chr16:15,070,150
INFO 2026-05-28 21:04:42 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:34:09s. Time for last 1,000,000: 19s. Last read position: chr16:16,321,237
INFO 2026-05-28 21:04:45 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:34:13s. Time for last 1,000,000: 3s. Last read position: chr16:20,741,613
INFO 2026-05-28 21:04:49 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:34:16s. Time for last 1,000,000: 3s. Last read position: chr16:21,904,516
INFO 2026-05-28 21:04:55 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:34:22s. Time for last 1,000,000: 6s. Last read position: chr16:28,380,509
INFO 2026-05-28 21:05:02 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:34:30s. Time for last 1,000,000: 7s. Last read position: chr16:29,807,527
INFO 2026-05-28 21:05:09 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:34:36s. Time for last 1,000,000: 6s. Last read position: chr16:30,905,052
INFO 2026-05-28 21:05:20 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:34:47s. Time for last 1,000,000: 11s. Last read position: chr16:57,521,110
INFO 2026-05-28 21:05:33 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:35:00s. Time for last 1,000,000: 12s. Last read position: chr16:70,463,739
INFO 2026-05-28 21:05:41 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:35:09s. Time for last 1,000,000: 8s. Last read position: chr16:85,292,995
INFO 2026-05-28 21:05:54 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:35:21s. Time for last 1,000,000: 12s. Last read position: chr17:1,423,573
INFO 2026-05-28 21:06:04 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:35:32s. Time for last 1,000,000: 10s. Last read position: chr17:7,220,477
INFO 2026-05-28 21:06:14 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:35:41s. Time for last 1,000,000: 9s. Last read position: chr17:7,884,911
INFO 2026-05-28 21:06:25 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:35:52s. Time for last 1,000,000: 11s. Last read position: chr17:17,814,660
INFO 2026-05-28 21:06:36 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:36:03s. Time for last 1,000,000: 11s. Last read position: chr17:30,776,883
INFO 2026-05-28 21:06:44 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:36:12s. Time for last 1,000,000: 8s. Last read position: chr17:38,914,466
INFO 2026-05-28 21:06:55 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:36:22s. Time for last 1,000,000: 10s. Last read position: chr17:43,201,725
INFO 2026-05-28 21:07:04 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:36:31s. Time for last 1,000,000: 8s. Last read position: chr17:47,916,617
INFO 2026-05-28 21:07:11 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:36:38s. Time for last 1,000,000: 7s. Last read position: chr17:50,186,850
INFO 2026-05-28 21:07:18 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:36:45s. Time for last 1,000,000: 7s. Last read position: chr17:50,189,858
INFO 2026-05-28 21:07:27 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:36:54s. Time for last 1,000,000: 8s. Last read position: chr17:50,195,467
INFO 2026-05-28 21:07:40 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:37:08s. Time for last 1,000,000: 13s. Last read position: chr17:50,383,035
INFO 2026-05-28 21:07:56 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:37:23s. Time for last 1,000,000: 15s. Last read position: chr17:64,504,047
INFO 2026-05-28 21:08:08 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:37:35s. Time for last 1,000,000: 11s. Last read position: chr17:75,590,878
INFO 2026-05-28 21:08:24 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:37:51s. Time for last 1,000,000: 16s. Last read position: chr17:80,995,721
INFO 2026-05-28 21:08:37 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:38:04s. Time for last 1,000,000: 13s. Last read position: chr18:10,471,651
INFO 2026-05-28 21:08:47 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:38:14s. Time for last 1,000,000: 9s. Last read position: chr18:51,196,942
INFO 2026-05-28 21:08:59 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:38:26s. Time for last 1,000,000: 12s. Last read position: chr18:79,923,286
INFO 2026-05-28 21:09:08 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:38:35s. Time for last 1,000,000: 8s. Last read position: chr19:2,512,151
INFO 2026-05-28 21:09:16 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:38:43s. Time for last 1,000,000: 8s. Last read position: chr19:6,413,916
INFO 2026-05-28 21:09:28 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:38:55s. Time for last 1,000,000: 11s. Last read position: chr19:9,974,342
INFO 2026-05-28 21:09:44 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:39:11s. Time for last 1,000,000: 16s. Last read position: chr19:12,949,289
INFO 2026-05-28 21:09:53 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:39:20s. Time for last 1,000,000: 8s. Last read position: chr19:15,403,498
INFO 2026-05-28 21:10:02 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:39:29s. Time for last 1,000,000: 8s. Last read position: chr19:18,891,271
INFO 2026-05-28 21:10:10 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:39:37s. Time for last 1,000,000: 7s. Last read position: chr19:35,786,797
INFO 2026-05-28 21:10:19 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:39:46s. Time for last 1,000,000: 9s. Last read position: chr19:40,242,671
INFO 2026-05-28 21:10:34 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:40:02s. Time for last 1,000,000: 15s. Last read position: chr19:42,291,340
INFO 2026-05-28 21:10:43 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:40:11s. Time for last 1,000,000: 8s. Last read position: chr19:46,387,360
INFO 2026-05-28 21:10:51 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:40:18s. Time for last 1,000,000: 7s. Last read position: chr19:49,497,560
INFO 2026-05-28 21:10:58 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:40:26s. Time for last 1,000,000: 7s. Last read position: chr19:54,121,900
INFO 2026-05-28 21:11:06 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:40:34s. Time for last 1,000,000: 8s. Last read position: chr19:57,336,815
INFO 2026-05-28 21:11:13 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:40:40s. Time for last 1,000,000: 6s. Last read position: chr20:6,778,770
INFO 2026-05-28 21:11:24 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:40:51s. Time for last 1,000,000: 10s. Last read position: chr20:33,644,488
INFO 2026-05-28 21:11:34 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:41:01s. Time for last 1,000,000: 10s. Last read position: chr20:43,460,756
INFO 2026-05-28 21:11:42 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:41:10s. Time for last 1,000,000: 8s. Last read position: chr20:57,709,552
INFO 2026-05-28 21:11:51 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:41:18s. Time for last 1,000,000: 8s. Last read position: chr21:8,210,326
INFO 2026-05-28 21:11:52 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:41:19s. Time for last 1,000,000: 0s. Last read position: chr21:8,216,085
INFO 2026-05-28 21:11:53 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:41:21s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,310
INFO 2026-05-28 21:11:54 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:41:21s. Time for last 1,000,000: 0s. Last read position: chr21:8,258,945
INFO 2026-05-28 21:11:55 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:41:22s. Time for last 1,000,000: 0s. Last read position: chr21:8,395,870
INFO 2026-05-28 21:11:56 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:41:23s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,875
INFO 2026-05-28 21:11:58 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:41:25s. Time for last 1,000,000: 1s. Last read position: chr21:8,401,708
INFO 2026-05-28 21:11:59 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:41:26s. Time for last 1,000,000: 0s. Last read position: chr21:8,441,999
INFO 2026-05-28 21:12:00 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:41:27s. Time for last 1,000,000: 0s. Last read position: chr21:8,444,138
INFO 2026-05-28 21:12:04 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:41:31s. Time for last 1,000,000: 4s. Last read position: chr21:25,975,109
INFO 2026-05-28 21:12:16 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:41:43s. Time for last 1,000,000: 11s. Last read position: chr21:44,984,084
INFO 2026-05-28 21:12:26 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:41:54s. Time for last 1,000,000: 10s. Last read position: chr22:17,548,855
INFO 2026-05-28 21:12:37 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 10s. Last read position: chr22:24,042,950
INFO 2026-05-28 21:12:49 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:42:17s. Time for last 1,000,000: 12s. Last read position: chr22:31,715,975
INFO 2026-05-28 21:13:00 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:42:27s. Time for last 1,000,000: 10s. Last read position: chr22:38,866,964
INFO 2026-05-28 21:13:08 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:42:35s. Time for last 1,000,000: 8s. Last read position: chr22:45,533,144
INFO 2026-05-28 21:13:16 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:42:43s. Time for last 1,000,000: 8s. Last read position: chrX:3,818,015
INFO 2026-05-28 21:13:29 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:42:56s. Time for last 1,000,000: 12s. Last read position: chrX:41,727,347
INFO 2026-05-28 21:13:41 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:43:09s. Time for last 1,000,000: 12s. Last read position: chrX:54,549,855
INFO 2026-05-28 21:13:55 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:43:23s. Time for last 1,000,000: 14s. Last read position: chrX:85,984,239
INFO 2026-05-28 21:14:03 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:43:31s. Time for last 1,000,000: 7s. Last read position: chrX:130,013,658
INFO 2026-05-28 21:14:13 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:43:41s. Time for last 1,000,000: 10s. Last read position: chrX:154,360,356
INFO 2026-05-28 21:14:25 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:43:52s. Time for last 1,000,000: 11s. Last read position: GL000220.1:109,774
INFO 2026-05-28 21:14:26 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:43:53s. Time for last 1,000,000: 0s. Last read position: GL000220.1:114,510
INFO 2026-05-28 21:14:27 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:43:54s. Time for last 1,000,000: 0s. Last read position: GL000220.1:116,465
INFO 2026-05-28 21:14:28 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:43:55s. Time for last 1,000,000: 0s. Last read position: GL000220.1:157,857
INFO 2026-05-28 21:14:29 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:43:56s. Time for last 1,000,000: 0s. Last read position: GL000220.1:159,541
INFO 2026-05-28 21:14:29 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:43:57s. Time for last 1,000,000: 0s. Last read position: GL000220.1:160,766
INFO 2026-05-28 21:14:30 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:43:58s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,015
INFO 2026-05-28 21:14:31 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:43:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,168
INFO 2026-05-28 21:14:32 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:44:00s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,977
INFO 2026-05-28 21:14:33 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:44:00s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,129
INFO 2026-05-28 21:14:34 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:44:01s. Time for last 1,000,000: 0s. Last read position: KI270733.1:178,267
INFO 2026-05-28 21:14:35 SinglePassSamProgram Processed 214,000,000 records. Elapsed time: 00:44:02s. Time for last 1,000,000: 0s. Last read position: */*
INFO 2026-05-28 21:14:36 SinglePassSamProgram Processed 215,000,000 records. Elapsed time: 00:44:03s. Time for last 1,000,000: 0s. Last read position: */*
INFO 2026-05-28 21:14:37 SinglePassSamProgram Processed 216,000,000 records. Elapsed time: 00:44:04s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 21:14:38 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 44.16 minutes.
Runtime.totalMemory()=3379036160