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/f9/9b7e7b2ef1237e3e9faba4ba632e7a/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0750d3b6bd7ad1407a0938d7a38a82/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0750d3b6bd7ad1407a0938d7a38a82/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/1b6839c2f11fb05d655d02c6eec5b1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> 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 8:07:13 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 20:07:13 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_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 20:07:13 GMT 2026] Executing as ?@nf-de0750d3b6bd7ad1407a0938d7a38a82-db051-q44wk 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 20:07:17 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:07:21 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr11:85,484,188
INFO 2026-05-28 20:07:25 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr21:8,397,817
INFO 2026-05-28 20:07:26 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,237
[Thu May 28 20:07:29 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=1714946048