/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 27, 2026 3:29:49 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 May 27 15:29:49 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_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 May 27 15:29:49 GMT 2026] Executing as ?@nf-3a10c0b8898089a85f3de039294cc406-8cc35-zsptn 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	2026-05-27 15:29:51	CollectRnaSeqMetrics	Loaded 58279 genes.
INFO	2026-05-27 15:30:05	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:   14s.  Last read position: chr1:111,230,487
INFO	2026-05-27 15:30:16	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:   10s.  Last read position: chr1:233,139,804
INFO	2026-05-27 15:30:28	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:   11s.  Last read position: chr2:177,215,659
INFO	2026-05-27 15:30:46	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:   18s.  Last read position: chr3:53,864,996
INFO	2026-05-27 15:31:00	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:   13s.  Last read position: chr4:143,538,860
INFO	2026-05-27 15:31:14	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   14s.  Last read position: chr5:181,237,672
INFO	2026-05-27 15:31:19	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    5s.  Last read position: chr6:43,499,011
INFO	2026-05-27 15:31:35	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:   15s.  Last read position: chr7:44,696,070
INFO	2026-05-27 15:31:46	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:   11s.  Last read position: chr8:100,706,769
INFO	2026-05-27 15:31:58	SinglePassSamProgram	Processed    10,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:   12s.  Last read position: chr9:136,454,161
INFO	2026-05-27 15:32:10	SinglePassSamProgram	Processed    11,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:   11s.  Last read position: chr11:46,547,131
INFO	2026-05-27 15:32:23	SinglePassSamProgram	Processed    12,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:   13s.  Last read position: chr12:8,605,335
INFO	2026-05-27 15:32:37	SinglePassSamProgram	Processed    13,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:   13s.  Last read position: chr12:124,911,968
INFO	2026-05-27 15:32:57	SinglePassSamProgram	Processed    14,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:   19s.  Last read position: chr15:34,904,443
INFO	2026-05-27 15:33:08	SinglePassSamProgram	Processed    15,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:   11s.  Last read position: chr16:22,513,880
INFO	2026-05-27 15:33:20	SinglePassSamProgram	Processed    16,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:   11s.  Last read position: chr17:7,311,406
INFO	2026-05-27 15:33:32	SinglePassSamProgram	Processed    17,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:   12s.  Last read position: chr17:76,047,903
INFO	2026-05-27 15:33:46	SinglePassSamProgram	Processed    18,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:   13s.  Last read position: chr19:10,689,198
INFO	2026-05-27 15:33:56	SinglePassSamProgram	Processed    19,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:   10s.  Last read position: chr20:3,755,548
INFO	2026-05-27 15:34:08	SinglePassSamProgram	Processed    20,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:   12s.  Last read position: chr22:36,518,625
INFO	2026-05-27 15:34:19	SinglePassSamProgram	Processed    21,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:   10s.  Last read position: chrX:154,360,515
[Wed May 27 15:34:22 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.56 minutes.
Runtime.totalMemory()=2372927488