/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 8:11:10 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 20:11:10 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_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 20:11:10 GMT 2026] Executing as ?@nf-637560919fe8c53679681fc7bb33a877-ee6e7-xh2lx 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 20:11:14 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:11:33 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 19s. Last read position: chr1:154,170,699
INFO 2026-05-28 20:11:49 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 15s. Last read position: chr2:55,232,826
INFO 2026-05-28 20:12:08 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 19s. Last read position: chr3:20,101,400
INFO 2026-05-28 20:12:26 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 18s. Last read position: chr3:195,784,165
INFO 2026-05-28 20:12:44 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 18s. Last read position: chr5:138,467,809
INFO 2026-05-28 20:12:57 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 12s. Last read position: chr6:138,424,240
INFO 2026-05-28 20:13:11 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 13s. Last read position: chr7:100,992,948
INFO 2026-05-28 20:13:14 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: chr7:100,996,313
INFO 2026-05-28 20:13:18 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: chr7:100,998,122
INFO 2026-05-28 20:13:21 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr7:101,000,813
INFO 2026-05-28 20:13:24 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr7:101,003,735
INFO 2026-05-28 20:13:36 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 12s. Last read position: chr8:143,859,092
INFO 2026-05-28 20:13:48 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 12s. Last read position: chr10:7,799,859
INFO 2026-05-28 20:14:05 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 16s. Last read position: chr11:3,702,314
INFO 2026-05-28 20:14:18 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 13s. Last read position: chr12:4,744,050
INFO 2026-05-28 20:14:33 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 14s. Last read position: chr13:49,746,972
INFO 2026-05-28 20:14:49 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 16s. Last read position: chr15:61,911,972
INFO 2026-05-28 20:15:03 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 14s. Last read position: chr16:21,599,760
INFO 2026-05-28 20:15:13 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 10s. Last read position: chr17:19,188,047
INFO 2026-05-28 20:15:28 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 14s. Last read position: chr18:76,379,957
INFO 2026-05-28 20:15:37 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 8s. Last read position: chr19:39,899,624
INFO 2026-05-28 20:15:50 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 13s. Last read position: chr20:62,324,486
INFO 2026-05-28 20:15:52 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,901
INFO 2026-05-28 20:15:59 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 6s. Last read position: chr22:31,104,234
INFO 2026-05-28 20:16:08 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 9s. Last read position: GL000220.1:114,342
INFO 2026-05-28 20:16:09 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,178
INFO 2026-05-28 20:16:11 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 20:16:12 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 5.03 minutes.
Runtime.totalMemory()=2536505344