Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/8ec4e7cd58f89d3391483001a1d88d/.command.sh
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/4a/8ec4e7cd58f89d3391483001a1d88d/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/9b2a539121712302115e2a0c1b983f/rna_s1200_S21.Aligned.sortedByCoord.out.bam
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/ab/4f1bf19fa18402d481892e6d1607c5/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
==> 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 03, 2026 4:03:14 AM 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 04:03:14 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_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 04:03:15 GMT 2026] Executing as ?@nf-4a8ec4e7cd58f89d3391483001a1d88d-08b2c-4smtt 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.XXXXug3alq/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXug3alq/rna_s1200_S21.Aligned.sortedByCoord.out.bam
INFO 2026-06-03 04:03:16 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-06-03 04:03:32 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:111,230,487
INFO 2026-06-03 04:03:44 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 12s. Last read position: chr1:233,139,804
INFO 2026-06-03 04:03:57 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 12s. Last read position: chr2:177,215,659
INFO 2026-06-03 04:04:16 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 19s. Last read position: chr3:53,864,996
INFO 2026-06-03 04:04:31 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 14s. Last read position: chr4:143,538,860
INFO 2026-06-03 04:04:46 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 15s. Last read position: chr5:181,237,672
INFO 2026-06-03 04:04:53 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 6s. Last read position: chr6:43,499,011
INFO 2026-06-03 04:05:11 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 18s. Last read position: chr7:44,696,070
INFO 2026-06-03 04:05:25 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 14s. Last read position: chr8:100,706,769
INFO 2026-06-03 04:05:43 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 17s. Last read position: chr9:136,454,161
INFO 2026-06-03 04:06:00 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 16s. Last read position: chr11:46,547,131
INFO 2026-06-03 04:06:21 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 20s. Last read position: chr12:8,605,335
INFO 2026-06-03 04:06:42 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 21s. Last read position: chr12:124,911,968
INFO 2026-06-03 04:07:12 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 29s. Last read position: chr15:34,904,443
INFO 2026-06-03 04:07:30 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 18s. Last read position: chr16:22,513,880
INFO 2026-06-03 04:07:48 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 17s. Last read position: chr17:7,311,406
INFO 2026-06-03 04:08:08 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 20s. Last read position: chr17:76,047,903
INFO 2026-06-03 04:08:30 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 21s. Last read position: chr19:10,689,198
INFO 2026-06-03 04:08:47 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 17s. Last read position: chr20:3,755,548
INFO 2026-06-03 04:09:07 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 19s. Last read position: chr22:36,518,625
INFO 2026-06-03 04:09:25 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 17s. Last read position: chrX:154,360,515
[Wed Jun 03 04:09:30 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 6.26 minutes.
Runtime.totalMemory()=2324168704