/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 8:09:11 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 20:09:11 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_3.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_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 20:09:11 GMT 2026] Executing as ?@nf-a15eb343c085a48cb3fb676564d3b2ac-0a4ed-vb679 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 20:09:14	CollectRnaSeqMetrics	Loaded 58279 genes.
INFO	2026-05-28 20:09:17	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr10:104,479,813
INFO	2026-05-28 20:09:20	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    2s.  Last read position: chr21:8,217,329
INFO	2026-05-28 20:09:22	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    2s.  Last read position: chr22:11,630,472
INFO	2026-05-28 20:09:24	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:131,106
[Thu May 28 20:09:25 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.24 minutes.
Runtime.totalMemory()=1570766848