/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 8:11:15 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 20:11:15 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_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_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 20:11:15 GMT 2026] Executing as ?@nf-04126bb592a14f19a6a72dd5aee527a7-95182-wf6rb 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 20:11:20 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:11:39 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:114,464,347
INFO 2026-05-28 20:11:57 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 18s. Last read position: chr2:13,227,518
INFO 2026-05-28 20:12:10 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 12s. Last read position: chr2:178,681,115
INFO 2026-05-28 20:12:30 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 20s. Last read position: chr3:105,577,790
INFO 2026-05-28 20:12:46 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 15s. Last read position: chr4:188,533,863
INFO 2026-05-28 20:12:59 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 13s. Last read position: chr6:3,224,944
INFO 2026-05-28 20:13:16 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 16s. Last read position: chr6:151,223,784
INFO 2026-05-28 20:13:34 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 17s. Last read position: chr7:137,908,315
INFO 2026-05-28 20:13:47 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 13s. Last read position: chr8:143,866,188
INFO 2026-05-28 20:14:02 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 15s. Last read position: chr10:11,096,338
INFO 2026-05-28 20:14:18 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 15s. Last read position: chr11:44,970,703
INFO 2026-05-28 20:14:36 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 17s. Last read position: chr12:6,581,150
INFO 2026-05-28 20:14:53 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 17s. Last read position: chr12:128,971,632
INFO 2026-05-28 20:15:09 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 15s. Last read position: chr14:104,893,056
INFO 2026-05-28 20:15:19 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 10s. Last read position: chr15:99,131,351
INFO 2026-05-28 20:15:30 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 10s. Last read position: chr16:66,604,864
INFO 2026-05-28 20:15:41 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 10s. Last read position: chr17:41,624,493
INFO 2026-05-28 20:15:52 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 11s. Last read position: chr18:44,949,891
INFO 2026-05-28 20:16:04 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 11s. Last read position: chr19:35,095,511
INFO 2026-05-28 20:16:13 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 8s. Last read position: chr20:17,825,458
INFO 2026-05-28 20:16:17 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 3s. Last read position: chr21:8,216,846
INFO 2026-05-28 20:16:18 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,478
INFO 2026-05-28 20:16:20 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr21:8,442,047
INFO 2026-05-28 20:16:24 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 3s. Last read position: chr22:20,566,657
INFO 2026-05-28 20:16:33 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 9s. Last read position: chrX:154,349,653
INFO 2026-05-28 20:16:35 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,801
INFO 2026-05-28 20:16:36 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 0s. Last read position: KI270733.1:126,207
INFO 2026-05-28 20:16:37 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 0s. Last read position: KI270733.1:173,231
INFO 2026-05-28 20:16:38 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 0s. Last read position: */*
[Thu May 28 20:16:39 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 5.40 minutes.
Runtime.totalMemory()=2781347840