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/cf/d696ff6932559540ebc80efea19ba5/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d696ff6932559540ebc80efea19ba5/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/4c2e7e617359a2c6f2b5010c9c6a5c/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/47/3533ec2869c235ff8bfe2f26d1c54e/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
May 27, 2026 10:00:59 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 May 27 22:00:59 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 May 27 22:00:59 GMT 2026] Executing as ?@nf-cfd696ff6932559540ebc80efea19ba5-76136-xzfsd 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 2026-05-27 22:01:02 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-27 22:01:15 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: chr1:111,230,487
INFO 2026-05-27 22:01:25 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 9s. Last read position: chr1:233,139,804
INFO 2026-05-27 22:01:38 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 12s. Last read position: chr2:177,215,659
INFO 2026-05-27 22:01:57 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 19s. Last read position: chr3:53,864,996
INFO 2026-05-27 22:02:11 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 14s. Last read position: chr4:143,538,860
INFO 2026-05-27 22:02:26 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 14s. Last read position: chr5:181,237,672
INFO 2026-05-27 22:02:32 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 6s. Last read position: chr6:43,499,011
INFO 2026-05-27 22:02:48 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 15s. Last read position: chr7:44,696,070
INFO 2026-05-27 22:02:59 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 11s. Last read position: chr8:100,706,769
INFO 2026-05-27 22:03:13 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 13s. Last read position: chr9:136,454,161
INFO 2026-05-27 22:03:25 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 12s. Last read position: chr11:46,547,131
INFO 2026-05-27 22:03:39 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 13s. Last read position: chr12:8,605,335
INFO 2026-05-27 22:03:54 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 14s. Last read position: chr12:124,911,968
INFO 2026-05-27 22:04:15 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 21s. Last read position: chr15:34,904,443
INFO 2026-05-27 22:04:28 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 12s. Last read position: chr16:22,513,880
INFO 2026-05-27 22:04:40 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 12s. Last read position: chr17:7,311,406
INFO 2026-05-27 22:04:53 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 13s. Last read position: chr17:76,047,903
INFO 2026-05-27 22:05:07 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 14s. Last read position: chr19:10,689,198
INFO 2026-05-27 22:05:19 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 11s. Last read position: chr20:3,755,548
INFO 2026-05-27 22:05:31 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 12s. Last read position: chr22:36,518,625
INFO 2026-05-27 22:05:43 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 11s. Last read position: chrX:154,360,515
[Wed May 27 22:05:46 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.78 minutes.
Runtime.totalMemory()=2464677888