/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 7:38:06 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 19:38:06 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 19:38:06 GMT 2026] Executing as ?@nf-1be76b6f6bf3813b869d2c5bc68ac522-3c28b-kqpts 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.XXXXLehBWq/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXLehBWq/rna_s1221_S42.Aligned.sortedByCoord.out.bam
INFO 2026-05-29 19:38:09 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-29 19:38:24 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:109,668,493
INFO 2026-05-29 19:38:36 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 11s. Last read position: chr1:228,097,688
INFO 2026-05-29 19:38:49 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 12s. Last read position: chr2:159,748,300
INFO 2026-05-29 19:39:09 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 19s. Last read position: chr3:51,969,471
INFO 2026-05-29 19:39:23 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 13s. Last read position: chr4:102,578,927
INFO 2026-05-29 19:39:38 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 14s. Last read position: chr5:175,965,027
INFO 2026-05-29 19:39:45 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 7s. Last read position: chr6:34,417,468
INFO 2026-05-29 19:39:59 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 14s. Last read position: chr7:26,196,874
INFO 2026-05-29 19:40:12 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 12s. Last read position: chr8:85,477,248
INFO 2026-05-29 19:40:26 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 13s. Last read position: chr9:133,348,921
INFO 2026-05-29 19:40:38 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 12s. Last read position: chr11:32,934,959
INFO 2026-05-29 19:40:52 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 14s. Last read position: chr12:6,934,175
INFO 2026-05-29 19:41:07 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 14s. Last read position: chr12:122,361,130
INFO 2026-05-29 19:41:26 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 19s. Last read position: chr15:22,577,157
INFO 2026-05-29 19:41:40 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 13s. Last read position: chr16:21,456,352
INFO 2026-05-29 19:41:51 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 11s. Last read position: chr17:7,252,517
INFO 2026-05-29 19:42:05 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 13s. Last read position: chr17:75,834,458
INFO 2026-05-29 19:42:20 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 14s. Last read position: chr19:12,666,543
INFO 2026-05-29 19:42:30 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 10s. Last read position: chr20:34,540,578
INFO 2026-05-29 19:42:35 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 4s. Last read position: chr21:8,397,807
INFO 2026-05-29 19:42:43 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 7s. Last read position: chr22:38,230,583
INFO 2026-05-29 19:42:55 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 12s. Last read position: chrY:12,912,799
INFO 2026-05-29 19:42:57 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,680
[Fri May 29 19:42:58 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.87 minutes.
Runtime.totalMemory()=2736259072