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/b5/a928f2dacaf0d0ead5a67b53133f9b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/369a4c1784fa5c8c1eb6124589dba9/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/a928f2dacaf0d0ead5a67b53133f9b/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/e750b7e0760a212602dfae8d940a92/BreastNP_FFPE_L03_RNA_01_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 8:16:05 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 20:16:05 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_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 20:16:05 GMT 2026] Executing as ?@nf-b5a928f2dacaf0d0ead5a67b53133f9b-be056-x29c6 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.XXXXhtBEbI/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXhtBEbI/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 20:16:07 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:16:23 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:19,074,799
INFO 2026-05-28 20:16:38 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 15s. Last read position: chr1:41,381,776
INFO 2026-05-28 20:16:49 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 10s. Last read position: chr1:103,617,952
INFO 2026-05-28 20:16:52 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:103,662,901
INFO 2026-05-28 20:16:54 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:103,714,755
INFO 2026-05-28 20:16:55 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:109,171,866
INFO 2026-05-28 20:17:05 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 9s. Last read position: chr1:155,187,775
INFO 2026-05-28 20:17:18 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 12s. Last read position: chr1:206,930,285
INFO 2026-05-28 20:17:28 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 10s. Last read position: chr2:10,047,883
INFO 2026-05-28 20:17:35 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 6s. Last read position: chr2:38,482,724
INFO 2026-05-28 20:17:45 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 9s. Last read position: chr2:95,276,231
INFO 2026-05-28 20:17:56 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 11s. Last read position: chr2:178,573,162
INFO 2026-05-28 20:18:19 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 23s. Last read position: chr2:241,063,676
INFO 2026-05-28 20:18:36 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 16s. Last read position: chr3:48,694,848
INFO 2026-05-28 20:18:48 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 12s. Last read position: chr3:127,660,820
INFO 2026-05-28 20:19:03 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 14s. Last read position: chr3:197,026,710
INFO 2026-05-28 20:19:13 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 9s. Last read position: chr4:69,999,670
INFO 2026-05-28 20:19:18 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 4s. Last read position: chr4:70,384,520
INFO 2026-05-28 20:19:21 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 3s. Last read position: chr4:70,389,866
INFO 2026-05-28 20:19:26 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 4s. Last read position: chr4:70,481,286
INFO 2026-05-28 20:19:30 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 4s. Last read position: chr4:70,481,656
INFO 2026-05-28 20:19:44 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 13s. Last read position: chr5:443,227
INFO 2026-05-28 20:19:55 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 11s. Last read position: chr5:132,591,235
INFO 2026-05-28 20:20:05 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 9s. Last read position: chr5:172,770,753
INFO 2026-05-28 20:20:15 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 10s. Last read position: chr6:30,910,858
INFO 2026-05-28 20:20:29 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 14s. Last read position: chr6:63,572,572
INFO 2026-05-28 20:20:41 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 11s. Last read position: chr6:158,783,657
INFO 2026-05-28 20:20:51 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 10s. Last read position: chr7:66,945,138
INFO 2026-05-28 20:21:05 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 14s. Last read position: chr7:100,694,318
INFO 2026-05-28 20:21:15 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 9s. Last read position: chr7:144,284,829
INFO 2026-05-28 20:21:31 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 15s. Last read position: chr8:70,148,423
INFO 2026-05-28 20:21:58 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 27s. Last read position: chr8:143,862,065
INFO 2026-05-28 20:22:14 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 15s. Last read position: chr9:35,398,214
INFO 2026-05-28 20:22:31 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 16s. Last read position: chr9:121,760,144
INFO 2026-05-28 20:22:48 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 17s. Last read position: chr10:3,163,756
INFO 2026-05-28 20:23:13 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 24s. Last read position: chr10:79,277,299
INFO 2026-05-28 20:23:34 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 21s. Last read position: chr10:122,589,028
INFO 2026-05-28 20:24:03 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 28s. Last read position: chr11:1,242,725
INFO 2026-05-28 20:24:09 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 5s. Last read position: chr11:1,245,049
INFO 2026-05-28 20:24:16 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 6s. Last read position: chr11:1,248,038
INFO 2026-05-28 20:24:26 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 9s. Last read position: chr11:1,250,478
INFO 2026-05-28 20:24:43 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 16s. Last read position: chr11:45,806,027
INFO 2026-05-28 20:24:59 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 16s. Last read position: chr11:65,503,409
INFO 2026-05-28 20:25:19 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 19s. Last read position: chr11:94,869,215
INFO 2026-05-28 20:25:38 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 18s. Last read position: chr12:7,091,519
INFO 2026-05-28 20:25:43 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 5s. Last read position: chr12:10,882,383
INFO 2026-05-28 20:25:49 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 5s. Last read position: chr12:10,929,258
INFO 2026-05-28 20:25:56 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 7s. Last read position: chr12:10,930,855
INFO 2026-05-28 20:26:07 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 11s. Last read position: chr12:40,487,305
INFO 2026-05-28 20:26:29 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 22s. Last read position: chr12:56,642,492
INFO 2026-05-28 20:26:46 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 16s. Last read position: chr12:110,445,482
INFO 2026-05-28 20:27:05 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 18s. Last read position: chr13:39,014,375
INFO 2026-05-28 20:27:33 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 27s. Last read position: chr14:32,545,812
INFO 2026-05-28 20:27:50 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 17s. Last read position: chr14:92,811,568
INFO 2026-05-28 20:28:09 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 19s. Last read position: chr14:105,707,164
INFO 2026-05-28 20:28:13 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 3s. Last read position: chr14:105,931,651
INFO 2026-05-28 20:28:30 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 17s. Last read position: chr15:66,518,855
INFO 2026-05-28 20:28:48 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 17s. Last read position: chr16:1,459,126
INFO 2026-05-28 20:29:10 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 21s. Last read position: chr16:4,469,456
INFO 2026-05-28 20:29:21 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 11s. Last read position: chr16:21,837,207
INFO 2026-05-28 20:29:32 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 11s. Last read position: chr16:30,711,836
INFO 2026-05-28 20:29:50 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 17s. Last read position: chr16:88,647,101
INFO 2026-05-28 20:30:11 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 21s. Last read position: chr17:16,382,161
INFO 2026-05-28 20:30:30 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 18s. Last read position: chr17:42,120,986
INFO 2026-05-28 20:30:48 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 18s. Last read position: chr17:64,504,244
INFO 2026-05-28 20:31:20 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 31s. Last read position: chr17:82,587,143
INFO 2026-05-28 20:31:38 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:15:30s. Time for last 1,000,000: 18s. Last read position: chr19:2,353,114
INFO 2026-05-28 20:31:58 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 19s. Last read position: chr19:13,137,356
INFO 2026-05-28 20:32:13 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 15s. Last read position: chr19:39,177,677
INFO 2026-05-28 20:32:31 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 17s. Last read position: chr19:49,497,270
INFO 2026-05-28 20:32:47 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 16s. Last read position: chr20:17,658,891
INFO 2026-05-28 20:32:56 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 8s. Last read position: chr20:23,685,944
INFO 2026-05-28 20:32:59 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:16:51s. Time for last 1,000,000: 3s. Last read position: chr20:23,747,843
INFO 2026-05-28 20:33:04 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 4s. Last read position: chr20:33,169,190
INFO 2026-05-28 20:33:16 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:17:08s. Time for last 1,000,000: 12s. Last read position: chr20:51,622,072
INFO 2026-05-28 20:33:37 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 20s. Last read position: chr21:8,214,783
INFO 2026-05-28 20:33:39 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:17:31s. Time for last 1,000,000: 1s. Last read position: chr21:8,254,558
INFO 2026-05-28 20:33:40 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,776
INFO 2026-05-28 20:33:43 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 2s. Last read position: chr21:8,400,997
INFO 2026-05-28 20:33:44 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:17:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,105
INFO 2026-05-28 20:33:55 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 10s. Last read position: chr21:45,992,208
INFO 2026-05-28 20:34:11 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 16s. Last read position: chr22:37,630,934
INFO 2026-05-28 20:34:27 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 15s. Last read position: chrX:40,073,338
INFO 2026-05-28 20:34:45 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:18:37s. Time for last 1,000,000: 17s. Last read position: chrX:153,694,863
INFO 2026-05-28 20:34:52 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:18:44s. Time for last 1,000,000: 6s. Last read position: GL000220.1:114,254
INFO 2026-05-28 20:34:53 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,231
INFO 2026-05-28 20:34:54 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:18:47s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,308
INFO 2026-05-28 20:34:56 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:18:48s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,108
INFO 2026-05-28 20:34:58 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:18:50s. Time for last 1,000,000: 1s. Last read position: KI270733.1:175,044
INFO 2026-05-28 20:34:59 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,276
INFO 2026-05-28 20:35:00 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:18:53s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 20:35:03 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 18.97 minutes.
Runtime.totalMemory()=2942828544