/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 8:23:08 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 20:23:08 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_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 20:23:08 GMT 2026] Executing as ?@nf-02f8247f7c685aaface742a4a79347c0-4fc46-tjwtd 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.XXXXepKRzS/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXepKRzS/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 20:23:11 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 20:23:31 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 19s. Last read position: chr1:11,099,736
INFO 2026-05-28 20:23:50 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 19s. Last read position: chr1:24,654,932
INFO 2026-05-28 20:24:07 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 16s. Last read position: chr1:35,841,527
INFO 2026-05-28 20:24:38 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 31s. Last read position: chr1:58,782,296
INFO 2026-05-28 20:24:53 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 14s. Last read position: chr1:119,948,519
INFO 2026-05-28 20:25:01 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 7s. Last read position: chr1:150,557,933
INFO 2026-05-28 20:25:20 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 19s. Last read position: chr1:155,751,817
INFO 2026-05-28 20:25:38 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 17s. Last read position: chr1:185,120,109
INFO 2026-05-28 20:25:51 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 13s. Last read position: chr1:226,736,010
INFO 2026-05-28 20:26:22 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 30s. Last read position: chr2:24,081,008
INFO 2026-05-28 20:26:32 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 10s. Last read position: chr2:32,916,406
INFO 2026-05-28 20:26:51 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 19s. Last read position: chr2:72,515,092
INFO 2026-05-28 20:27:02 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 10s. Last read position: chr2:108,762,131
INFO 2026-05-28 20:27:13 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 11s. Last read position: chr2:161,341,138
INFO 2026-05-28 20:27:47 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 33s. Last read position: chr2:189,005,382
INFO 2026-05-28 20:28:22 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 34s. Last read position: chr2:215,434,754
INFO 2026-05-28 20:28:46 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 24s. Last read position: chr2:237,493,429
INFO 2026-05-28 20:29:07 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 20s. Last read position: chr3:37,261,017
INFO 2026-05-28 20:29:29 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 22s. Last read position: chr3:49,691,422
INFO 2026-05-28 20:29:49 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 20s. Last read position: chr3:101,664,975
INFO 2026-05-28 20:30:05 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 15s. Last read position: chr3:150,546,052
INFO 2026-05-28 20:30:28 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 23s. Last read position: chr3:195,996,661
INFO 2026-05-28 20:30:49 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 20s. Last read position: chr4:41,990,661
INFO 2026-05-28 20:31:12 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 23s. Last read position: chr4:140,662,030
INFO 2026-05-28 20:31:35 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 23s. Last read position: chr5:14,488,041
INFO 2026-05-28 20:31:49 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 13s. Last read position: chr5:83,537,602
INFO 2026-05-28 20:32:03 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 14s. Last read position: chr5:141,215,586
INFO 2026-05-28 20:32:15 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 12s. Last read position: chr5:170,718,774
INFO 2026-05-28 20:32:32 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 17s. Last read position: chr6:7,231,444
INFO 2026-05-28 20:32:48 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 15s. Last read position: chr6:31,816,662
INFO 2026-05-28 20:33:08 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 20s. Last read position: chr6:36,211,295
INFO 2026-05-28 20:33:37 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 29s. Last read position: chr6:89,750,349
INFO 2026-05-28 20:33:51 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 14s. Last read position: chr6:150,936,829
INFO 2026-05-28 20:34:10 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 18s. Last read position: chr7:5,388,222
INFO 2026-05-28 20:34:26 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 15s. Last read position: chr7:55,019,114
INFO 2026-05-28 20:34:37 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 11s. Last read position: chr7:79,186,053
INFO 2026-05-28 20:35:09 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 31s. Last read position: chr7:100,157,903
INFO 2026-05-28 20:35:24 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 15s. Last read position: chr7:130,666,848
INFO 2026-05-28 20:35:36 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 11s. Last read position: chr7:151,376,730
INFO 2026-05-28 20:35:55 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 19s. Last read position: chr8:37,698,301
INFO 2026-05-28 20:36:18 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 23s. Last read position: chr8:97,686,684
INFO 2026-05-28 20:36:38 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 19s. Last read position: chr8:143,864,767
INFO 2026-05-28 20:36:57 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 19s. Last read position: chr9:19,378,895
INFO 2026-05-28 20:37:09 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 11s. Last read position: chr9:96,819,104
INFO 2026-05-28 20:37:28 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 19s. Last read position: chr9:128,180,469
INFO 2026-05-28 20:37:47 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 18s. Last read position: chr9:135,938,230
INFO 2026-05-28 20:38:04 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 17s. Last read position: chr10:24,619,805
INFO 2026-05-28 20:38:19 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 14s. Last read position: chr10:63,473,839
INFO 2026-05-28 20:38:38 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 19s. Last read position: chr10:98,435,340
INFO 2026-05-28 20:38:55 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 17s. Last read position: chr11:294,616
INFO 2026-05-28 20:39:12 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 17s. Last read position: chr11:9,437,918
INFO 2026-05-28 20:39:31 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:16:19s. Time for last 1,000,000: 18s. Last read position: chr11:61,329,558
INFO 2026-05-28 20:39:44 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 12s. Last read position: chr11:65,502,752
INFO 2026-05-28 20:39:56 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 11s. Last read position: chr11:72,003,420
INFO 2026-05-28 20:40:16 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 20s. Last read position: chr11:111,723,570
INFO 2026-05-28 20:40:35 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 19s. Last read position: chr12:3,274,017
INFO 2026-05-28 20:40:53 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 18s. Last read position: chr12:45,850,803
INFO 2026-05-28 20:41:13 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:18:01s. Time for last 1,000,000: 19s. Last read position: chr12:54,282,631
INFO 2026-05-28 20:41:35 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 22s. Last read position: chr12:65,326,905
INFO 2026-05-28 20:41:55 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:18:43s. Time for last 1,000,000: 19s. Last read position: chr12:116,019,848
INFO 2026-05-28 20:42:15 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:19:03s. Time for last 1,000,000: 20s. Last read position: chr12:132,640,312
INFO 2026-05-28 20:42:33 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 17s. Last read position: chr13:106,534,843
INFO 2026-05-28 20:42:52 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:19:40s. Time for last 1,000,000: 19s. Last read position: chr14:28,767,471
INFO 2026-05-28 20:43:16 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:20:04s. Time for last 1,000,000: 23s. Last read position: chr14:73,612,845
INFO 2026-05-28 20:43:45 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:20:34s. Time for last 1,000,000: 29s. Last read position: chr14:103,700,708
INFO 2026-05-28 20:44:03 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:20:51s. Time for last 1,000,000: 17s. Last read position: chr15:34,529,974
INFO 2026-05-28 20:44:22 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:21:10s. Time for last 1,000,000: 19s. Last read position: chr15:63,770,843
INFO 2026-05-28 20:44:36 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:21:24s. Time for last 1,000,000: 13s. Last read position: chr15:84,433,221
INFO 2026-05-28 20:44:49 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:21:37s. Time for last 1,000,000: 12s. Last read position: chr16:1,379,273
INFO 2026-05-28 20:45:11 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:21:59s. Time for last 1,000,000: 22s. Last read position: chr16:2,767,014
INFO 2026-05-28 20:45:21 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:22:09s. Time for last 1,000,000: 9s. Last read position: chr16:15,131,500
INFO 2026-05-28 20:45:27 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:22:15s. Time for last 1,000,000: 6s. Last read position: chr16:18,531,100
INFO 2026-05-28 20:45:34 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:22:23s. Time for last 1,000,000: 7s. Last read position: chr16:22,527,494
INFO 2026-05-28 20:45:47 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:22:35s. Time for last 1,000,000: 12s. Last read position: chr16:29,382,853
INFO 2026-05-28 20:45:55 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:22:43s. Time for last 1,000,000: 7s. Last read position: chr16:30,704,208
INFO 2026-05-28 20:46:12 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:23:00s. Time for last 1,000,000: 17s. Last read position: chr16:68,191,539
INFO 2026-05-28 20:46:23 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:23:11s. Time for last 1,000,000: 10s. Last read position: chr16:88,806,610
INFO 2026-05-28 20:46:47 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:23:35s. Time for last 1,000,000: 24s. Last read position: chr17:7,311,634
INFO 2026-05-28 20:47:05 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:23:53s. Time for last 1,000,000: 17s. Last read position: chr17:18,671,108
INFO 2026-05-28 20:47:17 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:24:05s. Time for last 1,000,000: 11s. Last read position: chr17:39,415,260
INFO 2026-05-28 20:47:37 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:24:25s. Time for last 1,000,000: 20s. Last read position: chr17:45,097,209
INFO 2026-05-28 20:47:50 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:24:38s. Time for last 1,000,000: 13s. Last read position: chr17:50,186,341
INFO 2026-05-28 20:48:01 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:24:49s. Time for last 1,000,000: 11s. Last read position: chr17:50,188,123
INFO 2026-05-28 20:48:11 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:24:59s. Time for last 1,000,000: 10s. Last read position: chr17:50,189,526
INFO 2026-05-28 20:48:24 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:25:12s. Time for last 1,000,000: 13s. Last read position: chr17:50,191,995
INFO 2026-05-28 20:48:40 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:25:28s. Time for last 1,000,000: 15s. Last read position: chr17:50,194,730
INFO 2026-05-28 20:48:55 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:25:43s. Time for last 1,000,000: 14s. Last read position: chr17:50,196,517
INFO 2026-05-28 20:49:07 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:25:55s. Time for last 1,000,000: 12s. Last read position: chr17:50,199,318
INFO 2026-05-28 20:49:28 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:26:16s. Time for last 1,000,000: 20s. Last read position: chr17:63,550,686
INFO 2026-05-28 20:49:50 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:26:38s. Time for last 1,000,000: 22s. Last read position: chr17:78,049,372
INFO 2026-05-28 20:50:12 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:27:00s. Time for last 1,000,000: 21s. Last read position: chr17:82,273,373
INFO 2026-05-28 20:50:31 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:27:19s. Time for last 1,000,000: 19s. Last read position: chr18:67,512,995
INFO 2026-05-28 20:50:44 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:27:32s. Time for last 1,000,000: 13s. Last read position: chr19:4,054,321
INFO 2026-05-28 20:50:58 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:27:46s. Time for last 1,000,000: 13s. Last read position: chr19:10,797,097
INFO 2026-05-28 20:51:22 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:28:10s. Time for last 1,000,000: 23s. Last read position: chr19:15,432,575
INFO 2026-05-28 20:51:36 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:28:24s. Time for last 1,000,000: 14s. Last read position: chr19:35,545,891
INFO 2026-05-28 20:51:55 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:28:43s. Time for last 1,000,000: 18s. Last read position: chr19:42,117,290
INFO 2026-05-28 20:52:09 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:28:57s. Time for last 1,000,000: 14s. Last read position: chr19:46,693,882
INFO 2026-05-28 20:52:20 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:29:08s. Time for last 1,000,000: 11s. Last read position: chr19:50,268,212
INFO 2026-05-28 20:52:29 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:29:17s. Time for last 1,000,000: 9s. Last read position: chr19:58,549,802
INFO 2026-05-28 20:52:39 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:29:27s. Time for last 1,000,000: 10s. Last read position: chr20:35,271,601
INFO 2026-05-28 20:52:57 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:29:45s. Time for last 1,000,000: 17s. Last read position: chr20:62,006,679
INFO 2026-05-28 20:53:04 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:29:52s. Time for last 1,000,000: 7s. Last read position: chr21:8,214,717
INFO 2026-05-28 20:53:05 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:29:53s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,073
INFO 2026-05-28 20:53:07 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:29:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,927
INFO 2026-05-28 20:53:09 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:29:57s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,746
INFO 2026-05-28 20:53:11 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:29:59s. Time for last 1,000,000: 2s. Last read position: chr21:8,400,295
INFO 2026-05-28 20:53:13 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:30:02s. Time for last 1,000,000: 2s. Last read position: chr21:8,441,966
INFO 2026-05-28 20:53:15 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:30:03s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,142
INFO 2026-05-28 20:53:22 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:30:11s. Time for last 1,000,000: 7s. Last read position: chr21:36,937,035
INFO 2026-05-28 20:53:40 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:30:28s. Time for last 1,000,000: 17s. Last read position: chr22:19,137,354
INFO 2026-05-28 20:53:57 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:30:45s. Time for last 1,000,000: 17s. Last read position: chr22:31,748,833
INFO 2026-05-28 20:54:11 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:30:59s. Time for last 1,000,000: 14s. Last read position: chr22:44,736,907
INFO 2026-05-28 20:54:26 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:31:14s. Time for last 1,000,000: 15s. Last read position: chrX:40,057,154
INFO 2026-05-28 20:54:47 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:31:35s. Time for last 1,000,000: 21s. Last read position: chrX:85,255,717
INFO 2026-05-28 20:55:07 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:31:55s. Time for last 1,000,000: 19s. Last read position: chrX:156,025,080
INFO 2026-05-28 20:55:08 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:31:56s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,202
INFO 2026-05-28 20:55:10 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:31:58s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,763
INFO 2026-05-28 20:55:11 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:31:59s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,157
INFO 2026-05-28 20:55:12 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:32:00s. Time for last 1,000,000: 0s. Last read position: GL000220.1:160,614
INFO 2026-05-28 20:55:13 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:32:01s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,014
INFO 2026-05-28 20:55:14 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:32:02s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,174
INFO 2026-05-28 20:55:15 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:32:03s. Time for last 1,000,000: 0s. Last read position: KI270733.1:175,851
INFO 2026-05-28 20:55:16 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:32:04s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,486
INFO 2026-05-28 20:55:17 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:32:06s. Time for last 1,000,000: 1s. Last read position: */*
INFO 2026-05-28 20:55:19 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:32:07s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 20:55:22 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 32.23 minutes.
Runtime.totalMemory()=3193962496