Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/e7e472702900f870eec5eb9cd82518/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.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/66/3231eeede2403a4f3cb44acb9111a7/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/58e14299ea9f2bba29297a61eaae25/.command.sh
  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/68/58e14299ea9f2bba29297a61eaae25/.command.run
==> 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 8:08:01 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 20:08:01 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_2.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_2_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 20:08:01 GMT 2026] Executing as ?@nf-6858e14299ea9f2bba29297a61eaae25-7fa04-pp4zn 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 20:08:03	CollectRnaSeqMetrics	Loaded 58279 genes.
INFO	2026-05-28 20:08:08	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr21:8,442,520
[Thu May 28 20:08:11 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=1594359808