/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 1:03:09 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 13:03:09 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
[Wed Jun 03 13:03:09 GMT 2026] Executing as ?@nf-2219863f5d07c85cc4ea6abb03bf8ee5-04484-86dnm 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 2026-06-03 13:03:11 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-06-03 13:03:25 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 2026-06-03 13:03:36 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 11s. Last read position: chr1:228,146,888
INFO 2026-06-03 13:03:48 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 11s. Last read position: chr2:159,759,241
INFO 2026-06-03 13:04:07 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 19s. Last read position: chr3:51,993,725
INFO 2026-06-03 13:04:21 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 13s. Last read position: chr4:102,597,542
INFO 2026-06-03 13:04:35 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 14s. Last read position: chr5:176,506,768
INFO 2026-06-03 13:04:42 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 6s. Last read position: chr6:34,421,771
INFO 2026-06-03 13:04:56 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 14s. Last read position: chr7:26,197,277
INFO 2026-06-03 13:05:09 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 12s. Last read position: chr8:89,914,196
INFO 2026-06-03 13:05:22 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 13s. Last read position: chr9:133,349,561
INFO 2026-06-03 13:05:34 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 11s. Last read position: chr11:33,068,720
INFO 2026-06-03 13:05:47 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 13s. Last read position: chr12:6,945,786
INFO 2026-06-03 13:06:01 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 13s. Last read position: chr12:122,752,900
INFO 2026-06-03 13:06:21 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 20s. Last read position: chr15:28,076,562
INFO 2026-06-03 13:06:33 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 11s. Last read position: chr16:21,834,735
INFO 2026-06-03 13:06:44 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 11s. Last read position: chr17:7,318,111
INFO 2026-06-03 13:06:58 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 13s. Last read position: chr17:76,039,898
INFO 2026-06-03 13:07:12 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 14s. Last read position: chr19:12,734,557
INFO 2026-06-03 13:07:21 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 9s. Last read position: chr20:35,277,516
INFO 2026-06-03 13:07:26 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 4s. Last read position: chr21:8,398,054
INFO 2026-06-03 13:07:34 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 7s. Last read position: chr22:38,495,046
INFO 2026-06-03 13:07:46 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 12s. Last read position: chrY:19,721,298
INFO 2026-06-03 13:07:47 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,152
[Wed Jun 03 13:07:49 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.66 minutes.
Runtime.totalMemory()=2799173632