Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8af83348c10fab5a0aa13fa2175d18/22Rv1_FFPE_RNA_0001_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/8d/d5c0160aa23847c7ec88d4d3ff3f1d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/d5c0160aa23847c7ec88d4d3ff3f1d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/fabb87851698c222da39b3d189853e/22Rv1_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 8:10:06 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 20:10:06 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_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 20:10:06 GMT 2026] Executing as ?@nf-8dd5c0160aa23847c7ec88d4d3ff3f1d-f1d6e-b7jms 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
INFO 2026-05-28 20:10:09 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:10:27 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 17s. Last read position: chr1:40,861,919
INFO 2026-05-28 20:10:42 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 15s. Last read position: chr1:155,942,448
INFO 2026-05-28 20:10:59 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 17s. Last read position: chr2:15,541,965
INFO 2026-05-28 20:11:09 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 9s. Last read position: chr2:96,276,932
INFO 2026-05-28 20:11:28 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 19s. Last read position: chr2:238,246,421
INFO 2026-05-28 20:11:46 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 18s. Last read position: chr3:113,632,779
INFO 2026-05-28 20:12:02 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 15s. Last read position: chr4:82,429,614
INFO 2026-05-28 20:12:21 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 19s. Last read position: chr5:134,371,536
INFO 2026-05-28 20:12:32 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 11s. Last read position: chr6:19,838,130
INFO 2026-05-28 20:12:51 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 18s. Last read position: chr6:73,466,596
INFO 2026-05-28 20:13:06 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 15s. Last read position: chr7:44,107,866
INFO 2026-05-28 20:13:19 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 12s. Last read position: chr7:144,365,132
INFO 2026-05-28 20:13:33 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 14s. Last read position: chr8:138,929,847
INFO 2026-05-28 20:13:44 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 11s. Last read position: chr9:87,967,563
INFO 2026-05-28 20:14:01 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 16s. Last read position: chr10:24,546,081
INFO 2026-05-28 20:14:17 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 16s. Last read position: chr11:862,567
INFO 2026-05-28 20:14:30 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 13s. Last read position: chr11:66,315,615
INFO 2026-05-28 20:14:46 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 16s. Last read position: chr12:9,165,193
INFO 2026-05-28 20:15:03 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 16s. Last read position: chr12:107,382,429
INFO 2026-05-28 20:15:17 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 13s. Last read position: chr14:23,957,084
INFO 2026-05-28 20:15:32 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 14s. Last read position: chr14:105,587,599
INFO 2026-05-28 20:15:39 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 7s. Last read position: chr15:75,356,397
INFO 2026-05-28 20:15:54 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 14s. Last read position: chr16:16,374,889
INFO 2026-05-28 20:16:01 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 7s. Last read position: chr16:78,582,099
INFO 2026-05-28 20:16:12 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 10s. Last read position: chr17:38,010,689
INFO 2026-05-28 20:16:20 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 8s. Last read position: chr17:50,199,816
INFO 2026-05-28 20:16:32 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 11s. Last read position: chr18:76,441,644
INFO 2026-05-28 20:16:41 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 9s. Last read position: chr19:15,265,438
INFO 2026-05-28 20:16:49 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 8s. Last read position: chr19:42,410,535
INFO 2026-05-28 20:16:58 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 9s. Last read position: chr20:35,716,793
INFO 2026-05-28 20:17:03 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 5s. Last read position: chr21:8,214,876
INFO 2026-05-28 20:17:05 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,727
INFO 2026-05-28 20:17:06 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,818
INFO 2026-05-28 20:17:07 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,654
INFO 2026-05-28 20:17:08 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 0s. Last read position: chr21:8,444,535
INFO 2026-05-28 20:17:16 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 8s. Last read position: chr22:32,066,989
INFO 2026-05-28 20:17:26 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 9s. Last read position: chrX:106,999,703
INFO 2026-05-28 20:17:29 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 3s. Last read position: GL000220.1:114,450
INFO 2026-05-28 20:17:30 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,121
INFO 2026-05-28 20:17:31 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 0s. Last read position: GL000220.1:160,819
INFO 2026-05-28 20:17:32 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,167
INFO 2026-05-28 20:17:33 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,186
INFO 2026-05-28 20:17:34 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 20:17:35 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 7.49 minutes.
Runtime.totalMemory()=2861563904