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/e5/531ce8eeed88d6bca2bd96f40e7f0c/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/0d5d055c6099e38620512b17b35dd6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/64bb71db35614ee027015bc4586297/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/0d5d055c6099e38620512b17b35dd6/.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 8:21:07 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 20:21:07 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L01_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 20:21:07 GMT 2026] Executing as ?@nf-8d0d5d055c6099e38620512b17b35dd6-08481-4gkpl 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.XXXXfhLNCL/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXfhLNCL/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 20:21:10 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:21:29 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:11,920,134
INFO 2026-05-28 20:21:49 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 20s. Last read position: chr1:26,696,776
INFO 2026-05-28 20:22:11 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 21s. Last read position: chr1:39,429,932
INFO 2026-05-28 20:22:38 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 26s. Last read position: chr1:69,537,416
INFO 2026-05-28 20:22:52 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 13s. Last read position: chr1:120,793,280
INFO 2026-05-28 20:23:05 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 13s. Last read position: chr1:151,428,287
INFO 2026-05-28 20:23:31 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 25s. Last read position: chr1:161,524,586
INFO 2026-05-28 20:23:48 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 17s. Last read position: chr1:206,478,985
INFO 2026-05-28 20:24:20 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 32s. Last read position: chr1:236,017,197
INFO 2026-05-28 20:24:39 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 18s. Last read position: chr2:32,916,257
INFO 2026-05-28 20:24:47 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 8s. Last read position: chr2:43,225,676
INFO 2026-05-28 20:25:12 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 24s. Last read position: chr2:86,914,418
INFO 2026-05-28 20:25:23 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 10s. Last read position: chr2:117,986,017
INFO 2026-05-28 20:25:57 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 34s. Last read position: chr2:188,994,233
INFO 2026-05-28 20:26:33 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 35s. Last read position: chr2:218,228,882
INFO 2026-05-28 20:27:02 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 29s. Last read position: chr2:241,633,854
INFO 2026-05-28 20:27:29 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 27s. Last read position: chr3:42,637,339
INFO 2026-05-28 20:27:56 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 26s. Last read position: chr3:50,066,310
INFO 2026-05-28 20:28:19 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 22s. Last read position: chr3:111,884,107
INFO 2026-05-28 20:28:36 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 16s. Last read position: chr3:170,137,720
INFO 2026-05-28 20:28:58 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 22s. Last read position: chr4:1,167,577
INFO 2026-05-28 20:29:16 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 18s. Last read position: chr4:74,038,542
INFO 2026-05-28 20:29:44 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 27s. Last read position: chr4:152,661,290
INFO 2026-05-28 20:30:07 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 22s. Last read position: chr5:40,633,298
INFO 2026-05-28 20:30:27 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 20s. Last read position: chr5:118,973,996
INFO 2026-05-28 20:30:44 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 17s. Last read position: chr5:150,132,700
INFO 2026-05-28 20:31:08 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 23s. Last read position: chr5:179,623,133
INFO 2026-05-28 20:31:23 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 14s. Last read position: chr6:28,232,571
INFO 2026-05-28 20:31:41 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 17s. Last read position: chr6:33,413,411
INFO 2026-05-28 20:32:18 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 36s. Last read position: chr6:73,387,193
INFO 2026-05-28 20:32:38 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 19s. Last read position: chr6:139,373,612
INFO 2026-05-28 20:33:03 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 24s. Last read position: chr7:5,199,555
INFO 2026-05-28 20:33:21 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 18s. Last read position: chr7:47,808,247
INFO 2026-05-28 20:33:35 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 13s. Last read position: chr7:77,059,227
INFO 2026-05-28 20:34:08 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 33s. Last read position: chr7:100,812,731
INFO 2026-05-28 20:34:29 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 20s. Last read position: chr7:137,513,842
INFO 2026-05-28 20:34:48 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 18s. Last read position: chr7:158,941,918
INFO 2026-05-28 20:35:07 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 19s. Last read position: chr8:41,303,484
INFO 2026-05-28 20:35:37 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 29s. Last read position: chr8:115,414,883
INFO 2026-05-28 20:35:54 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 16s. Last read position: chr8:143,860,825
INFO 2026-05-28 20:36:04 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 10s. Last read position: chr8:144,547,384
INFO 2026-05-28 20:36:25 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:15:14s. Time for last 1,000,000: 21s. Last read position: chr9:40,040,880
INFO 2026-05-28 20:36:42 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 16s. Last read position: chr9:106,926,796
INFO 2026-05-28 20:37:05 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 23s. Last read position: chr9:130,626,438
INFO 2026-05-28 20:37:19 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 13s. Last read position: chr9:137,253,274
INFO 2026-05-28 20:37:40 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 21s. Last read position: chr10:38,080,382
INFO 2026-05-28 20:37:59 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 18s. Last read position: chr10:77,835,737
INFO 2026-05-28 20:38:16 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 17s. Last read position: chr10:104,002,958
INFO 2026-05-28 20:38:34 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 17s. Last read position: chr11:799,200
INFO 2026-05-28 20:38:51 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 16s. Last read position: chr11:27,368,271
INFO 2026-05-28 20:39:05 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 14s. Last read position: chr11:62,524,379
INFO 2026-05-28 20:39:22 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 16s. Last read position: chr11:65,654,679
INFO 2026-05-28 20:39:47 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:18:36s. Time for last 1,000,000: 25s. Last read position: chr11:72,015,317
INFO 2026-05-28 20:40:08 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 21s. Last read position: chr11:114,064,373
INFO 2026-05-28 20:40:29 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:19:18s. Time for last 1,000,000: 21s. Last read position: chr12:6,561,671
INFO 2026-05-28 20:40:49 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:19:38s. Time for last 1,000,000: 19s. Last read position: chr12:48,776,252
INFO 2026-05-28 20:41:11 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:20:00s. Time for last 1,000,000: 21s. Last read position: chr12:56,164,404
INFO 2026-05-28 20:41:34 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:20:23s. Time for last 1,000,000: 23s. Last read position: chr12:91,157,114
INFO 2026-05-28 20:41:55 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:20:43s. Time for last 1,000,000: 20s. Last read position: chr12:121,819,868
INFO 2026-05-28 20:42:09 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:20:58s. Time for last 1,000,000: 14s. Last read position: chr13:31,288,395
INFO 2026-05-28 20:42:27 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:21:16s. Time for last 1,000,000: 18s. Last read position: chr13:113,363,834
INFO 2026-05-28 20:42:51 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:21:40s. Time for last 1,000,000: 23s. Last read position: chr14:49,894,134
INFO 2026-05-28 20:43:10 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:21:59s. Time for last 1,000,000: 19s. Last read position: chr14:92,071,011
INFO 2026-05-28 20:43:45 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:22:34s. Time for last 1,000,000: 34s. Last read position: chr15:25,719,100
INFO 2026-05-28 20:44:01 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:22:50s. Time for last 1,000,000: 16s. Last read position: chr15:45,962,064
INFO 2026-05-28 20:44:23 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:23:12s. Time for last 1,000,000: 21s. Last read position: chr15:75,307,282
INFO 2026-05-28 20:44:38 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:23:27s. Time for last 1,000,000: 14s. Last read position: chr15:99,131,880
INFO 2026-05-28 20:45:04 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:23:53s. Time for last 1,000,000: 26s. Last read position: chr16:2,475,528
INFO 2026-05-28 20:45:29 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:24:18s. Time for last 1,000,000: 24s. Last read position: chr16:11,232,426
INFO 2026-05-28 20:45:38 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:24:27s. Time for last 1,000,000: 9s. Last read position: chr16:18,318,177
INFO 2026-05-28 20:45:45 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:24:34s. Time for last 1,000,000: 6s. Last read position: chr16:21,836,981
INFO 2026-05-28 20:45:55 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:24:44s. Time for last 1,000,000: 10s. Last read position: chr16:28,866,442
INFO 2026-05-28 20:46:03 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:24:52s. Time for last 1,000,000: 7s. Last read position: chr16:30,720,919
INFO 2026-05-28 20:46:19 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:25:08s. Time for last 1,000,000: 16s. Last read position: chr16:69,357,523
INFO 2026-05-28 20:46:33 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:25:22s. Time for last 1,000,000: 14s. Last read position: chr16:89,561,664
INFO 2026-05-28 20:46:54 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:25:43s. Time for last 1,000,000: 20s. Last read position: chr17:7,512,793
INFO 2026-05-28 20:47:13 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:26:02s. Time for last 1,000,000: 19s. Last read position: chr17:28,056,417
INFO 2026-05-28 20:47:31 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:26:20s. Time for last 1,000,000: 17s. Last read position: chr17:39,717,339
INFO 2026-05-28 20:47:49 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:26:38s. Time for last 1,000,000: 17s. Last read position: chr17:45,547,727
INFO 2026-05-28 20:48:02 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:26:51s. Time for last 1,000,000: 13s. Last read position: chr17:50,189,241
INFO 2026-05-28 20:48:13 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:27:02s. Time for last 1,000,000: 10s. Last read position: chr17:50,196,500
INFO 2026-05-28 20:48:35 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:27:24s. Time for last 1,000,000: 22s. Last read position: chr17:64,895,939
INFO 2026-05-28 20:49:00 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 24s. Last read position: chr17:80,112,073
INFO 2026-05-28 20:49:24 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:28:13s. Time for last 1,000,000: 23s. Last read position: chr18:15,005,523
INFO 2026-05-28 20:49:43 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:28:32s. Time for last 1,000,000: 18s. Last read position: chr19:1,011,098
INFO 2026-05-28 20:49:59 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:28:48s. Time for last 1,000,000: 16s. Last read position: chr19:5,690,507
INFO 2026-05-28 20:50:20 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:29:09s. Time for last 1,000,000: 20s. Last read position: chr19:12,797,141
INFO 2026-05-28 20:50:34 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:29:23s. Time for last 1,000,000: 14s. Last read position: chr19:18,155,921
INFO 2026-05-28 20:50:47 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:29:36s. Time for last 1,000,000: 12s. Last read position: chr19:39,407,944
INFO 2026-05-28 20:51:03 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:29:52s. Time for last 1,000,000: 16s. Last read position: chr19:45,179,856
INFO 2026-05-28 20:51:18 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:30:07s. Time for last 1,000,000: 14s. Last read position: chr19:49,616,039
INFO 2026-05-28 20:51:32 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:30:21s. Time for last 1,000,000: 13s. Last read position: chr19:57,477,322
INFO 2026-05-28 20:51:48 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:30:37s. Time for last 1,000,000: 16s. Last read position: chr20:19,799,723
INFO 2026-05-28 20:52:05 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:30:54s. Time for last 1,000,000: 16s. Last read position: chr20:49,224,968
INFO 2026-05-28 20:52:21 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:31:09s. Time for last 1,000,000: 15s. Last read position: chr21:8,210,385
INFO 2026-05-28 20:52:23 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:31:11s. Time for last 1,000,000: 2s. Last read position: chr21:8,216,852
INFO 2026-05-28 20:52:24 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:31:13s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,913
INFO 2026-05-28 20:52:26 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:31:15s. Time for last 1,000,000: 1s. Last read position: chr21:8,390,749
INFO 2026-05-28 20:52:28 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:31:17s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,947
INFO 2026-05-28 20:52:30 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:31:19s. Time for last 1,000,000: 2s. Last read position: chr21:8,441,960
INFO 2026-05-28 20:52:32 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:31:21s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,115
INFO 2026-05-28 20:52:39 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:31:28s. Time for last 1,000,000: 7s. Last read position: chr21:33,555,064
INFO 2026-05-28 20:53:03 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:31:52s. Time for last 1,000,000: 23s. Last read position: chr22:17,864,944
INFO 2026-05-28 20:53:23 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:32:12s. Time for last 1,000,000: 19s. Last read position: chr22:31,125,270
INFO 2026-05-28 20:53:41 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:32:30s. Time for last 1,000,000: 18s. Last read position: chr22:42,211,205
INFO 2026-05-28 20:53:57 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:32:46s. Time for last 1,000,000: 15s. Last read position: chrX:31,147,423
INFO 2026-05-28 20:54:23 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:33:12s. Time for last 1,000,000: 26s. Last read position: chrX:77,951,770
INFO 2026-05-28 20:54:41 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:33:30s. Time for last 1,000,000: 17s. Last read position: chrY:7,606,334
INFO 2026-05-28 20:54:42 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:33:31s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,195
INFO 2026-05-28 20:54:44 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:33:33s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,776
INFO 2026-05-28 20:54:45 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:33:34s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,158
INFO 2026-05-28 20:54:46 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:33:35s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,692
INFO 2026-05-28 20:54:48 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:33:37s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,020
INFO 2026-05-28 20:54:49 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:33:38s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,174
INFO 2026-05-28 20:54:50 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:33:39s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,077
INFO 2026-05-28 20:54:51 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:33:40s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,455
INFO 2026-05-28 20:54:53 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:33:42s. Time for last 1,000,000: 1s. Last read position: */*
INFO 2026-05-28 20:54:54 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:33:43s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 20:54:57 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 33.84 minutes.
Runtime.totalMemory()=3330801664