/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 8:10:09 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 20:10:09 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_2.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_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 20:10:09 GMT 2026] Executing as ?@nf-1b896b15c310b8b78af6c1468f41903e-fdf27-26k87 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 20:10:12 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:10:34 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 22s. Last read position: chr1:45,341,086
INFO 2026-05-28 20:10:55 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 20s. Last read position: chr1:165,654,295
INFO 2026-05-28 20:11:12 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 16s. Last read position: chr2:32,916,406
INFO 2026-05-28 20:11:28 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 16s. Last read position: chr2:189,006,343
INFO 2026-05-28 20:11:53 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 24s. Last read position: chr3:50,297,159
INFO 2026-05-28 20:12:14 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 21s. Last read position: chr4:22,442,754
INFO 2026-05-28 20:12:34 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 20s. Last read position: chr5:118,973,773
INFO 2026-05-28 20:12:49 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 14s. Last read position: chr6:26,156,731
INFO 2026-05-28 20:13:12 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 23s. Last read position: chr6:111,274,281
INFO 2026-05-28 20:13:29 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 17s. Last read position: chr7:75,421,834
INFO 2026-05-28 20:13:46 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 16s. Last read position: chr8:30,504,372
INFO 2026-05-28 20:14:00 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 14s. Last read position: chr8:144,180,441
INFO 2026-05-28 20:14:17 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 17s. Last read position: chr9:134,765,706
INFO 2026-05-28 20:14:37 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 19s. Last read position: chr10:119,042,185
INFO 2026-05-28 20:14:55 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 18s. Last read position: chr11:65,554,300
INFO 2026-05-28 20:15:12 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 17s. Last read position: chr12:11,853,467
INFO 2026-05-28 20:15:30 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 17s. Last read position: chr12:119,179,587
INFO 2026-05-28 20:15:45 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 14s. Last read position: chr14:51,720,247
INFO 2026-05-28 20:15:59 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 14s. Last read position: chr14:105,708,566
INFO 2026-05-28 20:16:14 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 14s. Last read position: chr16:2,037,885
INFO 2026-05-28 20:16:25 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 11s. Last read position: chr16:30,700,847
INFO 2026-05-28 20:16:38 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 12s. Last read position: chr17:9,916,995
INFO 2026-05-28 20:16:49 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 11s. Last read position: chr17:50,190,354
INFO 2026-05-28 20:17:04 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 14s. Last read position: chr18:49,814,363
INFO 2026-05-28 20:17:16 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 12s. Last read position: chr19:15,257,094
INFO 2026-05-28 20:17:26 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 9s. Last read position: chr19:45,306,833
INFO 2026-05-28 20:17:37 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 10s. Last read position: chr20:50,191,214
INFO 2026-05-28 20:17:40 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 3s. Last read position: chr21:8,217,285
INFO 2026-05-28 20:17:41 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,111
INFO 2026-05-28 20:17:43 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,115
INFO 2026-05-28 20:17:51 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 8s. Last read position: chr22:31,260,007
INFO 2026-05-28 20:18:03 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 11s. Last read position: chrX:143,581,717
INFO 2026-05-28 20:18:06 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 3s. Last read position: GL000220.1:116,792
INFO 2026-05-28 20:18:07 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 0s. Last read position: KI270733.1:128,201
INFO 2026-05-28 20:18:08 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,024
INFO 2026-05-28 20:18:09 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 20:18:11 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 8.04 minutes.
Runtime.totalMemory()=2848980992