/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 7:06:02 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
[Wed Jun 03 19:06:02 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0754d2-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 19:06:02 GMT 2026] Executing as ?@nf-7de023522fbd2b4d4b4fb7eed45798ca-6d732-srq7b 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.XXXXcCKdO8/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXcCKdO8/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-06-03 19:06:04 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-06-03 19:06:16 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:18,916,969
INFO 2026-06-03 19:06:24 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 8s. Last read position: chr1:35,192,740
INFO 2026-06-03 19:06:38 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 14s. Last read position: chr1:58,577,046
INFO 2026-06-03 19:06:45 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 7s. Last read position: chr1:149,842,639
INFO 2026-06-03 19:06:58 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 12s. Last read position: chr1:161,072,695
INFO 2026-06-03 19:07:04 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 6s. Last read position: chr1:222,844,852
INFO 2026-06-03 19:07:14 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 10s. Last read position: chr2:28,778,918
INFO 2026-06-03 19:07:25 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 10s. Last read position: chr2:74,482,441
INFO 2026-06-03 19:07:35 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 10s. Last read position: chr2:177,212,771
INFO 2026-06-03 19:07:54 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 18s. Last read position: chr3:12,600,178
INFO 2026-06-03 19:08:12 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 18s. Last read position: chr3:52,492,122
INFO 2026-06-03 19:08:27 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 14s. Last read position: chr3:149,657,225
INFO 2026-06-03 19:08:47 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 20s. Last read position: chr3:188,866,335
INFO 2026-06-03 19:09:06 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 19s. Last read position: chr4:55,396,195
INFO 2026-06-03 19:09:23 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 16s. Last read position: chr5:14,358,246
INFO 2026-06-03 19:09:51 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 28s. Last read position: chr5:140,700,829
INFO 2026-06-03 19:10:09 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 17s. Last read position: chr6:3,015,538
INFO 2026-06-03 19:10:20 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 10s. Last read position: chr6:29,829,566
INFO 2026-06-03 19:10:27 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 6s. Last read position: chr6:31,816,768
INFO 2026-06-03 19:10:29 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr6:31,829,132
INFO 2026-06-03 19:10:39 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 10s. Last read position: chr6:43,770,792
INFO 2026-06-03 19:10:57 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 17s. Last read position: chr6:158,771,281
INFO 2026-06-03 19:11:14 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 17s. Last read position: chr7:44,884,635
INFO 2026-06-03 19:11:26 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 12s. Last read position: chr7:76,302,838
INFO 2026-06-03 19:11:45 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 19s. Last read position: chr7:128,947,818
INFO 2026-06-03 19:12:03 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 17s. Last read position: chr8:60,781,301
INFO 2026-06-03 19:12:27 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 24s. Last read position: chr8:133,262,118
INFO 2026-06-03 19:12:44 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 17s. Last read position: chr8:143,859,923
INFO 2026-06-03 19:12:46 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,064
INFO 2026-06-03 19:12:47 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,317
INFO 2026-06-03 19:13:04 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 16s. Last read position: chr8:144,095,079
INFO 2026-06-03 19:13:19 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 15s. Last read position: chr9:84,670,440
INFO 2026-06-03 19:13:33 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 13s. Last read position: chr9:128,166,267
INFO 2026-06-03 19:13:52 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 19s. Last read position: chr9:137,301,761
INFO 2026-06-03 19:14:10 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 17s. Last read position: chr10:79,296,576
INFO 2026-06-03 19:14:26 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 16s. Last read position: chr11:561,839
INFO 2026-06-03 19:14:46 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 19s. Last read position: chr11:46,397,744
INFO 2026-06-03 19:15:00 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 13s. Last read position: chr11:65,038,798
INFO 2026-06-03 19:15:19 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 19s. Last read position: chr11:117,392,494
INFO 2026-06-03 19:15:35 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 16s. Last read position: chr12:49,484,613
INFO 2026-06-03 19:15:48 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 12s. Last read position: chr12:57,156,093
INFO 2026-06-03 19:16:08 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 20s. Last read position: chr12:122,341,053
INFO 2026-06-03 19:16:24 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 15s. Last read position: chr14:20,343,235
INFO 2026-06-03 19:16:42 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 18s. Last read position: chr14:76,154,522
INFO 2026-06-03 19:17:06 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 23s. Last read position: chr14:104,948,580
INFO 2026-06-03 19:17:19 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 13s. Last read position: chr15:64,681,359
INFO 2026-06-03 19:17:37 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 17s. Last read position: chr16:2,208,547
INFO 2026-06-03 19:17:51 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 13s. Last read position: chr16:18,343,617
INFO 2026-06-03 19:18:04 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 13s. Last read position: chr16:30,225,615
INFO 2026-06-03 19:18:22 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 17s. Last read position: chr16:81,445,261
INFO 2026-06-03 19:18:41 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 19s. Last read position: chr17:7,587,190
INFO 2026-06-03 19:18:56 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 14s. Last read position: chr17:38,850,129
INFO 2026-06-03 19:19:09 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 13s. Last read position: chr17:47,531,262
INFO 2026-06-03 19:19:29 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 19s. Last read position: chr17:78,121,032
INFO 2026-06-03 19:19:53 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 24s. Last read position: chr18:49,992,348
INFO 2026-06-03 19:20:09 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 15s. Last read position: chr19:4,123,802
INFO 2026-06-03 19:20:34 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 25s. Last read position: chr19:13,993,690
INFO 2026-06-03 19:20:49 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 14s. Last read position: chr19:34,399,962
INFO 2026-06-03 19:21:08 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 19s. Last read position: chr19:40,367,709
INFO 2026-06-03 19:21:21 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:16s. Time for last 1,000,000: 12s. Last read position: chr19:49,090,293
INFO 2026-06-03 19:21:36 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 14s. Last read position: chr20:17,570,142
INFO 2026-06-03 19:21:51 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 15s. Last read position: chr20:62,813,465
INFO 2026-06-03 19:21:54 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,372
INFO 2026-06-03 19:21:56 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:15:51s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,314
INFO 2026-06-03 19:21:58 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 1s. Last read position: chr21:29,327,296
INFO 2026-06-03 19:22:11 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:16:06s. Time for last 1,000,000: 13s. Last read position: chr22:29,288,659
INFO 2026-06-03 19:22:26 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 15s. Last read position: chr22:46,263,083
INFO 2026-06-03 19:22:44 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 18s. Last read position: chrX:53,085,841
INFO 2026-06-03 19:23:05 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 20s. Last read position: GL000220.1:112,697
INFO 2026-06-03 19:23:06 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,559
INFO 2026-06-03 19:23:07 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,598
INFO 2026-06-03 19:23:08 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 1s. Last read position: */*
[Wed Jun 03 19:23:10 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 17.14 minutes.
Runtime.totalMemory()=2912419840