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/5e/3d5e5a6021ee2bfe710a278ab44f94/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/ec6324253da3f5ab04bed192af9730/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/3d5e5a6021ee2bfe710a278ab44f94/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/5a78798836aab0c355eab03c184d68/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
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
May 28, 2026 12:05:51 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
[Thu May 28 00:05:51 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bhK-T1-TRNA-1_B23WHTKLT4_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
[Thu May 28 00:05:51 GMT 2026] Executing as ?@nf-5e3d5e5a6021ee2bfe710a278ab44f94-396e4-lrb9n 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.XXXX21MCKG/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXX21MCKG/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
INFO 2026-05-28 00:05:53 CollectRnaSeqMetrics Loaded 58279 genes.
INFO 2026-05-28 00:06:08 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:3,628,471
INFO 2026-05-28 00:06:21 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 12s. Last read position: chr1:16,393,286
INFO 2026-05-28 00:06:35 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 14s. Last read position: chr1:22,639,070
INFO 2026-05-28 00:06:44 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 8s. Last read position: chr1:30,980,062
INFO 2026-05-28 00:06:59 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 14s. Last read position: chr1:39,295,793
INFO 2026-05-28 00:07:31 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 32s. Last read position: chr1:46,303,733
INFO 2026-05-28 00:07:44 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 12s. Last read position: chr1:88,813,619
INFO 2026-05-28 00:07:56 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 12s. Last read position: chr1:114,719,728
INFO 2026-05-28 00:08:05 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 8s. Last read position: chr1:146,156,771
INFO 2026-05-28 00:08:15 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 10s. Last read position: chr1:151,518,778
INFO 2026-05-28 00:08:27 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 12s. Last read position: chr1:155,190,124
INFO 2026-05-28 00:08:47 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 19s. Last read position: chr1:159,302,865
INFO 2026-05-28 00:08:57 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 10s. Last read position: chr1:179,126,490
INFO 2026-05-28 00:09:07 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 9s. Last read position: chr1:202,941,537
INFO 2026-05-28 00:09:15 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 8s. Last read position: chr1:223,864,016
INFO 2026-05-28 00:09:30 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 14s. Last read position: chr1:247,156,588
INFO 2026-05-28 00:09:40 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 10s. Last read position: chr2:27,929,849
INFO 2026-05-28 00:09:47 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 6s. Last read position: chr2:32,916,406
INFO 2026-05-28 00:09:54 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 7s. Last read position: chr2:47,799,909
INFO 2026-05-28 00:10:15 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 20s. Last read position: chr2:74,456,207
INFO 2026-05-28 00:10:23 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 8s. Last read position: chr2:95,856,001
INFO 2026-05-28 00:10:33 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 9s. Last read position: chr2:112,391,004
INFO 2026-05-28 00:10:44 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 11s. Last read position: chr2:144,404,909
INFO 2026-05-28 00:11:14 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 29s. Last read position: chr2:188,984,912
INFO 2026-05-28 00:11:26 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 12s. Last read position: chr2:189,005,397
INFO 2026-05-28 00:11:42 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 16s. Last read position: chr2:201,137,900
INFO 2026-05-28 00:11:55 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 12s. Last read position: chr2:215,361,554
INFO 2026-05-28 00:12:09 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 14s. Last read position: chr2:215,362,047
INFO 2026-05-28 00:12:25 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 16s. Last read position: chr2:215,365,564
INFO 2026-05-28 00:12:43 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 17s. Last read position: chr2:215,370,330
INFO 2026-05-28 00:13:07 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 23s. Last read position: chr2:215,371,987
INFO 2026-05-28 00:13:44 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 37s. Last read position: chr2:215,372,193
INFO 2026-05-28 00:14:15 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 30s. Last read position: chr2:215,373,347
INFO 2026-05-28 00:14:42 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 27s. Last read position: chr2:215,375,367
INFO 2026-05-28 00:15:16 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 33s. Last read position: chr2:215,376,560
INFO 2026-05-28 00:15:48 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 32s. Last read position: chr2:215,379,152
INFO 2026-05-28 00:16:27 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 38s. Last read position: chr2:215,380,969
INFO 2026-05-28 00:17:05 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 37s. Last read position: chr2:215,384,025
INFO 2026-05-28 00:17:45 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 40s. Last read position: chr2:215,386,767
INFO 2026-05-28 00:18:32 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 46s. Last read position: chr2:215,391,692
INFO 2026-05-28 00:19:22 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 49s. Last read position: chr2:215,394,695
INFO 2026-05-28 00:20:11 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 49s. Last read position: chr2:215,397,827
INFO 2026-05-28 00:21:08 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 57s. Last read position: chr2:215,404,540
INFO 2026-05-28 00:22:16 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 67s. Last read position: chr2:215,406,416
INFO 2026-05-28 00:23:32 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:17:39s. Time for last 1,000,000: 76s. Last read position: chr2:215,408,115
INFO 2026-05-28 00:24:57 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:19:04s. Time for last 1,000,000: 84s. Last read position: chr2:215,409,575
INFO 2026-05-28 00:26:17 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:20:23s. Time for last 1,000,000: 79s. Last read position: chr2:215,410,040
INFO 2026-05-28 00:27:38 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:21:45s. Time for last 1,000,000: 81s. Last read position: chr2:215,419,262
INFO 2026-05-28 00:29:05 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:23:11s. Time for last 1,000,000: 86s. Last read position: chr2:215,423,378
INFO 2026-05-28 00:30:34 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:24:40s. Time for last 1,000,000: 89s. Last read position: chr2:215,424,312
INFO 2026-05-28 00:32:02 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:26:08s. Time for last 1,000,000: 88s. Last read position: chr2:215,428,225
INFO 2026-05-28 00:33:36 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:27:43s. Time for last 1,000,000: 94s. Last read position: chr2:215,431,838
INFO 2026-05-28 00:35:10 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:29:17s. Time for last 1,000,000: 93s. Last read position: chr2:215,433,442
INFO 2026-05-28 00:36:50 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:30:56s. Time for last 1,000,000: 99s. Last read position: chr2:215,435,807
INFO 2026-05-28 00:37:11 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:31:17s. Time for last 1,000,000: 21s. Last read position: chr2:231,461,726
INFO 2026-05-28 00:37:37 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:31:43s. Time for last 1,000,000: 25s. Last read position: chr2:240,525,762
INFO 2026-05-28 00:37:52 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:31:58s. Time for last 1,000,000: 15s. Last read position: chr3:15,670,280
INFO 2026-05-28 00:38:07 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:32:13s. Time for last 1,000,000: 14s. Last read position: chr3:46,715,535
INFO 2026-05-28 00:38:23 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:32:29s. Time for last 1,000,000: 15s. Last read position: chr3:49,727,311
INFO 2026-05-28 00:38:36 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:32:42s. Time for last 1,000,000: 12s. Last read position: chr3:58,526,618
INFO 2026-05-28 00:38:48 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:32:54s. Time for last 1,000,000: 12s. Last read position: chr3:112,639,265
INFO 2026-05-28 00:38:56 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:33:02s. Time for last 1,000,000: 8s. Last read position: chr3:129,171,471
INFO 2026-05-28 00:39:08 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:33:14s. Time for last 1,000,000: 12s. Last read position: chr3:157,159,899
INFO 2026-05-28 00:39:25 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:33:32s. Time for last 1,000,000: 17s. Last read position: chr3:188,609,476
INFO 2026-05-28 00:39:42 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:33:48s. Time for last 1,000,000: 16s. Last read position: chr4:1,737,631
INFO 2026-05-28 00:39:56 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:34:03s. Time for last 1,000,000: 14s. Last read position: chr4:25,666,197
INFO 2026-05-28 00:40:07 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:34:13s. Time for last 1,000,000: 10s. Last read position: chr4:54,274,961
INFO 2026-05-28 00:40:19 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:34:26s. Time for last 1,000,000: 12s. Last read position: chr4:98,261,380
INFO 2026-05-28 00:40:38 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:34:45s. Time for last 1,000,000: 19s. Last read position: chr4:153,704,619
INFO 2026-05-28 00:40:49 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:34:56s. Time for last 1,000,000: 10s. Last read position: chr5:14,364,701
INFO 2026-05-28 00:41:07 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:35:14s. Time for last 1,000,000: 17s. Last read position: chr5:55,405,426
INFO 2026-05-28 00:41:19 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:35:25s. Time for last 1,000,000: 11s. Last read position: chr5:91,375,581
INFO 2026-05-28 00:41:38 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:35:44s. Time for last 1,000,000: 19s. Last read position: chr5:136,063,238
INFO 2026-05-28 00:41:49 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:35:55s. Time for last 1,000,000: 11s. Last read position: chr5:149,977,683
INFO 2026-05-28 00:41:56 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:36:03s. Time for last 1,000,000: 7s. Last read position: chr5:150,404,723
INFO 2026-05-28 00:42:06 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:36:12s. Time for last 1,000,000: 9s. Last read position: chr5:151,062,153
INFO 2026-05-28 00:42:17 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:36:23s. Time for last 1,000,000: 10s. Last read position: chr5:177,334,354
INFO 2026-05-28 00:42:29 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:36:36s. Time for last 1,000,000: 12s. Last read position: chr6:7,189,297
INFO 2026-05-28 00:42:37 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:36:43s. Time for last 1,000,000: 7s. Last read position: chr6:30,061,944
INFO 2026-05-28 00:42:46 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:36:52s. Time for last 1,000,000: 9s. Last read position: chr6:31,828,000
INFO 2026-05-28 00:42:53 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:36:59s. Time for last 1,000,000: 6s. Last read position: chr6:32,757,772
INFO 2026-05-28 00:43:00 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:37:07s. Time for last 1,000,000: 7s. Last read position: chr6:35,619,096
INFO 2026-05-28 00:43:12 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:37:18s. Time for last 1,000,000: 11s. Last read position: chr6:56,553,519
INFO 2026-05-28 00:43:34 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:37:40s. Time for last 1,000,000: 21s. Last read position: chr6:109,382,291
INFO 2026-05-28 00:43:45 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:37:52s. Time for last 1,000,000: 11s. Last read position: chr6:143,765,361
INFO 2026-05-28 00:44:00 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:38:07s. Time for last 1,000,000: 15s. Last read position: chr6:163,563,331
INFO 2026-05-28 00:44:13 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:38:19s. Time for last 1,000,000: 12s. Last read position: chr7:5,528,145
INFO 2026-05-28 00:44:26 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:38:32s. Time for last 1,000,000: 12s. Last read position: chr7:41,689,814
INFO 2026-05-28 00:44:35 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:38:41s. Time for last 1,000,000: 8s. Last read position: chr7:73,489,230
INFO 2026-05-28 00:44:53 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:38:59s. Time for last 1,000,000: 17s. Last read position: chr7:94,397,748
INFO 2026-05-28 00:45:06 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:39:12s. Time for last 1,000,000: 13s. Last read position: chr7:94,423,015
INFO 2026-05-28 00:45:23 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:39:29s. Time for last 1,000,000: 17s. Last read position: chr7:100,681,876
INFO 2026-05-28 00:45:39 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:39:45s. Time for last 1,000,000: 15s. Last read position: chr7:116,774,980
INFO 2026-05-28 00:45:48 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:39:54s. Time for last 1,000,000: 9s. Last read position: chr7:143,390,623
INFO 2026-05-28 00:46:00 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:40:06s. Time for last 1,000,000: 11s. Last read position: chr8:11,845,090
INFO 2026-05-28 00:46:21 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:40:27s. Time for last 1,000,000: 21s. Last read position: chr8:27,598,144
INFO 2026-05-28 00:46:29 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:40:35s. Time for last 1,000,000: 7s. Last read position: chr8:37,875,187
INFO 2026-05-28 00:46:44 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:40:50s. Time for last 1,000,000: 15s. Last read position: chr8:70,594,561
INFO 2026-05-28 00:46:58 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:41:04s. Time for last 1,000,000: 14s. Last read position: chr8:125,049,029
INFO 2026-05-28 00:47:10 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:41:17s. Time for last 1,000,000: 12s. Last read position: chr8:143,922,831
INFO 2026-05-28 00:47:27 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:41:33s. Time for last 1,000,000: 16s. Last read position: chr9:14,146,755
INFO 2026-05-28 00:47:37 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:41:43s. Time for last 1,000,000: 9s. Last read position: chr9:73,151,912
INFO 2026-05-28 00:47:47 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:41:54s. Time for last 1,000,000: 10s. Last read position: chr9:114,167,763
INFO 2026-05-28 00:48:02 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:42:08s. Time for last 1,000,000: 14s. Last read position: chr9:127,872,837
INFO 2026-05-28 00:48:13 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:42:20s. Time for last 1,000,000: 11s. Last read position: chr9:134,731,627
INFO 2026-05-28 00:48:29 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:42:35s. Time for last 1,000,000: 15s. Last read position: chr10:813,186
INFO 2026-05-28 00:48:40 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:42:47s. Time for last 1,000,000: 11s. Last read position: chr10:32,018,126
INFO 2026-05-28 00:48:51 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:42:57s. Time for last 1,000,000: 10s. Last read position: chr10:68,968,992
INFO 2026-05-28 00:49:06 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:43:12s. Time for last 1,000,000: 15s. Last read position: chr10:80,168,999
INFO 2026-05-28 00:49:17 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:43:23s. Time for last 1,000,000: 10s. Last read position: chr10:102,367,151
INFO 2026-05-28 00:49:35 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:43:41s. Time for last 1,000,000: 17s. Last read position: chr10:122,980,540
INFO 2026-05-28 00:49:44 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:43:50s. Time for last 1,000,000: 9s. Last read position: chr11:1,247,571
INFO 2026-05-28 00:49:58 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:44:04s. Time for last 1,000,000: 13s. Last read position: chr11:12,162,318
INFO 2026-05-28 00:50:08 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:44:14s. Time for last 1,000,000: 9s. Last read position: chr11:46,310,048
INFO 2026-05-28 00:50:22 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:44:28s. Time for last 1,000,000: 13s. Last read position: chr11:61,879,450
INFO 2026-05-28 00:50:27 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:44:34s. Time for last 1,000,000: 5s. Last read position: chr11:62,630,490
INFO 2026-05-28 00:50:39 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:44:46s. Time for last 1,000,000: 11s. Last read position: chr11:65,552,338
INFO 2026-05-28 00:50:51 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:44:57s. Time for last 1,000,000: 11s. Last read position: chr11:67,438,728
INFO 2026-05-28 00:51:06 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:45:12s. Time for last 1,000,000: 14s. Last read position: chr11:75,401,712
INFO 2026-05-28 00:51:18 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:45:24s. Time for last 1,000,000: 11s. Last read position: chr11:114,251,032
INFO 2026-05-28 00:51:28 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:45:35s. Time for last 1,000,000: 10s. Last read position: chr11:126,268,732
INFO 2026-05-28 00:51:48 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:45:55s. Time for last 1,000,000: 19s. Last read position: chr12:6,852,249
INFO 2026-05-28 00:51:57 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:46:03s. Time for last 1,000,000: 8s. Last read position: chr12:27,244,278
INFO 2026-05-28 00:52:12 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:46:18s. Time for last 1,000,000: 15s. Last read position: chr12:49,761,755
INFO 2026-05-28 00:52:23 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:46:29s. Time for last 1,000,000: 11s. Last read position: chr12:54,281,390
INFO 2026-05-28 00:52:39 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:46:45s. Time for last 1,000,000: 15s. Last read position: chr12:57,165,892
INFO 2026-05-28 00:52:53 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:46:59s. Time for last 1,000,000: 14s. Last read position: chr12:91,104,258
INFO 2026-05-28 00:53:05 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:47:11s. Time for last 1,000,000: 12s. Last read position: chr12:112,265,282
INFO 2026-05-28 00:53:18 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:47:24s. Time for last 1,000,000: 12s. Last read position: chr12:124,336,802
INFO 2026-05-28 00:53:29 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:47:35s. Time for last 1,000,000: 11s. Last read position: chr13:30,744,059
INFO 2026-05-28 00:53:40 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:47:46s. Time for last 1,000,000: 11s. Last read position: chr13:77,098,560
INFO 2026-05-28 00:53:56 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:48:02s. Time for last 1,000,000: 16s. Last read position: chr13:113,766,130
INFO 2026-05-28 00:54:09 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:48:15s. Time for last 1,000,000: 12s. Last read position: chr14:30,593,528
INFO 2026-05-28 00:54:28 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:48:34s. Time for last 1,000,000: 18s. Last read position: chr14:64,186,458
INFO 2026-05-28 00:54:43 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:48:50s. Time for last 1,000,000: 15s. Last read position: chr14:75,101,752
INFO 2026-05-28 00:54:57 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:49:04s. Time for last 1,000,000: 14s. Last read position: chr14:102,005,174
INFO 2026-05-28 00:55:33 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:49:39s. Time for last 1,000,000: 35s. Last read position: chr14:104,950,657
INFO 2026-05-28 00:55:37 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:49:43s. Time for last 1,000,000: 3s. Last read position: chr14:105,707,415
INFO 2026-05-28 00:55:46 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:49:53s. Time for last 1,000,000: 9s. Last read position: chr15:32,600,341
INFO 2026-05-28 00:55:55 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:50:01s. Time for last 1,000,000: 8s. Last read position: chr15:43,792,360
INFO 2026-05-28 00:56:12 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:50:19s. Time for last 1,000,000: 17s. Last read position: chr15:63,665,925
INFO 2026-05-28 00:56:23 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:50:30s. Time for last 1,000,000: 11s. Last read position: chr15:74,181,374
INFO 2026-05-28 00:56:38 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:50:44s. Time for last 1,000,000: 14s. Last read position: chr15:88,899,379
INFO 2026-05-28 00:56:49 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:50:55s. Time for last 1,000,000: 11s. Last read position: chr16:259,541
INFO 2026-05-28 00:57:08 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:51:14s. Time for last 1,000,000: 18s. Last read position: chr16:2,764,268
INFO 2026-05-28 00:57:20 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:51:26s. Time for last 1,000,000: 11s. Last read position: chr16:11,556,605
INFO 2026-05-28 00:57:27 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:51:33s. Time for last 1,000,000: 7s. Last read position: chr16:18,506,965
INFO 2026-05-28 00:57:34 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:51:40s. Time for last 1,000,000: 7s. Last read position: chr16:28,135,293
INFO 2026-05-28 00:57:43 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:51:49s. Time for last 1,000,000: 8s. Last read position: chr16:30,273,063
INFO 2026-05-28 00:57:52 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:51:58s. Time for last 1,000,000: 9s. Last read position: chr16:56,608,606
INFO 2026-05-28 00:58:05 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:52:12s. Time for last 1,000,000: 13s. Last read position: chr16:68,829,691
INFO 2026-05-28 00:58:15 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:52:21s. Time for last 1,000,000: 9s. Last read position: chr16:88,427,835
INFO 2026-05-28 00:58:27 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:52:33s. Time for last 1,000,000: 12s. Last read position: chr17:1,771,899
INFO 2026-05-28 00:58:38 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:52:44s. Time for last 1,000,000: 10s. Last read position: chr17:7,847,882
INFO 2026-05-28 00:58:51 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:52:57s. Time for last 1,000,000: 13s. Last read position: chr17:21,415,315
INFO 2026-05-28 00:59:03 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:53:10s. Time for last 1,000,000: 12s. Last read position: chr17:36,537,528
INFO 2026-05-28 00:59:15 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:53:21s. Time for last 1,000,000: 11s. Last read position: chr17:41,523,824
INFO 2026-05-28 00:59:27 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:53:33s. Time for last 1,000,000: 12s. Last read position: chr17:45,518,213
INFO 2026-05-28 00:59:36 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:53:43s. Time for last 1,000,000: 9s. Last read position: chr17:50,185,605
INFO 2026-05-28 00:59:41 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:53:48s. Time for last 1,000,000: 4s. Last read position: chr17:50,187,073
INFO 2026-05-28 00:59:47 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:53:54s. Time for last 1,000,000: 6s. Last read position: chr17:50,188,531
INFO 2026-05-28 00:59:54 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:54:00s. Time for last 1,000,000: 6s. Last read position: chr17:50,189,257
INFO 2026-05-28 01:00:00 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:54:07s. Time for last 1,000,000: 6s. Last read position: chr17:50,190,015
INFO 2026-05-28 01:00:08 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:54:14s. Time for last 1,000,000: 7s. Last read position: chr17:50,191,386
INFO 2026-05-28 01:00:16 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:54:22s. Time for last 1,000,000: 8s. Last read position: chr17:50,192,656
INFO 2026-05-28 01:00:26 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:54:33s. Time for last 1,000,000: 10s. Last read position: chr17:50,194,129
INFO 2026-05-28 01:00:37 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:54:43s. Time for last 1,000,000: 10s. Last read position: chr17:50,194,784
INFO 2026-05-28 01:00:49 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:54:55s. Time for last 1,000,000: 11s. Last read position: chr17:50,195,610
INFO 2026-05-28 01:01:02 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:55:08s. Time for last 1,000,000: 13s. Last read position: chr17:50,196,492
INFO 2026-05-28 01:01:16 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:55:22s. Time for last 1,000,000: 13s. Last read position: chr17:50,197,750
INFO 2026-05-28 01:01:30 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:55:37s. Time for last 1,000,000: 14s. Last read position: chr17:50,199,568
INFO 2026-05-28 01:01:48 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:55:54s. Time for last 1,000,000: 17s. Last read position: chr17:59,682,997
INFO 2026-05-28 01:02:01 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:56:07s. Time for last 1,000,000: 12s. Last read position: chr17:74,209,210
INFO 2026-05-28 01:02:17 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:56:23s. Time for last 1,000,000: 16s. Last read position: chr17:78,124,672
INFO 2026-05-28 01:02:36 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:56:43s. Time for last 1,000,000: 19s. Last read position: chr17:82,028,074
INFO 2026-05-28 01:02:48 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:56:55s. Time for last 1,000,000: 12s. Last read position: chr18:32,413,072
INFO 2026-05-28 01:03:02 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:57:09s. Time for last 1,000,000: 14s. Last read position: chr19:966,718
INFO 2026-05-28 01:03:13 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:57:19s. Time for last 1,000,000: 10s. Last read position: chr19:2,918,157
INFO 2026-05-28 01:03:21 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:57:28s. Time for last 1,000,000: 8s. Last read position: chr19:6,685,099
INFO 2026-05-28 01:03:33 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:57:39s. Time for last 1,000,000: 11s. Last read position: chr19:8,544,324
INFO 2026-05-28 01:03:53 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:57:59s. Time for last 1,000,000: 20s. Last read position: chr19:11,617,422
INFO 2026-05-28 01:04:02 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:58:09s. Time for last 1,000,000: 9s. Last read position: chr19:15,380,129
INFO 2026-05-28 01:04:12 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:58:18s. Time for last 1,000,000: 9s. Last read position: chr19:19,130,192
INFO 2026-05-28 01:04:22 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:58:28s. Time for last 1,000,000: 10s. Last read position: chr19:38,815,693
INFO 2026-05-28 01:04:26 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:58:33s. Time for last 1,000,000: 4s. Last read position: chr19:39,886,023
INFO 2026-05-28 01:04:31 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:58:37s. Time for last 1,000,000: 4s. Last read position: chr19:39,924,425
INFO 2026-05-28 01:04:43 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:58:50s. Time for last 1,000,000: 12s. Last read position: chr19:43,353,733
INFO 2026-05-28 01:04:49 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:58:55s. Time for last 1,000,000: 5s. Last read position: chr19:45,522,534
INFO 2026-05-28 01:04:57 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:59:03s. Time for last 1,000,000: 8s. Last read position: chr19:49,594,847
INFO 2026-05-28 01:05:09 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:59:15s. Time for last 1,000,000: 11s. Last read position: chr19:54,465,093
INFO 2026-05-28 01:05:16 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:59:22s. Time for last 1,000,000: 7s. Last read position: chr20:3,229,617
INFO 2026-05-28 01:05:26 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:59:32s. Time for last 1,000,000: 9s. Last read position: chr20:32,359,627
INFO 2026-05-28 01:05:37 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:59:43s. Time for last 1,000,000: 11s. Last read position: chr20:44,995,124
INFO 2026-05-28 01:05:46 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:59:52s. Time for last 1,000,000: 9s. Last read position: chr20:57,652,124
INFO 2026-05-28 01:05:58 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 01:00:05s. Time for last 1,000,000: 12s. Last read position: chr21:6,116,988
INFO 2026-05-28 01:06:04 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 01:00:10s. Time for last 1,000,000: 5s. Last read position: chr21:34,142,461
INFO 2026-05-28 01:06:19 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 01:00:25s. Time for last 1,000,000: 15s. Last read position: chr21:45,986,525
INFO 2026-05-28 01:06:31 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 01:00:37s. Time for last 1,000,000: 11s. Last read position: chr21:46,324,210
INFO 2026-05-28 01:06:42 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 01:00:48s. Time for last 1,000,000: 10s. Last read position: chr22:28,795,568
INFO 2026-05-28 01:06:53 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 01:01:00s. Time for last 1,000,000: 11s. Last read position: chr22:37,185,271
INFO 2026-05-28 01:07:02 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 01:01:09s. Time for last 1,000,000: 9s. Last read position: chr22:43,976,801
INFO 2026-05-28 01:07:14 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 01:01:20s. Time for last 1,000,000: 11s. Last read position: chrX:1,300,550
INFO 2026-05-28 01:07:24 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 01:01:31s. Time for last 1,000,000: 10s. Last read position: chrX:47,203,152
INFO 2026-05-28 01:07:38 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 01:01:44s. Time for last 1,000,000: 13s. Last read position: chrX:71,315,000
INFO 2026-05-28 01:07:48 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 01:01:54s. Time for last 1,000,000: 10s. Last read position: chrX:152,959,696
INFO 2026-05-28 01:08:10 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 01:02:16s. Time for last 1,000,000: 21s. Last read position: chrY:18,992,275
INFO 2026-05-28 01:08:11 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 01:02:17s. Time for last 1,000,000: 1s. Last read position: */*
[Thu May 28 01:08:12 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 62.36 minutes.
Runtime.totalMemory()=2925527040