/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 8:15:02 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 20:15:02 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L04_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 20:15:02 GMT 2026] Executing as ?@nf-d32e5fcef5a1fc656a73a83da6692805-f0e96-ztzr6 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 WARNING: BAM index file /tmp/nxf.XXXXIQtj7R/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXIQtj7R/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam INFO 2026-05-28 20:15:05 CollectRnaSeqMetrics Loaded 58279 genes. INFO 2026-05-28 20:15:17 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:17,687,621 INFO 2026-05-28 20:15:29 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 12s. Last read position: chr1:35,192,514 INFO 2026-05-28 20:15:44 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 15s. Last read position: chr1:77,129,495 INFO 2026-05-28 20:15:52 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 7s. Last read position: chr1:148,615,701 INFO 2026-05-28 20:16:07 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 14s. Last read position: chr1:156,670,333 INFO 2026-05-28 20:16:18 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 10s. Last read position: chr1:207,886,756 INFO 2026-05-28 20:16:33 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 15s. Last read position: chr2:24,683,110 INFO 2026-05-28 20:16:39 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 6s. Last read position: chr2:43,260,074 INFO 2026-05-28 20:16:51 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 11s. Last read position: chr2:101,859,736 INFO 2026-05-28 20:17:04 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 13s. Last read position: chr2:188,994,548 INFO 2026-05-28 20:17:21 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 16s. Last read position: chr2:219,558,386 INFO 2026-05-28 20:17:36 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 15s. Last read position: chr3:30,963,602 INFO 2026-05-28 20:17:49 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 12s. Last read position: chr3:52,480,337 INFO 2026-05-28 20:18:00 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 11s. Last read position: chr3:133,586,626 INFO 2026-05-28 20:18:13 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 12s. Last read position: chr4:1,823,023 INFO 2026-05-28 20:18:25 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 11s. Last read position: chr4:104,494,739 INFO 2026-05-28 20:18:40 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 15s. Last read position: chr5:31,526,590 INFO 2026-05-28 20:18:52 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 12s. Last read position: chr5:136,054,800 INFO 2026-05-28 20:19:01 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 8s. Last read position: chr5:157,744,023 INFO 2026-05-28 20:19:20 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 18s. Last read position: chr6:15,334,513 INFO 2026-05-28 20:19:35 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 15s. Last read position: chr6:32,081,604 INFO 2026-05-28 20:20:00 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 24s. Last read position: chr6:79,203,580 INFO 2026-05-28 20:20:14 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 14s. Last read position: chr6:151,353,644 INFO 2026-05-28 20:20:36 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 22s. Last read position: chr7:23,507,440 INFO 2026-05-28 20:20:52 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 15s. Last read position: chr7:75,557,706 INFO 2026-05-28 20:21:11 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 19s. Last read position: chr7:102,654,713 INFO 2026-05-28 20:21:22 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 11s. Last read position: chr7:152,154,034 INFO 2026-05-28 20:21:39 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 17s. Last read position: chr8:41,934,447 INFO 2026-05-28 20:21:56 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 16s. Last read position: chr8:127,740,760 INFO 2026-05-28 20:22:06 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 10s. Last read position: chr9:14,116,232 INFO 2026-05-28 20:22:17 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 10s. Last read position: chr9:96,937,240 INFO 2026-05-28 20:22:33 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 16s. Last read position: chr9:131,468,679 INFO 2026-05-28 20:22:45 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 11s. Last read position: chr10:17,359,539 INFO 2026-05-28 20:23:04 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 18s. Last read position: chr10:77,809,708 INFO 2026-05-28 20:23:15 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 11s. Last read position: chr10:125,838,278 INFO 2026-05-28 20:23:26 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 10s. Last read position: chr11:14,643,986 INFO 2026-05-28 20:23:40 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 14s. Last read position: chr11:62,528,929 INFO 2026-05-28 20:23:57 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 17s. Last read position: chr11:68,312,724 INFO 2026-05-28 20:24:18 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 20s. Last read position: chr11:114,064,077 INFO 2026-05-28 20:24:38 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 19s. Last read position: chr12:8,224,718 INFO 2026-05-28 20:24:49 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 11s. Last read position: chr12:52,520,045 INFO 2026-05-28 20:25:14 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 24s. Last read position: chr12:66,152,286 INFO 2026-05-28 20:25:33 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 19s. Last read position: chr12:122,133,452 INFO 2026-05-28 20:25:50 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 17s. Last read position: chr13:50,843,495 INFO 2026-05-28 20:26:12 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 21s. Last read position: chr14:39,181,488 INFO 2026-05-28 20:26:33 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 20s. Last read position: chr14:95,260,818 INFO 2026-05-28 20:26:57 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 24s. Last read position: chr15:42,746,053 INFO 2026-05-28 20:27:17 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 20s. Last read position: chr15:77,467,154 INFO 2026-05-28 20:27:40 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 22s. Last read position: chr16:2,093,614 INFO 2026-05-28 20:28:03 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 23s. Last read position: chr16:15,127,728 INFO 2026-05-28 20:28:12 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 8s. Last read position: chr16:22,523,832 INFO 2026-05-28 20:28:23 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 11s. Last read position: chr16:30,729,220 INFO 2026-05-28 20:28:40 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 16s. Last read position: chr16:83,161,630 INFO 2026-05-28 20:28:57 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 16s. Last read position: chr17:7,384,700 INFO 2026-05-28 20:29:12 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 15s. Last read position: chr17:28,701,573 INFO 2026-05-28 20:29:26 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 13s. Last read position: chr17:42,300,129 INFO 2026-05-28 20:29:41 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 15s. Last read position: chr17:50,187,967 INFO 2026-05-28 20:29:56 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 15s. Last read position: chr17:50,194,754 INFO 2026-05-28 20:30:15 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 18s. Last read position: chr17:62,573,302 INFO 2026-05-28 20:30:42 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:37s. Time for last 1,000,000: 27s. Last read position: chr17:81,512,113 INFO 2026-05-28 20:31:04 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:15:59s. Time for last 1,000,000: 21s. Last read position: chr18:77,017,032 INFO 2026-05-28 20:31:17 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 13s. Last read position: chr19:6,709,826 INFO 2026-05-28 20:31:35 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 17s. Last read position: chr19:15,244,267 INFO 2026-05-28 20:31:43 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 8s. Last read position: chr19:35,269,140 INFO 2026-05-28 20:31:55 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 12s. Last read position: chr19:42,287,204 INFO 2026-05-28 20:32:07 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 11s. Last read position: chr19:49,490,532 INFO 2026-05-28 20:32:21 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 14s. Last read position: chr20:2,484,216 INFO 2026-05-28 20:32:42 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 20s. Last read position: chr20:45,952,339 INFO 2026-05-28 20:32:55 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 12s. Last read position: chr21:8,214,701 INFO 2026-05-28 20:32:57 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,026 INFO 2026-05-28 20:32:58 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,948 INFO 2026-05-28 20:33:00 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:17:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,817 INFO 2026-05-28 20:33:02 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:17:57s. Time for last 1,000,000: 2s. Last read position: chr21:8,400,357 INFO 2026-05-28 20:33:04 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 1s. Last read position: chr21:8,442,047 INFO 2026-05-28 20:33:06 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:18:01s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,587 INFO 2026-05-28 20:33:21 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:18:16s. Time for last 1,000,000: 15s. Last read position: chr21:46,124,658 INFO 2026-05-28 20:33:36 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 15s. Last read position: chr22:37,312,105 INFO 2026-05-28 20:33:51 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 14s. Last read position: chrX:2,726,309 INFO 2026-05-28 20:34:07 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 16s. Last read position: chrX:101,391,503 INFO 2026-05-28 20:34:22 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:19:16s. Time for last 1,000,000: 14s. Last read position: GL000220.1:114,119 INFO 2026-05-28 20:34:23 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:19:18s. Time for last 1,000,000: 1s. Last read position: GL000220.1:115,558 INFO 2026-05-28 20:34:24 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:19:19s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,871 INFO 2026-05-28 20:34:26 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,525 INFO 2026-05-28 20:34:27 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:19:22s. Time for last 1,000,000: 1s. Last read position: KI270733.1:129,665 INFO 2026-05-28 20:34:29 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:19:24s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,403 INFO 2026-05-28 20:34:30 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 1s. Last read position: KI270733.1:171,711 INFO 2026-05-28 20:34:32 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,713 INFO 2026-05-28 20:34:33 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:19:28s. Time for last 1,000,000: 1s. Last read position: KI270733.1:179,526 INFO 2026-05-28 20:34:35 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 1s. Last read position: */* [Thu May 28 20:34:37 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 19.59 minutes. Runtime.totalMemory()=2837446656