Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/976a206c506e2bfc1dcdbe9906f9f4/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.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/3f/2c2f989dd79525e9f366c6a060621d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/2c2f989dd79525e9f366c6a060621d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/865b5c1e28a21171d2f43a3719ea8a/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.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 8:12:04 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 20:12:04 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_3.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_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 20:12:04 GMT 2026] Executing as ?@nf-3f2c2f989dd79525e9f366c6a060621d-baf69-97b52 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 20:12:07 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:12:28 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 20s. Last read position: chr1:43,415,997
INFO 2026-05-28 20:12:48 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 20s. Last read position: chr1:156,137,005
INFO 2026-05-28 20:13:08 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 19s. Last read position: chr2:27,366,774
INFO 2026-05-28 20:13:19 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 11s. Last read position: chr2:113,437,951
INFO 2026-05-28 20:13:46 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 26s. Last read position: chr3:13,637,781
INFO 2026-05-28 20:14:07 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 20s. Last read position: chr3:143,972,170
INFO 2026-05-28 20:14:28 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 21s. Last read position: chr4:153,788,504
INFO 2026-05-28 20:14:43 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 15s. Last read position: chr5:149,362,802
INFO 2026-05-28 20:15:00 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 16s. Last read position: chr6:32,052,785
INFO 2026-05-28 20:15:19 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 19s. Last read position: chr6:151,240,622
INFO 2026-05-28 20:15:35 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 16s. Last read position: chr7:94,430,251
INFO 2026-05-28 20:15:49 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 13s. Last read position: chr8:37,841,922
INFO 2026-05-28 20:16:03 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 14s. Last read position: chr8:144,512,966
INFO 2026-05-28 20:16:16 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 12s. Last read position: chr9:133,071,385
INFO 2026-05-28 20:16:29 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 12s. Last read position: chr10:102,656,900
INFO 2026-05-28 20:16:39 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 10s. Last read position: chr11:62,620,532
INFO 2026-05-28 20:16:51 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 12s. Last read position: chr11:129,892,789
INFO 2026-05-28 20:17:06 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 14s. Last read position: chr12:57,614,578
INFO 2026-05-28 20:17:19 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 12s. Last read position: chr13:110,419,985
INFO 2026-05-28 20:17:32 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 13s. Last read position: chr14:104,950,468
INFO 2026-05-28 20:17:39 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 6s. Last read position: chr15:68,187,090
INFO 2026-05-28 20:17:53 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 13s. Last read position: chr16:15,732,581
INFO 2026-05-28 20:18:01 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 8s. Last read position: chr16:70,664,225
INFO 2026-05-28 20:18:13 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 11s. Last read position: chr17:35,986,587
INFO 2026-05-28 20:18:24 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 11s. Last read position: chr17:50,863,177
INFO 2026-05-28 20:18:37 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 13s. Last read position: chr19:860,729
INFO 2026-05-28 20:18:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 10s. Last read position: chr19:17,511,738
INFO 2026-05-28 20:18:58 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 9s. Last read position: chr19:45,792,516
INFO 2026-05-28 20:19:07 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 9s. Last read position: chr20:51,488,531
INFO 2026-05-28 20:19:10 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 3s. Last read position: chr21:8,216,882
INFO 2026-05-28 20:19:11 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,444
INFO 2026-05-28 20:19:12 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,974
INFO 2026-05-28 20:19:16 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 3s. Last read position: chr21:44,456,542
INFO 2026-05-28 20:19:26 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 10s. Last read position: chrX:1,354,849
INFO 2026-05-28 20:19:35 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 8s. Last read position: GL000220.1:114,010
INFO 2026-05-28 20:19:36 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,088
INFO 2026-05-28 20:19:37 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 0s. Last read position: KI270733.1:130,991
INFO 2026-05-28 20:19:38 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 0s. Last read position: KI270733.1:175,897
INFO 2026-05-28 20:19:38 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 20:19:40 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 7.60 minutes.
Runtime.totalMemory()=2766667776