Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/f7c46891ee12480c88775c01ab5059/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
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/20/437a718b8e66d90a1a6549735c7d07/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2d6062a1134f981f2bd2faba13d16d/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/437a718b8e66d90a1a6549735c7d07/.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 8:55:09 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 20:55:09 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L03_RNA_01_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 20:55:09 GMT 2026] Executing as ?@nf-20437a718b8e66d90a1a6549735c7d07-43202-527p5 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.XXXXedQsBA/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXedQsBA/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 20:55:13 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:55:34 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 21s. Last read position: chr1:8,358,604
INFO 2026-05-28 20:55:52 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 18s. Last read position: chr1:16,953,304
INFO 2026-05-28 20:56:12 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 19s. Last read position: chr1:24,661,325
INFO 2026-05-28 20:56:33 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 20s. Last read position: chr1:32,204,578
INFO 2026-05-28 20:57:12 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 39s. Last read position: chr1:40,314,204
INFO 2026-05-28 20:57:30 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 17s. Last read position: chr1:55,071,877
INFO 2026-05-28 20:57:47 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 17s. Last read position: chr1:109,262,915
INFO 2026-05-28 20:57:57 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 10s. Last read position: chr1:143,599,120
INFO 2026-05-28 20:58:06 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 9s. Last read position: chr1:149,935,299
INFO 2026-05-28 20:58:23 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 16s. Last read position: chr1:154,489,268
INFO 2026-05-28 20:58:51 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 27s. Last read position: chr1:156,138,686
INFO 2026-05-28 20:59:06 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 15s. Last read position: chr1:171,557,636
INFO 2026-05-28 20:59:18 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 11s. Last read position: chr1:202,746,142
INFO 2026-05-28 20:59:31 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 13s. Last read position: chr1:225,828,834
INFO 2026-05-28 20:59:53 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 21s. Last read position: chr1:248,850,288
INFO 2026-05-28 21:00:09 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 15s. Last read position: chr2:29,193,418
INFO 2026-05-28 21:00:17 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 8s. Last read position: chr2:32,916,406
INFO 2026-05-28 21:00:31 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 13s. Last read position: chr2:55,049,873
INFO 2026-05-28 21:01:01 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 29s. Last read position: chr2:85,361,743
INFO 2026-05-28 21:01:17 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 16s. Last read position: chr2:106,073,968
INFO 2026-05-28 21:01:31 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 13s. Last read position: chr2:130,657,166
INFO 2026-05-28 21:01:48 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 16s. Last read position: chr2:178,537,855
INFO 2026-05-28 21:02:50 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 61s. Last read position: chr2:189,009,105
INFO 2026-05-28 21:03:11 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 20s. Last read position: chr2:215,386,766
INFO 2026-05-28 21:03:46 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 35s. Last read position: chr2:225,817,142
INFO 2026-05-28 21:04:07 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 21s. Last read position: chr2:240,014,816
INFO 2026-05-28 21:04:31 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 24s. Last read position: chr3:15,074,272
INFO 2026-05-28 21:04:49 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 17s. Last read position: chr3:46,995,966
INFO 2026-05-28 21:05:14 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 25s. Last read position: chr3:49,962,668
INFO 2026-05-28 21:05:31 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 17s. Last read position: chr3:58,170,690
INFO 2026-05-28 21:05:48 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 16s. Last read position: chr3:114,351,087
INFO 2026-05-28 21:06:04 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 16s. Last read position: chr3:138,010,188
INFO 2026-05-28 21:06:22 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 17s. Last read position: chr3:184,458,786
INFO 2026-05-28 21:06:38 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 16s. Last read position: chr4:1,212,219
INFO 2026-05-28 21:06:54 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 15s. Last read position: chr4:39,321,287
INFO 2026-05-28 21:07:14 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 20s. Last read position: chr4:88,523,499
INFO 2026-05-28 21:07:46 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 31s. Last read position: chr4:150,817,217
INFO 2026-05-28 21:08:00 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 14s. Last read position: chr5:14,316,647
INFO 2026-05-28 21:08:23 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 23s. Last read position: chr5:67,163,379
INFO 2026-05-28 21:08:41 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 17s. Last read position: chr5:114,362,648
INFO 2026-05-28 21:08:52 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 11s. Last read position: chr5:139,561,737
INFO 2026-05-28 21:09:02 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 9s. Last read position: chr5:150,123,180
INFO 2026-05-28 21:09:13 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 10s. Last read position: chr5:168,616,430
INFO 2026-05-28 21:09:31 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 18s. Last read position: chr5:179,822,965
INFO 2026-05-28 21:09:45 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 13s. Last read position: chr6:17,735,968
INFO 2026-05-28 21:09:58 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 13s. Last read position: chr6:31,632,916
INFO 2026-05-28 21:10:17 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:15:04s. Time for last 1,000,000: 18s. Last read position: chr6:32,195,892
INFO 2026-05-28 21:10:28 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 11s. Last read position: chr6:42,262,470
INFO 2026-05-28 21:10:52 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:15:38s. Time for last 1,000,000: 23s. Last read position: chr6:81,555,345
INFO 2026-05-28 21:11:02 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 10s. Last read position: chr6:129,791,548
INFO 2026-05-28 21:11:17 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 14s. Last read position: chr6:152,060,989
INFO 2026-05-28 21:11:35 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 17s. Last read position: chr7:2,433,473
INFO 2026-05-28 21:11:45 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 9s. Last read position: chr7:23,512,963
INFO 2026-05-28 21:12:03 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 18s. Last read position: chr7:55,201,279
INFO 2026-05-28 21:12:15 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 11s. Last read position: chr7:75,340,724
INFO 2026-05-28 21:12:35 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:17:22s. Time for last 1,000,000: 20s. Last read position: chr7:94,408,212
INFO 2026-05-28 21:13:00 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 24s. Last read position: chr7:100,430,873
INFO 2026-05-28 21:13:10 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 10s. Last read position: chr7:107,261,316
INFO 2026-05-28 21:13:22 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 12s. Last read position: chr7:139,583,979
INFO 2026-05-28 21:13:32 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 9s. Last read position: chr7:151,142,603
INFO 2026-05-28 21:13:52 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 20s. Last read position: chr8:22,556,875
INFO 2026-05-28 21:14:12 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 19s. Last read position: chr8:38,429,886
INFO 2026-05-28 21:14:27 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:19:14s. Time for last 1,000,000: 15s. Last read position: chr8:93,719,056
INFO 2026-05-28 21:14:44 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 17s. Last read position: chr8:140,152,291
INFO 2026-05-28 21:14:55 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:19:42s. Time for last 1,000,000: 10s. Last read position: chr8:143,924,181
INFO 2026-05-28 21:15:12 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:19:58s. Time for last 1,000,000: 16s. Last read position: chr9:14,307,087
INFO 2026-05-28 21:15:20 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:20:07s. Time for last 1,000,000: 8s. Last read position: chr9:66,920,522
INFO 2026-05-28 21:15:31 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:20:18s. Time for last 1,000,000: 10s. Last read position: chr9:99,062,260
INFO 2026-05-28 21:15:43 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 12s. Last read position: chr9:122,204,686
INFO 2026-05-28 21:15:59 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:20:45s. Time for last 1,000,000: 15s. Last read position: chr9:130,878,444
INFO 2026-05-28 21:16:10 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:20:57s. Time for last 1,000,000: 11s. Last read position: chr9:136,545,731
INFO 2026-05-28 21:16:21 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:21:07s. Time for last 1,000,000: 10s. Last read position: chr10:13,610,098
INFO 2026-05-28 21:16:35 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:21:22s. Time for last 1,000,000: 14s. Last read position: chr10:37,176,206
INFO 2026-05-28 21:16:44 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:21:30s. Time for last 1,000,000: 8s. Last read position: chr10:59,792,929
INFO 2026-05-28 21:16:58 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:21:44s. Time for last 1,000,000: 14s. Last read position: chr10:80,157,688
INFO 2026-05-28 21:17:07 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:21:54s. Time for last 1,000,000: 9s. Last read position: chr10:102,139,555
INFO 2026-05-28 21:17:22 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 14s. Last read position: chr10:128,069,721
INFO 2026-05-28 21:17:30 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:22:17s. Time for last 1,000,000: 8s. Last read position: chr11:1,757,323
INFO 2026-05-28 21:17:45 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:22:31s. Time for last 1,000,000: 14s. Last read position: chr11:17,288,881
INFO 2026-05-28 21:17:56 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:22:42s. Time for last 1,000,000: 11s. Last read position: chr11:57,313,676
INFO 2026-05-28 21:18:07 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:22:53s. Time for last 1,000,000: 10s. Last read position: chr11:62,529,844
INFO 2026-05-28 21:18:16 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:23:03s. Time for last 1,000,000: 9s. Last read position: chr11:65,424,585
INFO 2026-05-28 21:18:28 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:23:14s. Time for last 1,000,000: 11s. Last read position: chr11:67,286,378
INFO 2026-05-28 21:18:44 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:23:31s. Time for last 1,000,000: 16s. Last read position: chr11:73,309,317
INFO 2026-05-28 21:18:55 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:23:42s. Time for last 1,000,000: 11s. Last read position: chr11:103,909,785
INFO 2026-05-28 21:19:07 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:23:54s. Time for last 1,000,000: 11s. Last read position: chr11:119,744,039
INFO 2026-05-28 21:19:21 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:24:07s. Time for last 1,000,000: 13s. Last read position: chr12:6,573,095
INFO 2026-05-28 21:19:34 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:24:20s. Time for last 1,000,000: 12s. Last read position: chr12:14,947,899
INFO 2026-05-28 21:19:46 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:24:33s. Time for last 1,000,000: 12s. Last read position: chr12:49,055,014
INFO 2026-05-28 21:19:59 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:24:45s. Time for last 1,000,000: 12s. Last read position: chr12:53,063,243
INFO 2026-05-28 21:20:14 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:25:01s. Time for last 1,000,000: 15s. Last read position: chr12:56,721,309
INFO 2026-05-28 21:20:28 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:25:15s. Time for last 1,000,000: 14s. Last read position: chr12:68,689,534
INFO 2026-05-28 21:20:40 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:25:27s. Time for last 1,000,000: 11s. Last read position: chr12:110,028,511
INFO 2026-05-28 21:20:54 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:25:41s. Time for last 1,000,000: 14s. Last read position: chr12:122,133,659
INFO 2026-05-28 21:21:09 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:25:56s. Time for last 1,000,000: 14s. Last read position: chr12:132,748,176
INFO 2026-05-28 21:21:20 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 10s. Last read position: chr13:52,029,323
INFO 2026-05-28 21:21:32 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:26:19s. Time for last 1,000,000: 12s. Last read position: chr14:20,380,259
INFO 2026-05-28 21:21:47 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:26:34s. Time for last 1,000,000: 15s. Last read position: chr14:34,612,995
INFO 2026-05-28 21:22:03 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:26:49s. Time for last 1,000,000: 15s. Last read position: chr14:67,691,183
INFO 2026-05-28 21:22:13 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:27:00s. Time for last 1,000,000: 10s. Last read position: chr14:75,783,330
INFO 2026-05-28 21:22:38 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:27:24s. Time for last 1,000,000: 24s. Last read position: chr14:102,903,277
INFO 2026-05-28 21:22:54 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:27:41s. Time for last 1,000,000: 16s. Last read position: chr15:25,779,094
INFO 2026-05-28 21:23:02 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 8s. Last read position: chr15:41,835,065
INFO 2026-05-28 21:23:15 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:28:02s. Time for last 1,000,000: 12s. Last read position: chr15:61,907,327
INFO 2026-05-28 21:23:29 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:28:16s. Time for last 1,000,000: 13s. Last read position: chr15:74,043,075
INFO 2026-05-28 21:23:37 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:28:24s. Time for last 1,000,000: 8s. Last read position: chr15:85,579,623
INFO 2026-05-28 21:23:47 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:28:34s. Time for last 1,000,000: 10s. Last read position: chr16:381,792
INFO 2026-05-28 21:24:07 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:28:54s. Time for last 1,000,000: 19s. Last read position: chr16:2,757,556
INFO 2026-05-28 21:24:23 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:29:10s. Time for last 1,000,000: 15s. Last read position: chr16:4,652,016
INFO 2026-05-28 21:24:32 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:29:18s. Time for last 1,000,000: 8s. Last read position: chr16:15,363,810
INFO 2026-05-28 21:24:37 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:29:24s. Time for last 1,000,000: 5s. Last read position: chr16:18,351,271
INFO 2026-05-28 21:24:41 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:29:28s. Time for last 1,000,000: 3s. Last read position: chr16:21,404,973
INFO 2026-05-28 21:24:45 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:29:32s. Time for last 1,000,000: 4s. Last read position: chr16:22,527,565
INFO 2026-05-28 21:24:53 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:29:40s. Time for last 1,000,000: 8s. Last read position: chr16:27,776,901
INFO 2026-05-28 21:24:59 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:29:46s. Time for last 1,000,000: 6s. Last read position: chr16:29,485,485
INFO 2026-05-28 21:25:05 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:29:52s. Time for last 1,000,000: 6s. Last read position: chr16:30,664,846
INFO 2026-05-28 21:25:16 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:30:03s. Time for last 1,000,000: 10s. Last read position: chr16:56,502,329
INFO 2026-05-28 21:25:31 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:30:18s. Time for last 1,000,000: 15s. Last read position: chr16:70,664,597
INFO 2026-05-28 21:25:40 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:30:27s. Time for last 1,000,000: 8s. Last read position: chr16:88,624,045
INFO 2026-05-28 21:25:55 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:30:42s. Time for last 1,000,000: 15s. Last read position: chr17:3,577,628
INFO 2026-05-28 21:26:08 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:30:54s. Time for last 1,000,000: 12s. Last read position: chr17:7,513,489
INFO 2026-05-28 21:26:20 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:31:07s. Time for last 1,000,000: 12s. Last read position: chr17:17,217,159
INFO 2026-05-28 21:26:33 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:31:19s. Time for last 1,000,000: 12s. Last read position: chr17:31,865,385
INFO 2026-05-28 21:26:41 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:31:28s. Time for last 1,000,000: 8s. Last read position: chr17:39,710,346
INFO 2026-05-28 21:26:54 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:31:41s. Time for last 1,000,000: 13s. Last read position: chr17:42,991,465
INFO 2026-05-28 21:27:06 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:31:52s. Time for last 1,000,000: 11s. Last read position: chr17:50,149,167
INFO 2026-05-28 21:27:12 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:31:58s. Time for last 1,000,000: 5s. Last read position: chr17:50,186,913
INFO 2026-05-28 21:27:18 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:32:04s. Time for last 1,000,000: 6s. Last read position: chr17:50,188,930
INFO 2026-05-28 21:27:25 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:32:11s. Time for last 1,000,000: 7s. Last read position: chr17:50,190,077
INFO 2026-05-28 21:27:34 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:32:20s. Time for last 1,000,000: 8s. Last read position: chr17:50,193,992
INFO 2026-05-28 21:27:44 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:32:31s. Time for last 1,000,000: 10s. Last read position: chr17:50,195,960
INFO 2026-05-28 21:27:56 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:32:43s. Time for last 1,000,000: 12s. Last read position: chr17:50,199,226
INFO 2026-05-28 21:28:12 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:32:59s. Time for last 1,000,000: 15s. Last read position: chr17:56,981,182
INFO 2026-05-28 21:28:26 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:33:13s. Time for last 1,000,000: 14s. Last read position: chr17:68,528,864
INFO 2026-05-28 21:28:45 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:33:32s. Time for last 1,000,000: 18s. Last read position: chr17:78,091,504
INFO 2026-05-28 21:29:02 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:33:49s. Time for last 1,000,000: 17s. Last read position: chr17:82,079,185
INFO 2026-05-28 21:29:14 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:34:01s. Time for last 1,000,000: 11s. Last read position: chr18:36,198,901
INFO 2026-05-28 21:29:27 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:34:14s. Time for last 1,000,000: 12s. Last read position: chr19:860,683
INFO 2026-05-28 21:29:38 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:34:24s. Time for last 1,000,000: 10s. Last read position: chr19:3,387,249
INFO 2026-05-28 21:29:46 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:34:32s. Time for last 1,000,000: 7s. Last read position: chr19:6,415,018
INFO 2026-05-28 21:29:58 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:34:45s. Time for last 1,000,000: 12s. Last read position: chr19:10,986,954
INFO 2026-05-28 21:30:13 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:35:00s. Time for last 1,000,000: 15s. Last read position: chr19:15,161,606
INFO 2026-05-28 21:30:24 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:35:11s. Time for last 1,000,000: 10s. Last read position: chr19:17,862,161
INFO 2026-05-28 21:30:32 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:35:18s. Time for last 1,000,000: 7s. Last read position: chr19:35,267,234
INFO 2026-05-28 21:30:41 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:35:27s. Time for last 1,000,000: 8s. Last read position: chr19:39,408,339
INFO 2026-05-28 21:30:53 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:35:40s. Time for last 1,000,000: 12s. Last read position: chr19:42,273,799
INFO 2026-05-28 21:31:05 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:35:51s. Time for last 1,000,000: 11s. Last read position: chr19:45,472,915
INFO 2026-05-28 21:31:13 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:36:00s. Time for last 1,000,000: 8s. Last read position: chr19:49,061,352
INFO 2026-05-28 21:31:23 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:36:10s. Time for last 1,000,000: 10s. Last read position: chr19:52,415,139
INFO 2026-05-28 21:31:32 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:36:18s. Time for last 1,000,000: 8s. Last read position: chr19:57,390,017
INFO 2026-05-28 21:31:40 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:36:27s. Time for last 1,000,000: 8s. Last read position: chr20:17,659,071
INFO 2026-05-28 21:31:53 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:36:40s. Time for last 1,000,000: 13s. Last read position: chr20:36,786,551
INFO 2026-05-28 21:32:05 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:36:51s. Time for last 1,000,000: 11s. Last read position: chr20:53,254,486
INFO 2026-05-28 21:32:18 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:37:04s. Time for last 1,000,000: 13s. Last read position: chr20:64,069,360
INFO 2026-05-28 21:32:19 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:37:06s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,836
INFO 2026-05-28 21:32:20 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:37:07s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,898
INFO 2026-05-28 21:32:21 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:37:07s. Time for last 1,000,000: 0s. Last read position: chr21:8,389,269
INFO 2026-05-28 21:32:22 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:37:09s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,886
INFO 2026-05-28 21:32:24 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:37:10s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,948
INFO 2026-05-28 21:32:25 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:37:12s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,101
INFO 2026-05-28 21:32:27 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:37:13s. Time for last 1,000,000: 1s. Last read position: chr21:25,954,623
INFO 2026-05-28 21:32:40 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:37:27s. Time for last 1,000,000: 13s. Last read position: chr21:44,773,540
INFO 2026-05-28 21:32:52 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:37:38s. Time for last 1,000,000: 11s. Last read position: chr21:46,132,030
INFO 2026-05-28 21:33:03 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:37:50s. Time for last 1,000,000: 11s. Last read position: chr22:24,269,405
INFO 2026-05-28 21:33:18 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:38:05s. Time for last 1,000,000: 14s. Last read position: chr22:36,145,516
INFO 2026-05-28 21:33:27 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:38:13s. Time for last 1,000,000: 8s. Last read position: chr22:40,266,160
INFO 2026-05-28 21:33:37 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:38:24s. Time for last 1,000,000: 10s. Last read position: chr22:50,437,507
INFO 2026-05-28 21:33:48 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:38:34s. Time for last 1,000,000: 10s. Last read position: chrX:32,644,979
INFO 2026-05-28 21:34:05 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:38:51s. Time for last 1,000,000: 16s. Last read position: chrX:54,930,279
INFO 2026-05-28 21:34:16 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:39:02s. Time for last 1,000,000: 11s. Last read position: chrX:118,907,494
INFO 2026-05-28 21:34:30 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:39:17s. Time for last 1,000,000: 14s. Last read position: chrX:154,368,047
INFO 2026-05-28 21:34:34 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:39:20s. Time for last 1,000,000: 3s. Last read position: GL000220.1:114,176
INFO 2026-05-28 21:34:34 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:39:21s. Time for last 1,000,000: 0s. Last read position: GL000220.1:116,328
INFO 2026-05-28 21:34:35 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:39:22s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,127
INFO 2026-05-28 21:34:36 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:39:23s. Time for last 1,000,000: 0s. Last read position: GL000220.1:160,284
INFO 2026-05-28 21:34:37 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:39:23s. Time for last 1,000,000: 0s. Last read position: KI270733.1:129,682
INFO 2026-05-28 21:34:38 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:39:24s. Time for last 1,000,000: 0s. Last read position: KI270733.1:132,335
INFO 2026-05-28 21:34:39 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:39:25s. Time for last 1,000,000: 0s. Last read position: KI270733.1:148,214
INFO 2026-05-28 21:34:39 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:39:26s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,187
INFO 2026-05-28 21:34:40 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:39:27s. Time for last 1,000,000: 0s. Last read position: KI270733.1:178,729
INFO 2026-05-28 21:34:41 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:39:28s. Time for last 1,000,000: 0s. Last read position: */*
INFO 2026-05-28 21:34:43 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:39:29s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 21:34:44 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 39.58 minutes.
Runtime.totalMemory()=3270508544