/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Jun 03, 2026 7:07:29 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
[Wed Jun 03 19:07:29 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_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
[Wed Jun 03 19:07:29 GMT 2026] Executing as ?@nf-e0ed0c7b473469cf66a118f2ec9b5f93-62529-pm2mx 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.XXXXytozD8/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXytozD8/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-06-03 19:07:32 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-06-03 19:07:44 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:20,661,311
INFO 2026-06-03 19:07:55 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 10s. Last read position: chr1:35,883,358
INFO 2026-06-03 19:08:09 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 14s. Last read position: chr1:112,525,377
INFO 2026-06-03 19:08:16 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 7s. Last read position: chr1:155,060,725
INFO 2026-06-03 19:08:28 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 11s. Last read position: chr1:201,817,087
INFO 2026-06-03 19:08:39 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 10s. Last read position: chr2:17,931,676
INFO 2026-06-03 19:08:46 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 7s. Last read position: chr2:47,005,991
INFO 2026-06-03 19:08:58 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 11s. Last read position: chr2:108,534,554
INFO 2026-06-03 19:09:13 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 15s. Last read position: chr2:190,999,626
INFO 2026-06-03 19:09:43 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 29s. Last read position: chr2:219,418,482
INFO 2026-06-03 19:10:02 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 19s. Last read position: chr3:12,901,128
INFO 2026-06-03 19:10:15 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 13s. Last read position: chr3:52,516,735
INFO 2026-06-03 19:10:29 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 13s. Last read position: chr3:170,129,354
INFO 2026-06-03 19:10:51 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 21s. Last read position: chr4:10,098,990
INFO 2026-06-03 19:11:10 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 19s. Last read position: chr4:154,540,889
INFO 2026-06-03 19:11:29 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 19s. Last read position: chr5:122,775,099
INFO 2026-06-03 19:11:43 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 13s. Last read position: chr5:150,407,152
INFO 2026-06-03 19:11:59 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 16s. Last read position: chr6:495,294
INFO 2026-06-03 19:12:10 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 10s. Last read position: chr6:31,645,003
INFO 2026-06-03 19:12:22 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 12s. Last read position: chr6:43,051,419
INFO 2026-06-03 19:12:40 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 17s. Last read position: chr6:152,352,241
INFO 2026-06-03 19:12:57 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 17s. Last read position: chr7:6,501,816
INFO 2026-06-03 19:13:13 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 15s. Last read position: chr7:76,048,144
INFO 2026-06-03 19:13:29 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 15s. Last read position: chr7:100,994,326
INFO 2026-06-03 19:13:33 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 4s. Last read position: chr7:102,642,629
INFO 2026-06-03 19:13:47 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 13s. Last read position: chr7:151,079,853
INFO 2026-06-03 19:14:06 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 19s. Last read position: chr8:64,580,836
INFO 2026-06-03 19:14:20 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 13s. Last read position: chr8:143,862,590
INFO 2026-06-03 19:14:32 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 11s. Last read position: chr9:32,550,876
INFO 2026-06-03 19:14:46 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 13s. Last read position: chr9:115,086,604
INFO 2026-06-03 19:15:02 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 16s. Last read position: chr9:136,497,027
INFO 2026-06-03 19:15:16 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 14s. Last read position: chr10:69,415,941
INFO 2026-06-03 19:15:37 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 20s. Last read position: chr10:119,651,679
INFO 2026-06-03 19:15:49 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 12s. Last read position: chr11:2,928,915
INFO 2026-06-03 19:16:06 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 16s. Last read position: chr11:62,519,717
INFO 2026-06-03 19:16:20 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 13s. Last read position: chr11:66,599,243
INFO 2026-06-03 19:16:37 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 17s. Last read position: chr11:114,254,573
INFO 2026-06-03 19:16:57 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 20s. Last read position: chr12:7,921,550
INFO 2026-06-03 19:17:11 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 13s. Last read position: chr12:54,283,815
INFO 2026-06-03 19:17:26 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 14s. Last read position: chr12:108,591,851
INFO 2026-06-03 19:17:41 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 15s. Last read position: chr13:20,002,894
INFO 2026-06-03 19:17:55 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 13s. Last read position: chr14:22,998,445
INFO 2026-06-03 19:18:10 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 15s. Last read position: chr14:77,025,941
INFO 2026-06-03 19:18:34 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 23s. Last read position: chr14:105,643,216
INFO 2026-06-03 19:18:37 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr14:105,742,074
INFO 2026-06-03 19:18:43 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 6s. Last read position: chr15:39,581,196
INFO 2026-06-03 19:18:59 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 15s. Last read position: chr15:75,208,378
INFO 2026-06-03 19:19:13 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 14s. Last read position: chr16:1,777,287
INFO 2026-06-03 19:19:34 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 21s. Last read position: chr16:15,718,349
INFO 2026-06-03 19:19:56 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 22s. Last read position: chr16:21,834,866
INFO 2026-06-03 19:20:04 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 7s. Last read position: chr16:30,729,063
INFO 2026-06-03 19:20:18 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 14s. Last read position: chr16:79,599,116
INFO 2026-06-03 19:20:33 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 14s. Last read position: chr17:7,015,082
INFO 2026-06-03 19:20:47 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 14s. Last read position: chr17:35,441,773
INFO 2026-06-03 19:21:01 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 14s. Last read position: chr17:48,058,939
INFO 2026-06-03 19:21:07 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 6s. Last read position: chr17:50,189,266
INFO 2026-06-03 19:21:18 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 11s. Last read position: chr17:50,192,796
INFO 2026-06-03 19:21:33 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 14s. Last read position: chr17:50,196,185
INFO 2026-06-03 19:21:50 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 16s. Last read position: chr17:63,681,782
INFO 2026-06-03 19:22:09 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 19s. Last read position: chr17:81,846,475
INFO 2026-06-03 19:22:21 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 11s. Last read position: chr19:1,272,088
INFO 2026-06-03 19:22:31 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 10s. Last read position: chr19:10,713,167
INFO 2026-06-03 19:22:44 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 13s. Last read position: chr19:18,427,775
INFO 2026-06-03 19:22:53 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 8s. Last read position: chr19:39,913,812
INFO 2026-06-03 19:23:01 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 8s. Last read position: chr19:47,745,724
INFO 2026-06-03 19:23:11 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 10s. Last read position: chr19:57,280,724
INFO 2026-06-03 19:23:22 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 10s. Last read position: chr20:43,460,774
INFO 2026-06-03 19:23:32 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 10s. Last read position: chr21:5,163,565
INFO 2026-06-03 19:23:33 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,739
INFO 2026-06-03 19:23:35 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,618
INFO 2026-06-03 19:23:51 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 15s. Last read position: chr22:18,517,172
INFO 2026-06-03 19:24:02 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 11s. Last read position: chr22:37,128,650
INFO 2026-06-03 19:24:14 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 12s. Last read position: chrX:9,684,079
INFO 2026-06-03 19:24:26 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 11s. Last read position: chrX:136,207,097
INFO 2026-06-03 19:24:46 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 19s. Last read position: GL000220.1:114,146
INFO 2026-06-03 19:24:47 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,719
INFO 2026-06-03 19:24:48 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:17:15s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,463
INFO 2026-06-03 19:24:49 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 1s. Last read position: */*
[Wed Jun 03 19:24:51 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 17.36 minutes.
Runtime.totalMemory()=2812805120