/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 5:32:29 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
[Fri May 29 17:32:29 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 17:32:29 GMT 2026] Executing as ?@nf-74366f72e33fa34413085b66ee25a525-db1c1-9gtk4 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.XXXXIGF7Qx/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXIGF7Qx/rna_s1221_S42.Aligned.sortedByCoord.out.bam
INFO 2026-05-29 17:32:31 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-29 17:32:47 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:110,018,371
INFO 2026-05-29 17:32:59 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 11s. Last read position: chr1:228,146,888
INFO 2026-05-29 17:33:11 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 12s. Last read position: chr2:159,759,241
INFO 2026-05-29 17:33:31 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 20s. Last read position: chr3:51,993,725
INFO 2026-05-29 17:33:46 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 14s. Last read position: chr4:102,597,542
INFO 2026-05-29 17:34:00 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 14s. Last read position: chr5:176,506,768
INFO 2026-05-29 17:34:08 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 7s. Last read position: chr6:34,421,771
INFO 2026-05-29 17:34:22 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 14s. Last read position: chr7:26,197,277
INFO 2026-05-29 17:34:36 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 13s. Last read position: chr8:89,914,196
INFO 2026-05-29 17:34:49 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 13s. Last read position: chr9:133,349,561
INFO 2026-05-29 17:35:01 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 12s. Last read position: chr11:33,068,720
INFO 2026-05-29 17:35:15 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 14s. Last read position: chr12:6,945,786
INFO 2026-05-29 17:35:30 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 14s. Last read position: chr12:122,752,900
INFO 2026-05-29 17:35:51 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 20s. Last read position: chr15:28,076,562
INFO 2026-05-29 17:36:04 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 12s. Last read position: chr16:21,834,735
INFO 2026-05-29 17:36:15 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 11s. Last read position: chr17:7,318,111
INFO 2026-05-29 17:36:28 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 13s. Last read position: chr17:76,039,898
INFO 2026-05-29 17:36:44 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 15s. Last read position: chr19:12,734,557
INFO 2026-05-29 17:36:54 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 10s. Last read position: chr20:35,277,516
INFO 2026-05-29 17:36:59 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 5s. Last read position: chr21:8,398,054
INFO 2026-05-29 17:37:08 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 8s. Last read position: chr22:38,495,046
INFO 2026-05-29 17:37:21 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 12s. Last read position: chrY:19,721,298
INFO 2026-05-29 17:37:22 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,152
[Fri May 29 17:37:23 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.89 minutes.
Runtime.totalMemory()=2538078208