Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/0d6ef2d100723e3d49f92f6a034234/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ctat_ref_annot.interval_list
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/d5b53f9da95d1a0eaaff92defb9378/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/d5b53f9da95d1a0eaaff92defb9378/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/77f6521aa147bd4bf2fd365c3f16aa/rna_s1221_S42.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (6 inputs)
/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 3:29:18 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 15:29:18 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 15:29:18 GMT 2026] Executing as ?@nf-33d5b53f9da95d1a0eaaff92defb9378-55da9-7b6wq 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 15:29:20 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-06-02 15:29:33 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 2026-06-02 15:29:44 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 10s. Last read position: chr1:228,146,888
INFO 2026-06-02 15:29:55 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 11s. Last read position: chr2:159,759,241
INFO 2026-06-02 15:30:13 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 18s. Last read position: chr3:51,993,725
INFO 2026-06-02 15:30:25 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 12s. Last read position: chr4:102,597,542
INFO 2026-06-02 15:30:38 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 12s. Last read position: chr5:176,506,768
INFO 2026-06-02 15:30:45 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 6s. Last read position: chr6:34,421,771
INFO 2026-06-02 15:30:58 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 13s. Last read position: chr7:26,197,277
INFO 2026-06-02 15:31:09 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 11s. Last read position: chr8:89,914,196
INFO 2026-06-02 15:31:21 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 11s. Last read position: chr9:133,349,561
INFO 2026-06-02 15:31:32 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 10s. Last read position: chr11:33,068,720
INFO 2026-06-02 15:31:44 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 12s. Last read position: chr12:6,945,786
INFO 2026-06-02 15:31:57 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 13s. Last read position: chr12:122,752,900
INFO 2026-06-02 15:32:16 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 18s. Last read position: chr15:28,076,562
INFO 2026-06-02 15:32:26 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 10s. Last read position: chr16:21,834,735
INFO 2026-06-02 15:32:37 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 10s. Last read position: chr17:7,318,111
INFO 2026-06-02 15:32:48 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 11s. Last read position: chr17:76,039,898
INFO 2026-06-02 15:33:02 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 13s. Last read position: chr19:12,734,557
INFO 2026-06-02 15:33:11 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 8s. Last read position: chr20:35,277,516
INFO 2026-06-02 15:33:15 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 4s. Last read position: chr21:8,398,054
INFO 2026-06-02 15:33:22 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 6s. Last read position: chr22:38,495,046
INFO 2026-06-02 15:33:33 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 11s. Last read position: chrY:19,721,298
INFO 2026-06-02 15:33:34 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,152
[Tue Jun 02 15:33:35 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.28 minutes.
Runtime.totalMemory()=2520776704