/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Jun 02, 2026 2:48:35 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
[Tue Jun 02 14:48:35 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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
[Tue Jun 02 14:48:35 GMT 2026] Executing as ?@nf-6aa1662594efc653573b7cba85cd97af-f4e53-5r46l 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	2026-06-02 14:48:36	CollectRnaSeqMetrics	Loaded 58279 genes.
INFO	2026-06-02 14:48:50	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:   13s.  Last read position: chr1:109,668,493
INFO	2026-06-02 14:49:00	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:   10s.  Last read position: chr1:228,097,688
INFO	2026-06-02 14:49:14	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:   13s.  Last read position: chr2:159,748,300
INFO	2026-06-02 14:49:36	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:   22s.  Last read position: chr3:51,969,471
INFO	2026-06-02 14:49:51	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:   15s.  Last read position: chr4:102,578,927
INFO	2026-06-02 14:50:07	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:   15s.  Last read position: chr5:175,965,027
INFO	2026-06-02 14:50:14	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    7s.  Last read position: chr6:34,417,468
INFO	2026-06-02 14:50:30	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:   15s.  Last read position: chr7:26,196,874
INFO	2026-06-02 14:50:44	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:   14s.  Last read position: chr8:85,477,248
INFO	2026-06-02 14:50:59	SinglePassSamProgram	Processed    10,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:   14s.  Last read position: chr9:133,348,921
INFO	2026-06-02 14:51:12	SinglePassSamProgram	Processed    11,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   13s.  Last read position: chr11:32,934,959
INFO	2026-06-02 14:51:27	SinglePassSamProgram	Processed    12,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:   15s.  Last read position: chr12:6,934,175
INFO	2026-06-02 14:51:44	SinglePassSamProgram	Processed    13,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:   16s.  Last read position: chr12:122,361,130
INFO	2026-06-02 14:52:05	SinglePassSamProgram	Processed    14,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:   21s.  Last read position: chr15:22,577,157
INFO	2026-06-02 14:52:20	SinglePassSamProgram	Processed    15,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:   14s.  Last read position: chr16:21,456,352
INFO	2026-06-02 14:52:33	SinglePassSamProgram	Processed    16,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:   13s.  Last read position: chr17:7,252,517
INFO	2026-06-02 14:52:48	SinglePassSamProgram	Processed    17,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:   15s.  Last read position: chr17:75,834,458
INFO	2026-06-02 14:53:06	SinglePassSamProgram	Processed    18,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:   17s.  Last read position: chr19:12,666,543
INFO	2026-06-02 14:53:16	SinglePassSamProgram	Processed    19,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:   10s.  Last read position: chr20:34,540,578
INFO	2026-06-02 14:53:22	SinglePassSamProgram	Processed    20,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    5s.  Last read position: chr21:8,397,807
INFO	2026-06-02 14:53:30	SinglePassSamProgram	Processed    21,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    8s.  Last read position: chr22:38,230,583
INFO	2026-06-02 14:53:44	SinglePassSamProgram	Processed    22,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:   13s.  Last read position: chrY:12,912,799
INFO	2026-06-02 14:53:45	SinglePassSamProgram	Processed    23,000,000 records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:    1s.  Last read position: KI270733.1:133,680
[Tue Jun 02 14:53:46 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 5.20 minutes.
Runtime.totalMemory()=2460483584