Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/cd7cf4932c8aacd3ac2d7b4a0fa403/aih-tih-sc-ecc0bc-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/39/3611e3f6f01a71c7537379f1c15b14/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/bb80a9c53d741f1147ca5cc617504e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/bb80a9c53d741f1147ca5cc617504e/.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 8:24:49 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 20:24:49 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ecc0bc-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 20:24:49 GMT 2026] Executing as ?@nf-a0bb80a9c53d741f1147ca5cc617504e-e6861-b8dzm on Linux 6.12.88 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.XXXXRleGPy/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXRleGPy/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam INFO 2026-06-03 20:24:51 CollectRnaSeqMetrics Loaded 58279 genes. INFO 2026-06-03 20:25:03 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:1,318,954 INFO 2026-06-03 20:25:13 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 9s. Last read position: chr1:2,229,185 INFO 2026-06-03 20:25:24 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 10s. Last read position: chr1:6,599,274 INFO 2026-06-03 20:25:32 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 8s. Last read position: chr1:10,655,758 INFO 2026-06-03 20:25:44 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 11s. Last read position: chr1:15,659,893 INFO 2026-06-03 20:25:50 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 5s. Last read position: chr1:16,971,585 INFO 2026-06-03 20:26:02 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 12s. Last read position: chr1:20,744,947 INFO 2026-06-03 20:26:16 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 13s. Last read position: chr1:21,875,650 INFO 2026-06-03 20:26:24 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 7s. Last read position: chr1:23,794,454 INFO 2026-06-03 20:26:33 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 9s. Last read position: chr1:26,779,370 INFO 2026-06-03 20:26:40 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 7s. Last read position: chr1:29,148,592 INFO 2026-06-03 20:26:57 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 16s. Last read position: chr1:31,919,517 INFO 2026-06-03 20:27:05 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 7s. Last read position: chr1:35,192,525 INFO 2026-06-03 20:27:11 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 6s. Last read position: chr1:37,475,758 INFO 2026-06-03 20:28:02 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 50s. Last read position: chr1:39,844,205 INFO 2026-06-03 20:28:12 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 10s. Last read position: chr1:43,442,936 INFO 2026-06-03 20:28:26 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 13s. Last read position: chr1:45,511,192 INFO 2026-06-03 20:28:37 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 11s. Last read position: chr1:52,356,225 INFO 2026-06-03 20:28:44 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 7s. Last read position: chr1:59,512,414 INFO 2026-06-03 20:29:02 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 17s. Last read position: chr1:74,673,505 INFO 2026-06-03 20:29:10 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 8s. Last read position: chr1:89,892,622 INFO 2026-06-03 20:29:19 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 8s. Last read position: chr1:107,573,342 INFO 2026-06-03 20:29:29 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 10s. Last read position: chr1:110,339,855 INFO 2026-06-03 20:29:36 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 7s. Last read position: chr1:114,433,655 INFO 2026-06-03 20:29:43 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 7s. Last read position: chr1:119,920,295 INFO 2026-06-03 20:29:50 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 7s. Last read position: chr1:120,735,382 INFO 2026-06-03 20:29:55 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 4s. Last read position: chr1:145,995,404 INFO 2026-06-03 20:30:02 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 6s. Last read position: chr1:148,001,324 INFO 2026-06-03 20:30:11 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 8s. Last read position: chr1:149,430,961 INFO 2026-06-03 20:30:14 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr1:150,472,099 INFO 2026-06-03 20:30:23 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 8s. Last read position: chr1:150,968,975 INFO 2026-06-03 20:30:32 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 8s. Last read position: chr1:151,838,658 INFO 2026-06-03 20:30:39 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 6s. Last read position: chr1:153,976,698 INFO 2026-06-03 20:30:53 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 14s. Last read position: chr1:154,596,958 INFO 2026-06-03 20:31:12 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 18s. Last read position: chr1:155,188,310 INFO 2026-06-03 20:31:31 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 19s. Last read position: chr1:155,481,302 INFO 2026-06-03 20:31:46 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 15s. Last read position: chr1:156,115,070 INFO 2026-06-03 20:32:09 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 23s. Last read position: chr1:156,136,287 INFO 2026-06-03 20:32:41 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 31s. Last read position: chr1:156,293,013 INFO 2026-06-03 20:32:47 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 6s. Last read position: chr1:159,918,503 INFO 2026-06-03 20:32:58 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 10s. Last read position: chr1:161,191,373 INFO 2026-06-03 20:33:08 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 10s. Last read position: chr1:167,399,271 INFO 2026-06-03 20:33:19 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 10s. Last read position: chr1:172,132,934 INFO 2026-06-03 20:33:26 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 7s. Last read position: chr1:180,928,438 INFO 2026-06-03 20:33:33 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 6s. Last read position: chr1:186,038,015 INFO 2026-06-03 20:33:43 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 9s. Last read position: chr1:198,728,350 INFO 2026-06-03 20:33:54 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 11s. Last read position: chr1:203,184,604 INFO 2026-06-03 20:34:01 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 7s. Last read position: chr1:204,259,544 INFO 2026-06-03 20:34:08 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 6s. Last read position: chr1:207,761,367 INFO 2026-06-03 20:34:14 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 6s. Last read position: chr1:217,620,353 INFO 2026-06-03 20:34:22 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 8s. Last read position: chr1:225,498,356 INFO 2026-06-03 20:34:33 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 10s. Last read position: chr1:228,147,678 INFO 2026-06-03 20:35:00 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 27s. Last read position: chr1:233,258,591 INFO 2026-06-03 20:35:12 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 11s. Last read position: chr1:243,221,729 INFO 2026-06-03 20:35:25 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 13s. Last read position: chr2:277,259 INFO 2026-06-03 20:35:34 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 9s. Last read position: chr2:15,474,092 INFO 2026-06-03 20:35:44 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 9s. Last read position: chr2:25,742,741 INFO 2026-06-03 20:35:53 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 9s. Last read position: chr2:28,396,819 INFO 2026-06-03 20:36:00 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 7s. Last read position: chr2:32,916,260 INFO 2026-06-03 20:36:06 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 5s. Last read position: chr2:32,916,403 INFO 2026-06-03 20:36:08 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 2s. Last read position: chr2:36,356,480 INFO 2026-06-03 20:36:15 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 6s. Last read position: chr2:43,225,203 INFO 2026-06-03 20:36:26 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 11s. Last read position: chr2:54,255,566 INFO 2026-06-03 20:36:47 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 20s. Last read position: chr2:61,350,675 INFO 2026-06-03 20:37:06 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 19s. Last read position: chr2:70,275,576 INFO 2026-06-03 20:37:19 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 12s. Last read position: chr2:74,462,066 INFO 2026-06-03 20:37:27 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 7s. Last read position: chr2:86,620,346 INFO 2026-06-03 20:37:33 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 6s. Last read position: chr2:96,365,971 INFO 2026-06-03 20:37:43 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 10s. Last read position: chr2:101,002,709 INFO 2026-06-03 20:37:50 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 6s. Last read position: chr2:108,765,693 INFO 2026-06-03 20:37:55 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 4s. Last read position: chr2:112,389,980 INFO 2026-06-03 20:38:03 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 8s. Last read position: chr2:127,650,864 INFO 2026-06-03 20:38:10 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 6s. Last read position: chr2:134,954,477 INFO 2026-06-03 20:38:21 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 11s. Last read position: chr2:157,766,172 INFO 2026-06-03 20:38:33 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 11s. Last read position: chr2:171,554,620 INFO 2026-06-03 20:38:56 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 23s. Last read position: chr2:178,594,466 INFO 2026-06-03 20:39:30 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 33s. Last read position: chr2:188,993,418 INFO 2026-06-03 20:39:41 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:14:49s. Time for last 1,000,000: 11s. Last read position: chr2:189,006,363 INFO 2026-06-03 20:39:54 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 13s. Last read position: chr2:189,561,924 INFO 2026-06-03 20:40:07 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 12s. Last read position: chr2:200,857,857 INFO 2026-06-03 20:40:23 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 15s. Last read position: chr2:207,977,306 INFO 2026-06-03 20:40:36 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 12s. Last read position: chr2:215,371,996 INFO 2026-06-03 20:41:00 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 24s. Last read position: chr2:215,379,308 INFO 2026-06-03 20:41:36 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 36s. Last read position: chr2:215,399,334 INFO 2026-06-03 20:42:33 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 56s. Last read position: chr2:215,422,129 INFO 2026-06-03 20:43:41 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 67s. Last read position: chr2:216,499,961 INFO 2026-06-03 20:43:54 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 13s. Last read position: chr2:219,174,158 INFO 2026-06-03 20:44:04 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 9s. Last read position: chr2:229,767,528 INFO 2026-06-03 20:44:22 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 18s. Last read position: chr2:235,040,979 INFO 2026-06-03 20:44:37 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 14s. Last read position: chr2:237,366,922 INFO 2026-06-03 20:45:08 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:20:16s. Time for last 1,000,000: 30s. Last read position: chr2:237,762,971 INFO 2026-06-03 20:45:21 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:20:29s. Time for last 1,000,000: 13s. Last read position: chr2:241,256,353 INFO 2026-06-03 20:45:45 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:20:53s. Time for last 1,000,000: 24s. Last read position: chr3:9,678,012 INFO 2026-06-03 20:45:57 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:21:05s. Time for last 1,000,000: 11s. Last read position: chr3:12,946,403 INFO 2026-06-03 20:46:05 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:21:12s. Time for last 1,000,000: 7s. Last read position: chr3:22,382,241 INFO 2026-06-03 20:46:18 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 13s. Last read position: chr3:37,326,054 INFO 2026-06-03 20:46:33 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:21:41s. Time for last 1,000,000: 15s. Last read position: chr3:42,531,787 INFO 2026-06-03 20:46:43 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:21:51s. Time for last 1,000,000: 9s. Last read position: chr3:47,121,608 INFO 2026-06-03 20:46:55 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:22:03s. Time for last 1,000,000: 11s. Last read position: chr3:48,564,241 INFO 2026-06-03 20:47:11 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:22:19s. Time for last 1,000,000: 15s. Last read position: chr3:49,123,151 INFO 2026-06-03 20:47:21 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:22:29s. Time for last 1,000,000: 10s. Last read position: chr3:50,077,016 INFO 2026-06-03 20:47:30 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:22:38s. Time for last 1,000,000: 8s. Last read position: chr3:52,278,296 INFO 2026-06-03 20:47:45 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:22:53s. Time for last 1,000,000: 14s. Last read position: chr3:53,823,700 INFO 2026-06-03 20:48:01 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:23:09s. Time for last 1,000,000: 16s. Last read position: chr3:63,990,067 INFO 2026-06-03 20:48:17 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:23:25s. Time for last 1,000,000: 15s. Last read position: chr3:93,879,276 INFO 2026-06-03 20:48:31 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:23:39s. Time for last 1,000,000: 14s. Last read position: chr3:111,884,616 INFO 2026-06-03 20:48:37 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:23:45s. Time for last 1,000,000: 6s. Last read position: chr3:120,399,888 INFO 2026-06-03 20:48:46 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:23:54s. Time for last 1,000,000: 8s. Last read position: chr3:125,107,617 INFO 2026-06-03 20:48:54 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:24:02s. Time for last 1,000,000: 8s. Last read position: chr3:129,571,744 INFO 2026-06-03 20:49:06 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:24:14s. Time for last 1,000,000: 11s. Last read position: chr3:139,379,394 INFO 2026-06-03 20:49:14 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:24:22s. Time for last 1,000,000: 8s. Last read position: chr3:151,511,587 INFO 2026-06-03 20:49:23 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:24:31s. Time for last 1,000,000: 9s. Last read position: chr3:172,506,900 INFO 2026-06-03 20:49:38 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:24:46s. Time for last 1,000,000: 14s. Last read position: chr3:184,323,583 INFO 2026-06-03 20:49:53 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:25:01s. Time for last 1,000,000: 14s. Last read position: chr3:193,615,723 INFO 2026-06-03 20:50:09 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:25:17s. Time for last 1,000,000: 16s. Last read position: chr3:197,681,280 INFO 2026-06-03 20:50:18 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:25:26s. Time for last 1,000,000: 9s. Last read position: chr4:1,312,034 INFO 2026-06-03 20:50:32 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:25:40s. Time for last 1,000,000: 14s. Last read position: chr4:3,199,774 INFO 2026-06-03 20:50:43 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:25:51s. Time for last 1,000,000: 10s. Last read position: chr4:10,075,428 INFO 2026-06-03 20:50:52 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:26:00s. Time for last 1,000,000: 9s. Last read position: chr4:38,103,051 INFO 2026-06-03 20:51:02 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:26:10s. Time for last 1,000,000: 10s. Last read position: chr4:54,272,400 INFO 2026-06-03 20:51:10 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:26:18s. Time for last 1,000,000: 7s. Last read position: chr4:74,446,590 INFO 2026-06-03 20:51:22 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:26:30s. Time for last 1,000,000: 12s. Last read position: chr4:84,583,081 INFO 2026-06-03 20:51:41 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:26:49s. Time for last 1,000,000: 18s. Last read position: chr4:99,316,050 INFO 2026-06-03 20:52:41 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 60s. Last read position: chr4:113,360,844 INFO 2026-06-03 20:53:06 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:28:14s. Time for last 1,000,000: 24s. Last read position: chr4:139,071,883 INFO 2026-06-03 20:53:19 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:28:27s. Time for last 1,000,000: 12s. Last read position: chr4:150,905,839 INFO 2026-06-03 20:53:29 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:28:37s. Time for last 1,000,000: 10s. Last read position: chr4:165,493,195 INFO 2026-06-03 20:53:40 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:28:48s. Time for last 1,000,000: 10s. Last read position: chr5:140,488 INFO 2026-06-03 20:53:49 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:28:57s. Time for last 1,000,000: 8s. Last read position: chr5:14,290,973 INFO 2026-06-03 20:54:15 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:29:23s. Time for last 1,000,000: 25s. Last read position: chr5:19,802,897 INFO 2026-06-03 20:54:26 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:29:34s. Time for last 1,000,000: 11s. Last read position: chr5:39,202,528 INFO 2026-06-03 20:54:34 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:29:42s. Time for last 1,000,000: 7s. Last read position: chr5:55,960,401 INFO 2026-06-03 20:54:45 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:29:53s. Time for last 1,000,000: 10s. Last read position: chr5:70,123,320 INFO 2026-06-03 20:54:54 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:30:02s. Time for last 1,000,000: 8s. Last read position: chr5:77,463,211 INFO 2026-06-03 20:55:02 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:30:10s. Time for last 1,000,000: 8s. Last read position: chr5:86,619,385 INFO 2026-06-03 20:55:21 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:30:29s. Time for last 1,000,000: 19s. Last read position: chr5:112,819,300 INFO 2026-06-03 20:55:33 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:30:41s. Time for last 1,000,000: 11s. Last read position: chr5:132,761,531 INFO 2026-06-03 20:55:41 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:30:49s. Time for last 1,000,000: 7s. Last read position: chr5:138,341,847 INFO 2026-06-03 20:55:45 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:30:53s. Time for last 1,000,000: 4s. Last read position: chr5:138,758,316 INFO 2026-06-03 20:55:56 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:31:04s. Time for last 1,000,000: 11s. Last read position: chr5:141,102,487 INFO 2026-06-03 20:56:01 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:31:09s. Time for last 1,000,000: 5s. Last read position: chr5:143,399,906 INFO 2026-06-03 20:56:12 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:31:20s. Time for last 1,000,000: 10s. Last read position: chr5:150,125,460 INFO 2026-06-03 20:56:19 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:31:27s. Time for last 1,000,000: 7s. Last read position: chr5:150,402,596 INFO 2026-06-03 20:56:27 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:31:35s. Time for last 1,000,000: 7s. Last read position: chr5:150,406,315 INFO 2026-06-03 20:56:35 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:31:43s. Time for last 1,000,000: 8s. Last read position: chr5:151,133,165 INFO 2026-06-03 20:56:44 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:31:52s. Time for last 1,000,000: 8s. Last read position: chr5:167,922,971 INFO 2026-06-03 20:56:58 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:32:06s. Time for last 1,000,000: 14s. Last read position: chr5:172,768,830 INFO 2026-06-03 20:57:03 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:32:11s. Time for last 1,000,000: 4s. Last read position: chr5:177,305,901 INFO 2026-06-03 20:57:14 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:32:22s. Time for last 1,000,000: 10s. Last read position: chr5:179,706,310 INFO 2026-06-03 20:57:27 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:32:35s. Time for last 1,000,000: 13s. Last read position: chr5:180,574,102 INFO 2026-06-03 20:57:35 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:32:43s. Time for last 1,000,000: 8s. Last read position: chr6:7,189,180 INFO 2026-06-03 20:57:43 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:32:51s. Time for last 1,000,000: 7s. Last read position: chr6:12,161,889 INFO 2026-06-03 20:57:50 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:32:57s. Time for last 1,000,000: 6s. Last read position: chr6:26,124,413 INFO 2026-06-03 20:57:54 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:33:02s. Time for last 1,000,000: 4s. Last read position: chr6:30,489,571 INFO 2026-06-03 20:58:05 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:33:13s. Time for last 1,000,000: 10s. Last read position: chr6:31,271,708 INFO 2026-06-03 20:58:15 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:33:23s. Time for last 1,000,000: 10s. Last read position: chr6:31,696,969 INFO 2026-06-03 20:58:21 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:33:29s. Time for last 1,000,000: 5s. Last read position: chr6:31,980,360 INFO 2026-06-03 20:58:31 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:33:39s. Time for last 1,000,000: 9s. Last read position: chr6:32,055,966 INFO 2026-06-03 20:58:51 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:33:59s. Time for last 1,000,000: 20s. Last read position: chr6:32,182,869 INFO 2026-06-03 20:58:58 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:34:05s. Time for last 1,000,000: 6s. Last read position: chr6:33,068,711 INFO 2026-06-03 20:59:04 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:34:11s. Time for last 1,000,000: 5s. Last read position: chr6:33,415,078 INFO 2026-06-03 20:59:12 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:34:20s. Time for last 1,000,000: 8s. Last read position: chr6:36,899,438 INFO 2026-06-03 20:59:18 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:34:26s. Time for last 1,000,000: 6s. Last read position: chr6:43,048,229 INFO 2026-06-03 20:59:28 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:34:36s. Time for last 1,000,000: 9s. Last read position: chr6:46,708,062 INFO 2026-06-03 21:00:10 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:35:18s. Time for last 1,000,000: 42s. Last read position: chr6:63,576,436 INFO 2026-06-03 21:00:32 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:35:40s. Time for last 1,000,000: 22s. Last read position: chr6:80,069,575 INFO 2026-06-03 21:00:42 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:35:50s. Time for last 1,000,000: 9s. Last read position: chr6:99,414,588 INFO 2026-06-03 21:00:53 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:36:01s. Time for last 1,000,000: 10s. Last read position: chr6:113,857,793 INFO 2026-06-03 21:01:03 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:36:11s. Time for last 1,000,000: 9s. Last read position: chr6:130,880,166 INFO 2026-06-03 21:01:29 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:36:37s. Time for last 1,000,000: 26s. Last read position: chr6:136,389,416 INFO 2026-06-03 21:01:37 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:36:45s. Time for last 1,000,000: 7s. Last read position: chr6:145,922,773 INFO 2026-06-03 21:01:42 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:36:50s. Time for last 1,000,000: 5s. Last read position: chr6:151,865,894 INFO 2026-06-03 21:02:08 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:37:16s. Time for last 1,000,000: 26s. Last read position: chr6:158,584,032 INFO 2026-06-03 21:02:16 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:37:24s. Time for last 1,000,000: 7s. Last read position: chr6:163,478,780 INFO 2026-06-03 21:02:31 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:37:39s. Time for last 1,000,000: 15s. Last read position: chr7:726,855 INFO 2026-06-03 21:02:41 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:37:49s. Time for last 1,000,000: 9s. Last read position: chr7:2,731,447 INFO 2026-06-03 21:02:48 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:37:56s. Time for last 1,000,000: 7s. Last read position: chr7:5,415,071 INFO 2026-06-03 21:02:57 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:38:05s. Time for last 1,000,000: 8s. Last read position: chr7:5,741,524 INFO 2026-06-03 21:03:04 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:38:12s. Time for last 1,000,000: 6s. Last read position: chr7:20,331,811 INFO 2026-06-03 21:03:20 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:38:28s. Time for last 1,000,000: 16s. Last read position: chr7:30,912,005 INFO 2026-06-03 21:03:28 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:38:36s. Time for last 1,000,000: 7s. Last read position: chr7:43,919,597 INFO 2026-06-03 21:03:36 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:38:44s. Time for last 1,000,000: 7s. Last read position: chr7:44,760,387 INFO 2026-06-03 21:03:46 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:38:54s. Time for last 1,000,000: 10s. Last read position: chr7:56,011,681 INFO 2026-06-03 21:03:54 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:39:02s. Time for last 1,000,000: 8s. Last read position: chr7:72,941,921 INFO 2026-06-03 21:03:58 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:39:06s. Time for last 1,000,000: 3s. Last read position: chr7:73,831,241 INFO 2026-06-03 21:04:23 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:39:31s. Time for last 1,000,000: 25s. Last read position: chr7:74,912,028 INFO 2026-06-03 21:04:28 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:39:36s. Time for last 1,000,000: 4s. Last read position: chr7:76,054,835 INFO 2026-06-03 21:04:33 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:39:41s. Time for last 1,000,000: 5s. Last read position: chr7:80,656,620 INFO 2026-06-03 21:05:19 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:40:27s. Time for last 1,000,000: 46s. Last read position: chr7:92,089,415 INFO 2026-06-03 21:05:58 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:41:06s. Time for last 1,000,000: 38s. Last read position: chr7:94,408,806 INFO 2026-06-03 21:06:12 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:41:20s. Time for last 1,000,000: 14s. Last read position: chr7:94,425,610 INFO 2026-06-03 21:06:34 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:41:42s. Time for last 1,000,000: 21s. Last read position: chr7:99,030,494 INFO 2026-06-03 21:06:43 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:41:51s. Time for last 1,000,000: 9s. Last read position: chr7:100,310,367 INFO 2026-06-03 21:06:50 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:41:58s. Time for last 1,000,000: 6s. Last read position: chr7:100,855,758 INFO 2026-06-03 21:06:57 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:42:05s. Time for last 1,000,000: 7s. Last read position: chr7:102,538,318 INFO 2026-06-03 21:07:01 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:42:09s. Time for last 1,000,000: 4s. Last read position: chr7:105,051,218 INFO 2026-06-03 21:07:22 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:42:30s. Time for last 1,000,000: 20s. Last read position: chr7:117,129,806 INFO 2026-06-03 21:07:30 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:42:38s. Time for last 1,000,000: 8s. Last read position: chr7:128,767,458 INFO 2026-06-03 21:07:39 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:42:47s. Time for last 1,000,000: 9s. Last read position: chr7:137,905,773 INFO 2026-06-03 21:07:47 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:42:55s. Time for last 1,000,000: 7s. Last read position: chr7:140,801,466 INFO 2026-06-03 21:07:54 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:43:02s. Time for last 1,000,000: 6s. Last read position: chr7:144,284,841 INFO 2026-06-03 21:07:58 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:43:06s. Time for last 1,000,000: 4s. Last read position: chr7:150,477,189 INFO 2026-06-03 21:08:18 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:43:25s. Time for last 1,000,000: 19s. Last read position: chr7:152,229,997 INFO 2026-06-03 21:08:30 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:43:38s. Time for last 1,000,000: 12s. Last read position: chr8:11,826,028 INFO 2026-06-03 21:08:49 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:43:57s. Time for last 1,000,000: 19s. Last read position: chr8:22,197,358 INFO 2026-06-03 21:08:58 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:44:06s. Time for last 1,000,000: 9s. Last read position: chr8:27,491,250 INFO 2026-06-03 21:09:04 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:44:12s. Time for last 1,000,000: 5s. Last read position: chr8:37,839,525 INFO 2026-06-03 21:09:21 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:44:29s. Time for last 1,000,000: 17s. Last read position: chr8:38,836,188 INFO 2026-06-03 21:09:34 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:44:42s. Time for last 1,000,000: 13s. Last read position: chr8:47,837,373