/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 29, 2026 5:20:38 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
[Fri May 29 17:20:38 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
[Fri May 29 17:20:38 GMT 2026] Executing as ?@nf-f03e3f06211a64626491627b336faeb7-09298-j4hfc 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 2026-05-29 17:20:41 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-29 17:20:55 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: chr1:110,018,371
INFO 2026-05-29 17:21:05 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 10s. Last read position: chr1:228,146,888
INFO 2026-05-29 17:21:16 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 10s. Last read position: chr2:159,759,241
INFO 2026-05-29 17:21:33 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 17s. Last read position: chr3:51,993,725
INFO 2026-05-29 17:21:45 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 11s. Last read position: chr4:102,597,542
INFO 2026-05-29 17:21:58 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 12s. Last read position: chr5:176,506,768
INFO 2026-05-29 17:22:04 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 6s. Last read position: chr6:34,421,771
INFO 2026-05-29 17:22:17 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 13s. Last read position: chr7:26,197,277
INFO 2026-05-29 17:22:28 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 10s. Last read position: chr8:89,914,196
INFO 2026-05-29 17:22:40 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 11s. Last read position: chr9:133,349,561
INFO 2026-05-29 17:22:50 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 10s. Last read position: chr11:33,068,720
INFO 2026-05-29 17:23:02 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 12s. Last read position: chr12:6,945,786
INFO 2026-05-29 17:23:15 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 12s. Last read position: chr12:122,752,900
INFO 2026-05-29 17:23:32 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 17s. Last read position: chr15:28,076,562
INFO 2026-05-29 17:23:43 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 10s. Last read position: chr16:21,834,735
INFO 2026-05-29 17:23:53 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 9s. Last read position: chr17:7,318,111
INFO 2026-05-29 17:24:04 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 11s. Last read position: chr17:76,039,898
INFO 2026-05-29 17:24:17 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 12s. Last read position: chr19:12,734,557
INFO 2026-05-29 17:24:26 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 8s. Last read position: chr20:35,277,516
INFO 2026-05-29 17:24:30 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 4s. Last read position: chr21:8,398,054
INFO 2026-05-29 17:24:37 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 6s. Last read position: chr22:38,495,046
INFO 2026-05-29 17:24:48 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 10s. Last read position: chrY:19,721,298
INFO 2026-05-29 17:24:49 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,152
[Fri May 29 17:24:50 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.20 minutes.
Runtime.totalMemory()=2736783360