Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/1df1663baebbd37ee71760bb555a15/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/06bc43b7a8e03ba958f3ba94bebbb5/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.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/e0/ed0c7b473469cf66a118f2ec9b5f93/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/ed0c7b473469cf66a118f2ec9b5f93/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat ==> 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 7:07:29 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 19:07:29 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_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 19:07:29 GMT 2026] Executing as ?@nf-e0ed0c7b473469cf66a118f2ec9b5f93-62529-pm2mx 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.XXXXytozD8/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXytozD8/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam INFO 2026-06-03 19:07:32 CollectRnaSeqMetrics Loaded 58279 genes. INFO 2026-06-03 19:07:44 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:20,661,311 INFO 2026-06-03 19:07:55 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 10s. Last read position: chr1:35,883,358 INFO 2026-06-03 19:08:09 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 14s. Last read position: chr1:112,525,377 INFO 2026-06-03 19:08:16 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 7s. Last read position: chr1:155,060,725 INFO 2026-06-03 19:08:28 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 11s. Last read position: chr1:201,817,087 INFO 2026-06-03 19:08:39 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 10s. Last read position: chr2:17,931,676 INFO 2026-06-03 19:08:46 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 7s. Last read position: chr2:47,005,991 INFO 2026-06-03 19:08:58 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 11s. Last read position: chr2:108,534,554 INFO 2026-06-03 19:09:13 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 15s. Last read position: chr2:190,999,626 INFO 2026-06-03 19:09:43 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 29s. Last read position: chr2:219,418,482 INFO 2026-06-03 19:10:02 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 19s. Last read position: chr3:12,901,128 INFO 2026-06-03 19:10:15 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 13s. Last read position: chr3:52,516,735 INFO 2026-06-03 19:10:29 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 13s. Last read position: chr3:170,129,354 INFO 2026-06-03 19:10:51 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 21s. Last read position: chr4:10,098,990 INFO 2026-06-03 19:11:10 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 19s. Last read position: chr4:154,540,889 INFO 2026-06-03 19:11:29 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 19s. Last read position: chr5:122,775,099 INFO 2026-06-03 19:11:43 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 13s. Last read position: chr5:150,407,152 INFO 2026-06-03 19:11:59 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 16s. Last read position: chr6:495,294 INFO 2026-06-03 19:12:10 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 10s. Last read position: chr6:31,645,003 INFO 2026-06-03 19:12:22 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 12s. Last read position: chr6:43,051,419 INFO 2026-06-03 19:12:40 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 17s. Last read position: chr6:152,352,241 INFO 2026-06-03 19:12:57 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 17s. Last read position: chr7:6,501,816 INFO 2026-06-03 19:13:13 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 15s. Last read position: chr7:76,048,144 INFO 2026-06-03 19:13:29 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 15s. Last read position: chr7:100,994,326 INFO 2026-06-03 19:13:33 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 4s. Last read position: chr7:102,642,629 INFO 2026-06-03 19:13:47 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 13s. Last read position: chr7:151,079,853 INFO 2026-06-03 19:14:06 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 19s. Last read position: chr8:64,580,836 INFO 2026-06-03 19:14:20 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 13s. Last read position: chr8:143,862,590 INFO 2026-06-03 19:14:32 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 11s. Last read position: chr9:32,550,876 INFO 2026-06-03 19:14:46 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 13s. Last read position: chr9:115,086,604 INFO 2026-06-03 19:15:02 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 16s. Last read position: chr9:136,497,027 INFO 2026-06-03 19:15:16 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 14s. Last read position: chr10:69,415,941 INFO 2026-06-03 19:15:37 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 20s. Last read position: chr10:119,651,679 INFO 2026-06-03 19:15:49 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 12s. Last read position: chr11:2,928,915 INFO 2026-06-03 19:16:06 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 16s. Last read position: chr11:62,519,717 INFO 2026-06-03 19:16:20 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 13s. Last read position: chr11:66,599,243 INFO 2026-06-03 19:16:37 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 17s. Last read position: chr11:114,254,573 INFO 2026-06-03 19:16:57 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 20s. Last read position: chr12:7,921,550 INFO 2026-06-03 19:17:11 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 13s. Last read position: chr12:54,283,815 INFO 2026-06-03 19:17:26 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 14s. Last read position: chr12:108,591,851 INFO 2026-06-03 19:17:41 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 15s. Last read position: chr13:20,002,894 INFO 2026-06-03 19:17:55 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 13s. Last read position: chr14:22,998,445 INFO 2026-06-03 19:18:10 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 15s. Last read position: chr14:77,025,941 INFO 2026-06-03 19:18:34 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 23s. Last read position: chr14:105,643,216 INFO 2026-06-03 19:18:37 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr14:105,742,074 INFO 2026-06-03 19:18:43 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 6s. Last read position: chr15:39,581,196 INFO 2026-06-03 19:18:59 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 15s. Last read position: chr15:75,208,378 INFO 2026-06-03 19:19:13 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 14s. Last read position: chr16:1,777,287 INFO 2026-06-03 19:19:34 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 21s. Last read position: chr16:15,718,349 INFO 2026-06-03 19:19:56 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 22s. Last read position: chr16:21,834,866 INFO 2026-06-03 19:20:04 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 7s. Last read position: chr16:30,729,063 INFO 2026-06-03 19:20:18 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 14s. Last read position: chr16:79,599,116 INFO 2026-06-03 19:20:33 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 14s. Last read position: chr17:7,015,082 INFO 2026-06-03 19:20:47 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 14s. Last read position: chr17:35,441,773 INFO 2026-06-03 19:21:01 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 14s. Last read position: chr17:48,058,939 INFO 2026-06-03 19:21:07 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 6s. Last read position: chr17:50,189,266 INFO 2026-06-03 19:21:18 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 11s. Last read position: chr17:50,192,796 INFO 2026-06-03 19:21:33 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 14s. Last read position: chr17:50,196,185 INFO 2026-06-03 19:21:50 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 16s. Last read position: chr17:63,681,782 INFO 2026-06-03 19:22:09 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 19s. Last read position: chr17:81,846,475 INFO 2026-06-03 19:22:21 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 11s. Last read position: chr19:1,272,088 INFO 2026-06-03 19:22:31 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 10s. Last read position: chr19:10,713,167 INFO 2026-06-03 19:22:44 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 13s. Last read position: chr19:18,427,775 INFO 2026-06-03 19:22:53 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 8s. Last read position: chr19:39,913,812 INFO 2026-06-03 19:23:01 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 8s. Last read position: chr19:47,745,724 INFO 2026-06-03 19:23:11 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 10s. Last read position: chr19:57,280,724 INFO 2026-06-03 19:23:22 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 10s. Last read position: chr20:43,460,774 INFO 2026-06-03 19:23:32 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 10s. Last read position: chr21:5,163,565 INFO 2026-06-03 19:23:33 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,739 INFO 2026-06-03 19:23:35 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,618 INFO 2026-06-03 19:23:51 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 15s. Last read position: chr22:18,517,172 INFO 2026-06-03 19:24:02 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 11s. Last read position: chr22:37,128,650 INFO 2026-06-03 19:24:14 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 12s. Last read position: chrX:9,684,079 INFO 2026-06-03 19:24:26 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 11s. Last read position: chrX:136,207,097 INFO 2026-06-03 19:24:46 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 19s. Last read position: GL000220.1:114,146 INFO 2026-06-03 19:24:47 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,719 INFO 2026-06-03 19:24:48 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:17:15s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,463 INFO 2026-06-03 19:24:49 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 1s. Last read position: */* [Wed Jun 03 19:24:51 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 17.36 minutes. Runtime.totalMemory()=2812805120