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/9a/42ebaf549f566984dfe50050c1c452/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/42ebaf549f566984dfe50050c1c452/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/ce426489fe8f62557e6ec077b9f0d5/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 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/90/184faea4f130c0eae580ccd3e890be/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam ==> 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 7:45:36 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 19:45:36 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-31d31f-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 19:45:37 GMT 2026] Executing as ?@nf-9a42ebaf549f566984dfe50050c1c452-be268-2hpz4 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.XXXXweQklg/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXXweQklg/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam INFO 2026-06-03 19:45:40 CollectRnaSeqMetrics Loaded 58279 genes. INFO 2026-06-03 19:45:58 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 17s. Last read position: chr1:1,472,007 INFO 2026-06-03 19:46:17 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 19s. Last read position: chr1:6,253,768 INFO 2026-06-03 19:46:34 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 17s. Last read position: chr1:9,744,613 INFO 2026-06-03 19:46:57 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 22s. Last read position: chr1:13,782,367 INFO 2026-06-03 19:47:09 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 12s. Last read position: chr1:17,069,133 INFO 2026-06-03 19:47:30 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 20s. Last read position: chr1:20,941,734 INFO 2026-06-03 19:47:57 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 26s. Last read position: chr1:22,639,312 INFO 2026-06-03 19:48:07 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 10s. Last read position: chr1:25,829,606 INFO 2026-06-03 19:48:21 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 14s. Last read position: chr1:27,552,007 INFO 2026-06-03 19:48:37 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 16s. Last read position: chr1:32,226,415 INFO 2026-06-03 19:48:50 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 12s. Last read position: chr1:35,192,643 INFO 2026-06-03 19:49:18 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 28s. Last read position: chr1:39,387,236 INFO 2026-06-03 19:50:01 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 42s. Last read position: chr1:43,312,370 INFO 2026-06-03 19:50:28 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 27s. Last read position: chr1:45,676,842 INFO 2026-06-03 19:50:46 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 18s. Last read position: chr1:52,950,776 INFO 2026-06-03 19:51:08 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 22s. Last read position: chr1:67,269,552 INFO 2026-06-03 19:51:24 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 15s. Last read position: chr1:93,582,725 INFO 2026-06-03 19:51:41 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 17s. Last read position: chr1:110,341,327 INFO 2026-06-03 19:51:50 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 9s. Last read position: chr1:115,976,658 INFO 2026-06-03 19:52:01 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 10s. Last read position: chr1:143,904,241 INFO 2026-06-03 19:52:08 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 7s. Last read position: chr1:148,564,860 INFO 2026-06-03 19:52:16 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 7s. Last read position: chr1:150,338,236 INFO 2026-06-03 19:52:34 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 18s. Last read position: chr1:151,520,226 INFO 2026-06-03 19:52:46 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 11s. Last read position: chr1:154,170,419 INFO 2026-06-03 19:53:13 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 26s. Last read position: chr1:155,181,854 INFO 2026-06-03 19:53:35 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 22s. Last read position: chr1:156,042,285 INFO 2026-06-03 19:53:54 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 19s. Last read position: chr1:156,969,302 INFO 2026-06-03 19:54:06 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 11s. Last read position: chr1:167,054,274 INFO 2026-06-03 19:54:16 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 10s. Last read position: chr1:178,024,040 INFO 2026-06-03 19:54:23 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 6s. Last read position: chr1:186,339,745 INFO 2026-06-03 19:54:33 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 9s. Last read position: chr1:202,422,672 INFO 2026-06-03 19:54:45 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 12s. Last read position: chr1:206,685,211 INFO 2026-06-03 19:54:49 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 3s. Last read position: chr1:207,336,807 INFO 2026-06-03 19:54:58 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 9s. Last read position: chr1:223,619,357 INFO 2026-06-03 19:55:14 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 15s. Last read position: chr1:228,271,963 INFO 2026-06-03 19:55:33 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 19s. Last read position: chr1:236,064,882 INFO 2026-06-03 19:55:45 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 11s. Last read position: chr2:3,388,596 INFO 2026-06-03 19:55:54 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 9s. Last read position: chr2:20,278,599 INFO 2026-06-03 19:56:03 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 9s. Last read position: chr2:27,234,628 INFO 2026-06-03 19:56:12 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 9s. Last read position: chr2:32,916,254 INFO 2026-06-03 19:56:16 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,273 INFO 2026-06-03 19:56:18 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,444 INFO 2026-06-03 19:56:24 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 6s. Last read position: chr2:43,225,006 INFO 2026-06-03 19:56:35 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 10s. Last read position: chr2:54,626,099 INFO 2026-06-03 19:56:54 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 18s. Last read position: chr2:61,348,354 INFO 2026-06-03 19:57:11 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 17s. Last read position: chr2:71,388,662 INFO 2026-06-03 19:57:23 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 11s. Last read position: chr2:74,878,916 INFO 2026-06-03 19:57:28 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 5s. Last read position: chr2:88,126,308 INFO 2026-06-03 19:57:37 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 8s. Last read position: chr2:97,792,436 INFO 2026-06-03 19:57:45 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 8s. Last read position: chr2:108,754,937 INFO 2026-06-03 19:57:50 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 4s. Last read position: chr2:111,873,329 INFO 2026-06-03 19:57:58 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 7s. Last read position: chr2:127,605,899 INFO 2026-06-03 19:58:10 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 11s. Last read position: chr2:148,483,657 INFO 2026-06-03 19:58:25 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 15s. Last read position: chr2:170,965,794 INFO 2026-06-03 19:59:02 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 36s. Last read position: chr2:181,531,742 INFO 2026-06-03 19:59:21 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 19s. Last read position: chr2:190,998,271 INFO 2026-06-03 19:59:45 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 24s. Last read position: chr2:203,112,042 INFO 2026-06-03 20:00:01 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 15s. Last read position: chr2:215,379,269 INFO 2026-06-03 20:00:52 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 50s. Last read position: chr2:218,392,980 INFO 2026-06-03 20:01:06 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 14s. Last read position: chr2:224,862,694 INFO 2026-06-03 20:01:25 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 18s. Last read position: chr2:231,521,013 INFO 2026-06-03 20:01:45 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 20s. Last read position: chr2:237,377,165 INFO 2026-06-03 20:02:03 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 18s. Last read position: chr2:241,240,065 INFO 2026-06-03 20:02:25 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 21s. Last read position: chr3:9,933,056 INFO 2026-06-03 20:02:35 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:16:55s. Time for last 1,000,000: 10s. Last read position: chr3:18,349,426 INFO 2026-06-03 20:02:47 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:17:06s. Time for last 1,000,000: 11s. Last read position: chr3:38,020,230 INFO 2026-06-03 20:03:05 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 18s. Last read position: chr3:45,118,457 INFO 2026-06-03 20:03:17 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 12s. Last read position: chr3:47,916,804 INFO 2026-06-03 20:03:44 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:18:04s. Time for last 1,000,000: 26s. Last read position: chr3:49,006,123 INFO 2026-06-03 20:03:59 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 14s. Last read position: chr3:49,972,125 INFO 2026-06-03 20:04:10 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:18:30s. Time for last 1,000,000: 11s. Last read position: chr3:52,502,009 INFO 2026-06-03 20:04:26 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:18:46s. Time for last 1,000,000: 16s. Last read position: chr3:58,524,588 INFO 2026-06-03 20:04:41 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:19:01s. Time for last 1,000,000: 14s. Last read position: chr3:100,386,886 INFO 2026-06-03 20:04:54 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 12s. Last read position: chr3:121,694,567 INFO 2026-06-03 20:05:03 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 9s. Last read position: chr3:127,014,711 INFO 2026-06-03 20:05:13 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:19:33s. Time for last 1,000,000: 10s. Last read position: chr3:134,486,543 INFO 2026-06-03 20:05:24 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:19:44s. Time for last 1,000,000: 10s. Last read position: chr3:158,665,346 INFO 2026-06-03 20:05:35 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:19:54s. Time for last 1,000,000: 10s. Last read position: chr3:184,142,321 INFO 2026-06-03 20:05:56 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:20:16s. Time for last 1,000,000: 21s. Last read position: chr3:188,524,726 INFO 2026-06-03 20:06:03 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:20:23s. Time for last 1,000,000: 6s. Last read position: chr3:195,725,206 INFO 2026-06-03 20:06:19 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:20:39s. Time for last 1,000,000: 16s. Last read position: chr3:195,779,581 INFO 2026-06-03 20:06:47 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:21:07s. Time for last 1,000,000: 27s. Last read position: chr3:195,783,512 INFO 2026-06-03 20:07:18 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:21:38s. Time for last 1,000,000: 31s. Last read position: chr3:195,787,869 INFO 2026-06-03 20:07:51 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 32s. Last read position: chr3:197,951,157 INFO 2026-06-03 20:08:04 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:22:24s. Time for last 1,000,000: 13s. Last read position: chr4:1,804,946 INFO 2026-06-03 20:08:20 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:22:40s. Time for last 1,000,000: 16s. Last read position: chr4:6,863,295 INFO 2026-06-03 20:08:29 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:22:48s. Time for last 1,000,000: 8s. Last read position: chr4:25,662,552 INFO 2026-06-03 20:08:41 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:23:01s. Time for last 1,000,000: 12s. Last read position: chr4:54,064,190 INFO 2026-06-03 20:08:50 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:23:10s. Time for last 1,000,000: 8s. Last read position: chr4:73,156,044 INFO 2026-06-03 20:09:02 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:23:22s. Time for last 1,000,000: 11s. Last read position: chr4:83,094,744 INFO 2026-06-03 20:09:20 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:23:40s. Time for last 1,000,000: 18s. Last read position: chr4:106,328,115 INFO 2026-06-03 20:09:39 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:23:58s. Time for last 1,000,000: 18s. Last read position: chr4:139,147,812 INFO 2026-06-03 20:09:52 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:24:11s. Time for last 1,000,000: 13s. Last read position: chr4:153,168,487 INFO 2026-06-03 20:10:08 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:24:27s. Time for last 1,000,000: 16s. Last read position: chr4:186,611,388 INFO 2026-06-03 20:10:16 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:24:35s. Time for last 1,000,000: 7s. Last read position: chr5:10,258,278 INFO 2026-06-03 20:10:40 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:24:59s. Time for last 1,000,000: 24s. Last read position: chr5:16,475,044 INFO 2026-06-03 20:10:50 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:25:09s. Time for last 1,000,000: 9s. Last read position: chr5:42,801,093 INFO 2026-06-03 20:11:02 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:25:21s. Time for last 1,000,000: 11s. Last read position: chr5:69,365,259 INFO 2026-06-03 20:11:09 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:25:29s. Time for last 1,000,000: 7s. Last read position: chr5:82,269,947 INFO 2026-06-03 20:11:35 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:25:54s. Time for last 1,000,000: 25s. Last read position: chr5:113,018,370 INFO 2026-06-03 20:11:47 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 11s. Last read position: chr5:132,822,999 INFO 2026-06-03 20:12:00 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:26:19s. Time for last 1,000,000: 13s. Last read position: chr5:138,466,995 INFO 2026-06-03 20:12:13 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:26:33s. Time for last 1,000,000: 13s. Last read position: chr5:141,102,404 INFO 2026-06-03 20:12:27 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:26:47s. Time for last 1,000,000: 14s. Last read position: chr5:146,459,124 INFO 2026-06-03 20:12:36 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:26:56s. Time for last 1,000,000: 8s. Last read position: chr5:150,402,568 INFO 2026-06-03 20:12:45 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:27:04s. Time for last 1,000,000: 8s. Last read position: chr5:154,792,679 INFO 2026-06-03 20:12:56 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:27:16s. Time for last 1,000,000: 11s. Last read position: chr5:171,392,962 INFO 2026-06-03 20:13:05 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:27:25s. Time for last 1,000,000: 8s. Last read position: chr5:177,366,195 INFO 2026-06-03 20:13:22 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:27:41s. Time for last 1,000,000: 16s. Last read position: chr5:179,797,997 INFO 2026-06-03 20:13:31 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:27:51s. Time for last 1,000,000: 9s. Last read position: chr5:181,260,264 INFO 2026-06-03 20:13:44 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:28:04s. Time for last 1,000,000: 12s. Last read position: chr6:7,247,193 INFO 2026-06-03 20:13:54 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:28:14s. Time for last 1,000,000: 9s. Last read position: chr6:21,594,598 INFO 2026-06-03 20:14:00 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:28:20s. Time for last 1,000,000: 6s. Last read position: chr6:29,610,960 INFO 2026-06-03 20:14:09 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:28:28s. Time for last 1,000,000: 8s. Last read position: chr6:30,720,432 INFO 2026-06-03 20:14:25 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:28:45s. Time for last 1,000,000: 16s. Last read position: chr6:31,631,828 INFO 2026-06-03 20:14:35 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:28:55s. Time for last 1,000,000: 10s. Last read position: chr6:31,956,979 INFO 2026-06-03 20:14:45 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:29:05s. Time for last 1,000,000: 9s. Last read position: chr6:33,290,755 INFO 2026-06-03 20:14:54 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:29:13s. Time for last 1,000,000: 8s. Last read position: chr6:35,470,578 INFO 2026-06-03 20:15:00 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:29:20s. Time for last 1,000,000: 6s. Last read position: chr6:43,019,125 INFO 2026-06-03 20:15:09 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:29:29s. Time for last 1,000,000: 9s. Last read position: chr6:47,286,210 INFO 2026-06-03 20:16:00 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:30:19s. Time for last 1,000,000: 50s. Last read position: chr6:63,685,295 INFO 2026-06-03 20:16:15 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:30:34s. Time for last 1,000,000: 15s. Last read position: chr6:89,352,548 INFO 2026-06-03 20:16:23 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:30:43s. Time for last 1,000,000: 8s. Last read position: chr6:110,967,613 INFO 2026-06-03 20:16:34 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:30:54s. Time for last 1,000,000: 11s. Last read position: chr6:130,869,797 INFO 2026-06-03 20:16:54 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:31:14s. Time for last 1,000,000: 20s. Last read position: chr6:138,945,360 INFO 2026-06-03 20:17:08 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:31:28s. Time for last 1,000,000: 13s. Last read position: chr6:154,832,966 INFO 2026-06-03 20:17:17 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:31:37s. Time for last 1,000,000: 9s. Last read position: chr6:160,069,907 INFO 2026-06-03 20:17:36 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:31:56s. Time for last 1,000,000: 18s. Last read position: chr7:1,435,148 INFO 2026-06-03 20:17:43 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:32:03s. Time for last 1,000,000: 6s. Last read position: chr7:5,362,689 INFO 2026-06-03 20:17:53 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:32:13s. Time for last 1,000,000: 9s. Last read position: chr7:5,923,945 INFO 2026-06-03 20:18:07 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:32:26s. Time for last 1,000,000: 13s. Last read position: chr7:27,145,607 INFO 2026-06-03 20:18:15 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:32:35s. Time for last 1,000,000: 8s. Last read position: chr7:44,104,844 INFO 2026-06-03 20:18:25 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:32:45s. Time for last 1,000,000: 10s. Last read position: chr7:55,687,835 INFO 2026-06-03 20:18:31 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:32:51s. Time for last 1,000,000: 6s. Last read position: chr7:73,296,877 INFO 2026-06-03 20:18:39 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:32:58s. Time for last 1,000,000: 7s. Last read position: chr7:75,395,285 INFO 2026-06-03 20:18:43 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:33:02s. Time for last 1,000,000: 4s. Last read position: chr7:77,053,106 INFO 2026-06-03 20:19:32 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:33:51s. Time for last 1,000,000: 49s. Last read position: chr7:93,926,138 INFO 2026-06-03 20:19:46 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:34:05s. Time for last 1,000,000: 13s. Last read position: chr7:99,666,994 INFO 2026-06-03 20:19:54 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:34:14s. Time for last 1,000,000: 8s. Last read position: chr7:100,805,561 INFO 2026-06-03 20:19:58 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:34:18s. Time for last 1,000,000: 4s. Last read position: chr7:100,991,457 INFO 2026-06-03 20:20:01 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:34:21s. Time for last 1,000,000: 2s. Last read position: chr7:100,992,360 INFO 2026-06-03 20:20:03 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:34:23s. Time for last 1,000,000: 2s. Last read position: chr7:100,992,858 INFO 2026-06-03 20:20:05 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:34:25s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,161 INFO 2026-06-03 20:20:06 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:34:26s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,592 INFO 2026-06-03 20:20:07 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:34:27s. Time for last 1,000,000: 0s. Last read position: chr7:100,993,772 INFO 2026-06-03 20:20:09 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:34:28s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,136 INFO 2026-06-03 20:20:10 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:34:29s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,655 INFO 2026-06-03 20:20:10 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:34:30s. Time for last 1,000,000: 0s. Last read position: chr7:100,994,929 INFO 2026-06-03 20:20:11 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:34:31s. Time for last 1,000,000: 0s. Last read position: chr7:100,995,220 INFO 2026-06-03 20:20:12 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:34:32s. Time for last 1,000,000: 1s. Last read position: chr7:100,995,664 INFO 2026-06-03 20:20:13 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:34:33s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,041 INFO 2026-06-03 20:20:14 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:34:34s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,280 INFO 2026-06-03 20:20:15 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:34:35s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,400 INFO 2026-06-03 20:20:17 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:34:37s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,518 INFO 2026-06-03 20:20:19 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:34:39s. Time for last 1,000,000: 2s. Last read position: chr7:100,996,743 INFO 2026-06-03 20:20:22 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:34:42s. Time for last 1,000,000: 2s. Last read position: chr7:100,996,843 INFO 2026-06-03 20:20:24 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:34:44s. Time for last 1,000,000: 2s. Last read position: chr7:100,997,030 INFO 2026-06-03 20:20:26 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:34:46s. Time for last 1,000,000: 2s. Last read position: chr7:100,997,234 INFO 2026-06-03 20:20:29 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:34:49s. Time for last 1,000,000: 2s. Last read position: chr7:100,997,504 INFO 2026-06-03 20:20:31 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:34:51s. Time for last 1,000,000: 2s. Last read position: chr7:100,997,809 INFO 2026-06-03 20:20:32 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:34:52s. Time for last 1,000,000: 0s. Last read position: chr7:100,997,928 INFO 2026-06-03 20:20:34 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:34:53s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,064 INFO 2026-06-03 20:20:34 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:34:54s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,266 INFO 2026-06-03 20:20:35 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:34:55s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,458 INFO 2026-06-03 20:20:36 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:34:55s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,646 INFO 2026-06-03 20:20:37 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:34:57s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,822 INFO 2026-06-03 20:20:38 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:34:58s. Time for last 1,000,000: 0s. Last read position: chr7:100,999,010 INFO 2026-06-03 20:20:40 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:34:59s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,440 INFO 2026-06-03 20:20:42 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:35:01s. Time for last 1,000,000: 2s. Last read position: chr7:100,999,694 INFO 2026-06-03 20:20:44 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:35:03s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,961 INFO 2026-06-03 20:20:46 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:35:06s. Time for last 1,000,000: 2s. Last read position: chr7:101,000,168 INFO 2026-06-03 20:20:48 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:35:07s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,415 INFO 2026-06-03 20:20:49 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:35:09s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,662 INFO 2026-06-03 20:20:51 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:35:11s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,871 INFO 2026-06-03 20:20:54 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:35:13s. Time for last 1,000,000: 2s. Last read position: chr7:101,001,048 INFO 2026-06-03 20:20:55 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:35:15s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,316 INFO 2026-06-03 20:20:56 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:35:16s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,436 INFO 2026-06-03 20:20:57 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:35:17s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,556 INFO 2026-06-03 20:20:58 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:35:17s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,778 INFO 2026-06-03 20:20:58 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:35:18s. Time for last 1,000,000: 0s. Last read position: chr7:101,002,055 INFO 2026-06-03 20:20:59 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:35:19s. Time for last 1,000,000: 0s. Last read position: chr7:101,002,345 INFO 2026-06-03 20:21:01 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:35:21s. Time for last 1,000,000: 2s. Last read position: chr7:101,002,577 INFO 2026-06-03 20:21:03 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:35:23s. Time for last 1,000,000: 1s. Last read position: chr7:101,003,173 INFO 2026-06-03 20:21:05 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:35:24s. Time for last 1,000,000: 1s. Last read position: chr7:101,003,741 INFO 2026-06-03 20:21:06 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:35:25s. Time for last 1,000,000: 0s. Last read position: chr7:101,004,046 INFO 2026-06-03 20:21:08 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:35:27s. Time for last 1,000,000: 1s. Last read position: chr7:101,008,737 INFO 2026-06-03 20:21:16 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:35:36s. Time for last 1,000,000: 8s. Last read position: chr7:102,640,231 INFO 2026-06-03 20:21:35 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:35:55s. Time for last 1,000,000: 19s. Last read position: chr7:108,565,848 INFO 2026-06-03 20:21:44 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:36:04s. Time for last 1,000,000: 8s. Last read position: chr7:128,846,758 INFO 2026-06-03 20:21:52 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:36:11s. Time for last 1,000,000: 7s. Last read position: chr7:139,572,962 INFO 2026-06-03 20:21:58 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:36:18s. Time for last 1,000,000: 6s. Last read position: chr7:144,282,267 INFO 2026-06-03 20:22:01 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:36:21s. Time for last 1,000,000: 3s. Last read position: chr7:150,369,765 INFO 2026-06-03 20:22:17 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:36:37s. Time for last 1,000,000: 16s. Last read position: chr7:152,263,063 INFO 2026-06-03 20:22:27 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:36:46s. Time for last 1,000,000: 9s. Last read position: chr8:9,556,443 INFO 2026-06-03 20:22:41 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:37:01s. Time for last 1,000,000: 14s. Last read position: chr8:22,572,400 INFO 2026-06-03 20:22:51 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:37:11s. Time for last 1,000,000: 10s. Last read position: chr8:29,092,775 INFO 2026-06-03 20:22:58 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:37:17s. Time for last 1,000,000: 6s. Last read position: chr8:38,110,401 INFO 2026-06-03 20:23:14 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:37:34s. Time for last 1,000,000: 16s. Last read position: chr8:47,599,159 INFO 2026-06-03 20:23:27 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:37:46s. Time for last 1,000,000: 12s. Last read position: chr8:70,131,891 INFO 2026-06-03 20:23:35 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:37:54s. Time for last 1,000,000: 7s. Last read position: chr8:94,865,457 INFO 2026-06-03 20:23:54 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:38:13s. Time for last 1,000,000: 19s. Last read position: chr8:116,645,086 INFO 2026-06-03 20:24:03 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:38:23s. Time for last 1,000,000: 9s. Last read position: chr8:133,259,205 INFO 2026-06-03 20:24:16 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:38:36s. Time for last 1,000,000: 13s. Last read position: chr8:143,728,498 INFO 2026-06-03 20:24:20 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:38:40s. Time for last 1,000,000: 3s. Last read position: chr8:143,859,877 INFO 2026-06-03 20:24:21 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:38:41s. Time for last 1,000,000: 0s. Last read position: chr8:143,862,053 INFO 2026-06-03 20:24:22 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:38:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,400 INFO 2026-06-03 20:24:23 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:38:42s. Time for last 1,000,000: 0s. Last read position: chr8:143,867,772 INFO 2026-06-03 20:24:28 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:38:48s. Time for last 1,000,000: 5s. Last read position: chr8:143,924,547 INFO 2026-06-03 20:24:44 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:39:04s. Time for last 1,000,000: 16s. Last read position: chr8:144,318,304 INFO 2026-06-03 20:24:52 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:39:12s. Time for last 1,000,000: 8s. Last read position: chr9:730,170 INFO 2026-06-03 20:25:08 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:39:27s. Time for last 1,000,000: 15s. Last read position: chr9:20,622,288 INFO 2026-06-03 20:25:17 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:39:36s. Time for last 1,000,000: 9s. Last read position: chr9:35,377,664 INFO 2026-06-03 20:25:24 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:39:43s. Time for last 1,000,000: 7s. Last read position: chr9:64,842,206 INFO 2026-06-03 20:25:36 SinglePassSamProgram Processed 214,000,000 records. Elapsed time: 00:39:55s. Time for last 1,000,000: 11s. Last read position: chr9:83,971,293 INFO 2026-06-03 20:25:46 SinglePassSamProgram Processed 215,000,000 records. Elapsed time: 00:40:06s. Time for last 1,000,000: 10s. Last read position: chr9:93,292,788 INFO 2026-06-03 20:25:54 SinglePassSamProgram Processed 216,000,000 records. Elapsed time: 00:40:14s. Time for last 1,000,000: 7s. Last read position: chr9:101,390,837 INFO 2026-06-03 20:26:03 SinglePassSamProgram Processed 217,000,000 records. Elapsed time: 00:40:23s. Time for last 1,000,000: 9s. Last read position: chr9:113,193,441 INFO 2026-06-03 20:26:15 SinglePassSamProgram Processed 218,000,000 records. Elapsed time: 00:40:35s. Time for last 1,000,000: 11s. Last read position: chr9:121,759,980 INFO 2026-06-03 20:26:25 SinglePassSamProgram Processed 219,000,000 records. Elapsed time: 00:40:44s. Time for last 1,000,000: 9s. Last read position: chr9:127,867,963 INFO 2026-06-03 20:26:43 SinglePassSamProgram Processed 220,000,000 records. Elapsed time: 00:41:02s. Time for last 1,000,000: 18s. Last read position: chr9:128,633,220 INFO 2026-06-03 20:26:50 SinglePassSamProgram Processed 221,000,000 records. Elapsed time: 00:41:09s. Time for last 1,000,000: 6s. Last read position: chr9:131,066,995 INFO 2026-06-03 20:26:59 SinglePassSamProgram Processed 222,000,000 records. Elapsed time: 00:41:19s. Time for last 1,000,000: 9s. Last read position: chr9:133,797,800 INFO 2026-06-03 20:27:10 SinglePassSamProgram Processed 223,000,000 records. Elapsed time: 00:41:30s. Time for last 1,000,000: 11s. Last read position: chr9:136,476,871 INFO 2026-06-03 20:27:25 SinglePassSamProgram Processed 224,000,000 records. Elapsed time: 00:41:45s. Time for last 1,000,000: 14s. Last read position: chr9:137,015,752 INFO 2026-06-03 20:27:33 SinglePassSamProgram Processed 225,000,000 records. Elapsed time: 00:41:53s. Time for last 1,000,000: 7s. Last read position: chr9:137,551,929 INFO 2026-06-03 20:27:44 SinglePassSamProgram Processed 226,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 11s. Last read position: chr10:12,374,611 INFO 2026-06-03 20:27:57 SinglePassSamProgram Processed 227,000,000 records. Elapsed time: 00:42:16s. Time for last 1,000,000: 12s. Last read position: chr10:28,595,853 INFO 2026-06-03 20:28:09 SinglePassSamProgram Processed 228,000,000 records. Elapsed time: 00:42:28s. Time for last 1,000,000: 12s. Last read position: chr10:43,387,054 INFO 2026-06-03 20:28:13 SinglePassSamProgram Processed 229,000,000 records. Elapsed time: 00:42:33s. Time for last 1,000,000: 4s. Last read position: chr10:50,068,162 INFO 2026-06-03 20:28:23 SinglePassSamProgram Processed 230,000,000 records. Elapsed time: 00:42:42s. Time for last 1,000,000: 9s. Last read position: chr10:70,153,850 INFO 2026-06-03 20:28:34 SinglePassSamProgram Processed 231,000,000 records. Elapsed time: 00:42:54s. Time for last 1,000,000: 11s. Last read position: chr10:75,211,140 INFO 2026-06-03 20:28:48 SinglePassSamProgram Processed 232,000,000 records. Elapsed time: 00:43:08s. Time for last 1,000,000: 14s. Last read position: chr10:86,943,397 INFO 2026-06-03 20:28:56 SinglePassSamProgram Processed 233,000,000 records. Elapsed time: 00:43:16s. Time for last 1,000,000: 7s. Last read position: chr10:95,271,716 INFO 2026-06-03 20:29:07 SinglePassSamProgram Processed 234,000,000 records. Elapsed time: 00:43:27s. Time for last 1,000,000: 11s. Last read position: chr10:100,984,737 INFO 2026-06-03 20:29:26 SinglePassSamProgram Processed 235,000,000 records. Elapsed time: 00:43:45s. Time for last 1,000,000: 18s. Last read position: chr10:103,661,018 INFO 2026-06-03 20:29:39 SinglePassSamProgram Processed 236,000,000 records. Elapsed time: 00:43:58s. Time for last 1,000,000: 13s. Last read position: chr10:116,944,965 INFO 2026-06-03 20:29:49 SinglePassSamProgram Processed 237,000,000 records. Elapsed time: 00:44:08s. Time for last 1,000,000: 10s. Last read position: chr10:124,992,785 INFO 2026-06-03 20:29:55 SinglePassSamProgram Processed 238,000,000 records. Elapsed time: 00:44:15s. Time for last 1,000,000: 6s. Last read position: chr11:314,943 INFO 2026-06-03 20:30:02 SinglePassSamProgram Processed 239,000,000 records. Elapsed time: 00:44:22s. Time for last 1,000,000: 6s. Last read position: chr11:618,845 INFO 2026-06-03 20:30:12 SinglePassSamProgram Processed 240,000,000 records. Elapsed time: 00:44:32s. Time for last 1,000,000: 9s. Last read position: chr11:1,075,773 INFO 2026-06-03 20:30:17 SinglePassSamProgram Processed 241,000,000 records. Elapsed time: 00:44:37s. Time for last 1,000,000: 5s. Last read position: chr11:1,085,826 INFO 2026-06-03 20:30:26 SinglePassSamProgram Processed 242,000,000 records. Elapsed time: 00:44:46s. Time for last 1,000,000: 9s. Last read position: chr11:1,098,949 INFO 2026-06-03 20:30:34 SinglePassSamProgram Processed 243,000,000 records. Elapsed time: 00:44:53s. Time for last 1,000,000: 7s. Last read position: chr11:1,243,068 INFO 2026-06-03 20:30:38 SinglePassSamProgram Processed 244,000,000 records. Elapsed time: 00:44:58s. Time for last 1,000,000: 4s. Last read position: chr11:1,244,379 INFO 2026-06-03 20:30:41 SinglePassSamProgram Processed 245,000,000 records. Elapsed time: 00:45:01s. Time for last 1,000,000: 3s. Last read position: chr11:1,245,252 INFO 2026-06-03 20:30:47 SinglePassSamProgram Processed 246,000,000 records. Elapsed time: 00:45:07s. Time for last 1,000,000: 6s. Last read position: chr11:1,247,003 INFO 2026-06-03 20:30:52 SinglePassSamProgram Processed 247,000,000 records. Elapsed time: 00:45:12s. Time for last 1,000,000: 4s. Last read position: chr11:1,248,264 INFO 2026-06-03 20:31:00 SinglePassSamProgram Processed 248,000,000 records. Elapsed time: 00:45:19s. Time for last 1,000,000: 7s. Last read position: chr11:1,249,463 INFO 2026-06-03 20:31:08 SinglePassSamProgram Processed 249,000,000 records. Elapsed time: 00:45:27s. Time for last 1,000,000: 7s. Last read position: chr11:1,250,918 INFO 2026-06-03 20:31:16 SinglePassSamProgram Processed 250,000,000 records. Elapsed time: 00:45:36s. Time for last 1,000,000: 8s. Last read position: chr11:2,929,108 INFO 2026-06-03 20:31:26 SinglePassSamProgram Processed 251,000,000 records. Elapsed time: 00:45:46s. Time for last 1,000,000: 9s. Last read position: chr11:8,707,102 INFO 2026-06-03 20:31:43 SinglePassSamProgram Processed 252,000,000 records. Elapsed time: 00:46:02s. Time for last 1,000,000: 16s. Last read position: chr11:17,074,415 INFO 2026-06-03 20:31:52 SinglePassSamProgram Processed 253,000,000 records. Elapsed time: 00:46:11s. Time for last 1,000,000: 8s. Last read position: chr11:43,443,366 INFO 2026-06-03 20:32:00 SinglePassSamProgram Processed 254,000,000 records. Elapsed time: 00:46:20s. Time for last 1,000,000: 8s. Last read position: chr11:46,899,882 INFO 2026-06-03 20:32:11 SinglePassSamProgram Processed 255,000,000 records. Elapsed time: 00:46:30s. Time for last 1,000,000: 10s. Last read position: chr11:57,796,833 INFO 2026-06-03 20:32:28 SinglePassSamProgram Processed 256,000,000 records. Elapsed time: 00:46:48s. Time for last 1,000,000: 17s. Last read position: chr11:61,967,320 INFO 2026-06-03 20:32:32 SinglePassSamProgram Processed 257,000,000 records. Elapsed time: 00:46:51s. Time for last 1,000,000: 3s. Last read position: chr11:62,593,916 INFO 2026-06-03 20:32:41 SinglePassSamProgram Processed 258,000,000 records. Elapsed time: 00:47:01s. Time for last 1,000,000: 9s. Last read position: chr11:64,258,941 INFO 2026-06-03 20:32:50 SinglePassSamProgram Processed 259,000,000 records. Elapsed time: 00:47:10s. Time for last 1,000,000: 8s. Last read position: chr11:65,120,759 INFO 2026-06-03 20:32:58 SinglePassSamProgram Processed 260,000,000 records. Elapsed time: 00:47:18s. Time for last 1,000,000: 8s. Last read position: chr11:65,654,413 INFO 2026-06-03 20:33:06 SinglePassSamProgram Processed 261,000,000 records. Elapsed time: 00:47:26s. Time for last 1,000,000: 8s. Last read position: chr11:66,643,564 INFO 2026-06-03 20:33:18 SinglePassSamProgram Processed 262,000,000 records. Elapsed time: 00:47:37s. Time for last 1,000,000: 11s. Last read position: chr11:68,045,008 INFO 2026-06-03 20:33:26 SinglePassSamProgram Processed 263,000,000 records. Elapsed time: 00:47:46s. Time for last 1,000,000: 8s. Last read position: chr11:70,820,647 INFO 2026-06-03 20:33:48 SinglePassSamProgram Processed 264,000,000 records. Elapsed time: 00:48:08s. Time for last 1,000,000: 22s. Last read position: chr11:73,311,058 INFO 2026-06-03 20:33:58 SinglePassSamProgram Processed 265,000,000 records. Elapsed time: 00:48:18s. Time for last 1,000,000: 10s. Last read position: chr11:83,157,510 INFO 2026-06-03 20:34:10 SinglePassSamProgram Processed 266,000,000 records. Elapsed time: 00:48:30s. Time for last 1,000,000: 11s. Last read position: chr11:102,205,911 INFO 2026-06-03 20:34:19 SinglePassSamProgram Processed 267,000,000 records. Elapsed time: 00:48:38s. Time for last 1,000,000: 8s. Last read position: chr11:117,207,965 INFO 2026-06-03 20:34:30 SinglePassSamProgram Processed 268,000,000 records. Elapsed time: 00:48:49s. Time for last 1,000,000: 10s. Last read position: chr11:119,056,092 INFO 2026-06-03 20:34:39 SinglePassSamProgram Processed 269,000,000 records. Elapsed time: 00:48:58s. Time for last 1,000,000: 9s. Last read position: chr11:126,271,525 INFO 2026-06-03 20:34:46 SinglePassSamProgram Processed 270,000,000 records. Elapsed time: 00:49:06s. Time for last 1,000,000: 7s. Last read position: chr12:754,065 INFO 2026-06-03 20:35:01 SinglePassSamProgram Processed 271,000,000 records. Elapsed time: 00:49:21s. Time for last 1,000,000: 15s. Last read position: chr12:6,374,705 INFO 2026-06-03 20:35:22 SinglePassSamProgram Processed 272,000,000 records. Elapsed time: 00:49:42s. Time for last 1,000,000: 20s. Last read position: chr12:6,970,939 INFO 2026-06-03 20:35:28 SinglePassSamProgram Processed 273,000,000 records. Elapsed time: 00:49:48s. Time for last 1,000,000: 6s. Last read position: chr12:12,721,035 INFO 2026-06-03 20:35:38 SinglePassSamProgram Processed 274,000,000 records. Elapsed time: 00:49:58s. Time for last 1,000,000: 9s. Last read position: chr12:31,103,769 INFO 2026-06-03 20:35:51 SinglePassSamProgram Processed 275,000,000 records. Elapsed time: 00:50:10s. Time for last 1,000,000: 12s. Last read position: chr12:48,938,971 INFO 2026-06-03 20:35:58 SinglePassSamProgram Processed 276,000,000 records. Elapsed time: 00:50:18s. Time for last 1,000,000: 7s. Last read position: chr12:49,642,243 INFO 2026-06-03 20:36:06 SinglePassSamProgram Processed 277,000,000 records. Elapsed time: 00:50:26s. Time for last 1,000,000: 8s. Last read position: chr12:52,904,801 INFO 2026-06-03 20:36:18 SinglePassSamProgram Processed 278,000,000 records. Elapsed time: 00:50:38s. Time for last 1,000,000: 12s. Last read position: chr12:54,183,740 INFO 2026-06-03 20:36:33 SinglePassSamProgram Processed 279,000,000 records. Elapsed time: 00:50:53s. Time for last 1,000,000: 14s. Last read position: chr12:56,163,753 INFO 2026-06-03 20:36:46 SinglePassSamProgram Processed 280,000,000 records. Elapsed time: 00:51:06s. Time for last 1,000,000: 12s. Last read position: chr12:57,096,581 INFO 2026-06-03 20:37:03 SinglePassSamProgram Processed 281,000,000 records. Elapsed time: 00:51:23s. Time for last 1,000,000: 16s. Last read position: chr12:57,474,872 INFO 2026-06-03 20:37:14 SinglePassSamProgram Processed 282,000,000 records. Elapsed time: 00:51:33s. Time for last 1,000,000: 10s. Last read position: chr12:68,731,707 INFO 2026-06-03 20:37:24 SinglePassSamProgram Processed 283,000,000 records. Elapsed time: 00:51:44s. Time for last 1,000,000: 10s. Last read position: chr12:93,395,487 INFO 2026-06-03 20:37:34 SinglePassSamProgram Processed 284,000,000 records. Elapsed time: 00:51:54s. Time for last 1,000,000: 10s. Last read position: chr12:108,526,443 INFO 2026-06-03 20:37:48 SinglePassSamProgram Processed 285,000,000 records. Elapsed time: 00:52:08s. Time for last 1,000,000: 13s. Last read position: chr12:112,265,956 INFO 2026-06-03 20:38:02 SinglePassSamProgram Processed 286,000,000 records. Elapsed time: 00:52:22s. Time for last 1,000,000: 13s. Last read position: chr12:120,178,852 INFO 2026-06-03 20:38:11 SinglePassSamProgram Processed 287,000,000 records. Elapsed time: 00:52:30s. Time for last 1,000,000: 8s. Last read position: chr12:122,133,424 INFO 2026-06-03 20:38:19 SinglePassSamProgram Processed 288,000,000 records. Elapsed time: 00:52:39s. Time for last 1,000,000: 8s. Last read position: chr12:124,336,758 INFO 2026-06-03 20:38:37 SinglePassSamProgram Processed 289,000,000 records. Elapsed time: 00:52:56s. Time for last 1,000,000: 17s. Last read position: chr12:132,066,880 INFO 2026-06-03 20:38:46 SinglePassSamProgram Processed 290,000,000 records. Elapsed time: 00:53:05s. Time for last 1,000,000: 9s. Last read position: chr13:20,189,225 INFO 2026-06-03 20:38:52 SinglePassSamProgram Processed 291,000,000 records. Elapsed time: 00:53:12s. Time for last 1,000,000: 6s. Last read position: chr13:33,185,860 INFO 2026-06-03 20:39:00 SinglePassSamProgram Processed 292,000,000 records. Elapsed time: 00:53:20s. Time for last 1,000,000: 7s. Last read position: chr13:49,196,925 INFO 2026-06-03 20:39:10 SinglePassSamProgram Processed 293,000,000 records. Elapsed time: 00:53:30s. Time for last 1,000,000: 10s. Last read position: chr13:77,899,960 INFO 2026-06-03 20:39:21 SinglePassSamProgram Processed 294,000,000 records. Elapsed time: 00:53:41s. Time for last 1,000,000: 11s. Last read position: chr13:110,183,252 INFO 2026-06-03 20:39:36 SinglePassSamProgram Processed 295,000,000 records. Elapsed time: 00:53:56s. Time for last 1,000,000: 14s. Last read position: chr13:113,319,605 INFO 2026-06-03 20:39:50 SinglePassSamProgram Processed 296,000,000 records. Elapsed time: 00:54:09s. Time for last 1,000,000: 13s. Last read position: chr14:22,845,991 INFO 2026-06-03 20:39:59 SinglePassSamProgram Processed 297,000,000 records. Elapsed time: 00:54:19s. Time for last 1,000,000: 9s. Last read position: chr14:24,210,457 INFO 2026-06-03 20:40:12 SinglePassSamProgram Processed 298,000,000 records. Elapsed time: 00:54:32s. Time for last 1,000,000: 12s. Last read position: chr14:39,181,105 INFO 2026-06-03 20:40:19 SinglePassSamProgram Processed 299,000,000 records. Elapsed time: 00:54:39s. Time for last 1,000,000: 7s. Last read position: chr14:55,145,137 INFO 2026-06-03 20:40:50 SinglePassSamProgram Processed 300,000,000 records. Elapsed time: 00:55:09s. Time for last 1,000,000: 30s. Last read position: chr14:64,932,202 INFO 2026-06-03 20:41:01 SinglePassSamProgram Processed 301,000,000 records. Elapsed time: 00:55:21s. Time for last 1,000,000: 11s. Last read position: chr14:73,217,233 INFO 2026-06-03 20:41:09 SinglePassSamProgram Processed 302,000,000 records. Elapsed time: 00:55:29s. Time for last 1,000,000: 8s. Last read position: chr14:76,082,299 INFO 2026-06-03 20:41:18 SinglePassSamProgram Processed 303,000,000 records. Elapsed time: 00:55:37s. Time for last 1,000,000: 8s. Last read position: chr14:93,294,758 INFO 2026-06-03 20:42:19 SinglePassSamProgram Processed 304,000,000 records. Elapsed time: 00:56:38s. Time for last 1,000,000: 60s. Last read position: chr14:102,082,158 INFO 2026-06-03 20:42:32 SinglePassSamProgram Processed 305,000,000 records. Elapsed time: 00:56:51s. Time for last 1,000,000: 13s. Last read position: chr14:104,152,266 INFO 2026-06-03 20:42:50 SinglePassSamProgram Processed 306,000,000 records. Elapsed time: 00:57:10s. Time for last 1,000,000: 18s. Last read position: chr14:105,460,774 INFO 2026-06-03 20:42:53 SinglePassSamProgram Processed 307,000,000 records. Elapsed time: 00:57:13s. Time for last 1,000,000: 2s. Last read position: chr14:105,742,190 INFO 2026-06-03 20:43:09 SinglePassSamProgram Processed 308,000,000 records. Elapsed time: 00:57:29s. Time for last 1,000,000: 15s. Last read position: chr15:31,372,200 INFO 2026-06-03 20:43:15 SinglePassSamProgram Processed 309,000,000 records. Elapsed time: 00:57:34s. Time for last 1,000,000: 5s. Last read position: chr15:40,353,257 INFO 2026-06-03 20:43:21 SinglePassSamProgram Processed 310,000,000 records. Elapsed time: 00:57:41s. Time for last 1,000,000: 6s. Last read position: chr15:41,900,660 INFO 2026-06-03 20:43:30 SinglePassSamProgram Processed 311,000,000 records. Elapsed time: 00:57:50s. Time for last 1,000,000: 9s. Last read position: chr15:44,566,221 INFO 2026-06-03 20:43:42 SinglePassSamProgram Processed 312,000,000 records. Elapsed time: 00:58:01s. Time for last 1,000,000: 11s. Last read position: chr15:56,443,676 INFO 2026-06-03 20:43:59 SinglePassSamProgram Processed 313,000,000 records. Elapsed time: 00:58:19s. Time for last 1,000,000: 17s. Last read position: chr15:63,677,927 INFO 2026-06-03 20:44:07 SinglePassSamProgram Processed 314,000,000 records. Elapsed time: 00:58:27s. Time for last 1,000,000: 8s. Last read position: chr15:70,666,947 INFO 2026-06-03 20:44:19 SinglePassSamProgram Processed 315,000,000 records. Elapsed time: 00:58:39s. Time for last 1,000,000: 12s. Last read position: chr15:74,923,657 INFO 2026-06-03 20:44:30 SinglePassSamProgram Processed 316,000,000 records. Elapsed time: 00:58:49s. Time for last 1,000,000: 10s. Last read position: chr15:78,965,700 INFO 2026-06-03 20:44:34 SinglePassSamProgram Processed 317,000,000 records. Elapsed time: 00:58:53s. Time for last 1,000,000: 4s. Last read position: chr15:85,244,836 INFO 2026-06-03 20:44:45 SinglePassSamProgram Processed 318,000,000 records. Elapsed time: 00:59:05s. Time for last 1,000,000: 11s. Last read position: chr15:90,910,273 INFO 2026-06-03 20:44:55 SinglePassSamProgram Processed 319,000,000 records. Elapsed time: 00:59:15s. Time for last 1,000,000: 10s. Last read position: chr16:371,920 INFO 2026-06-03 20:45:08 SinglePassSamProgram Processed 320,000,000 records. Elapsed time: 00:59:27s. Time for last 1,000,000: 12s. Last read position: chr16:1,446,517 INFO 2026-06-03 20:45:33 SinglePassSamProgram Processed 321,000,000 records. Elapsed time: 00:59:53s. Time for last 1,000,000: 25s. Last read position: chr16:2,108,480 INFO 2026-06-03 20:45:47 SinglePassSamProgram Processed 322,000,000 records. Elapsed time: 01:00:07s. Time for last 1,000,000: 14s. Last read position: chr16:2,765,021 INFO 2026-06-03 20:45:59 SinglePassSamProgram Processed 323,000,000 records. Elapsed time: 01:00:19s. Time for last 1,000,000: 11s. Last read position: chr16:3,727,899 INFO 2026-06-03 20:46:11 SinglePassSamProgram Processed 324,000,000 records. Elapsed time: 01:00:31s. Time for last 1,000,000: 12s. Last read position: chr16:11,060,963 INFO 2026-06-03 20:46:17 SinglePassSamProgram Processed 325,000,000 records. Elapsed time: 01:00:36s. Time for last 1,000,000: 5s. Last read position: chr16:15,006,572 INFO 2026-06-03 20:46:29 SinglePassSamProgram Processed 326,000,000 records. Elapsed time: 01:00:49s. Time for last 1,000,000: 12s. Last read position: chr16:16,350,409 INFO 2026-06-03 20:46:32 SinglePassSamProgram Processed 327,000,000 records. Elapsed time: 01:00:52s. Time for last 1,000,000: 2s. Last read position: chr16:18,571,278 INFO 2026-06-03 20:46:38 SinglePassSamProgram Processed 328,000,000 records. Elapsed time: 01:00:57s. Time for last 1,000,000: 5s. Last read position: chr16:21,404,782 INFO 2026-06-03 20:46:41 SinglePassSamProgram Processed 329,000,000 records. Elapsed time: 01:01:00s. Time for last 1,000,000: 3s. Last read position: chr16:21,836,460 INFO 2026-06-03 20:46:44 SinglePassSamProgram Processed 330,000,000 records. Elapsed time: 01:01:04s. Time for last 1,000,000: 3s. Last read position: chr16:22,533,777 INFO 2026-06-03 20:46:49 SinglePassSamProgram Processed 331,000,000 records. Elapsed time: 01:01:09s. Time for last 1,000,000: 5s. Last read position: chr16:23,623,006 INFO 2026-06-03 20:47:02 SinglePassSamProgram Processed 332,000,000 records. Elapsed time: 01:01:22s. Time for last 1,000,000: 12s. Last read position: chr16:28,496,422 INFO 2026-06-03 20:47:11 SinglePassSamProgram Processed 333,000,000 records. Elapsed time: 01:01:30s. Time for last 1,000,000: 8s. Last read position: chr16:29,381,828 INFO 2026-06-03 20:47:12 SinglePassSamProgram Processed 334,000,000 records. Elapsed time: 01:01:32s. Time for last 1,000,000: 1s. Last read position: chr16:29,499,313 INFO 2026-06-03 20:47:18 SinglePassSamProgram Processed 335,000,000 records. Elapsed time: 01:01:38s. Time for last 1,000,000: 6s. Last read position: chr16:29,991,070 INFO 2026-06-03 20:47:24 SinglePassSamProgram Processed 336,000,000 records. Elapsed time: 01:01:43s. Time for last 1,000,000: 5s. Last read position: chr16:30,245,459 INFO 2026-06-03 20:47:31 SinglePassSamProgram Processed 337,000,000 records. Elapsed time: 01:01:50s. Time for last 1,000,000: 7s. Last read position: chr16:30,756,706 INFO 2026-06-03 20:47:37 SinglePassSamProgram Processed 338,000,000 records. Elapsed time: 01:01:57s. Time for last 1,000,000: 6s. Last read position: chr16:46,691,008 INFO 2026-06-03 20:47:48 SinglePassSamProgram Processed 339,000,000 records. Elapsed time: 01:02:07s. Time for last 1,000,000: 10s. Last read position: chr16:57,059,497 INFO 2026-06-03 20:48:02 SinglePassSamProgram Processed 340,000,000 records. Elapsed time: 01:02:21s. Time for last 1,000,000: 13s. Last read position: chr16:67,195,822 INFO 2026-06-03 20:48:12 SinglePassSamProgram Processed 341,000,000 records. Elapsed time: 01:02:32s. Time for last 1,000,000: 10s. Last read position: chr16:68,829,679 INFO 2026-06-03 20:48:22 SinglePassSamProgram Processed 342,000,000 records. Elapsed time: 01:02:41s. Time for last 1,000,000: 9s. Last read position: chr16:71,649,984 INFO 2026-06-03 20:48:29 SinglePassSamProgram Processed 343,000,000 records. Elapsed time: 01:02:49s. Time for last 1,000,000: 7s. Last read position: chr16:79,598,898 INFO 2026-06-03 20:48:37 SinglePassSamProgram Processed 344,000,000 records. Elapsed time: 01:02:56s. Time for last 1,000,000: 7s. Last read position: chr16:87,602,535 INFO 2026-06-03 20:48:44 SinglePassSamProgram Processed 345,000,000 records. Elapsed time: 01:03:04s. Time for last 1,000,000: 7s. Last read position: chr16:89,280,867 INFO 2026-06-03 20:49:04 SinglePassSamProgram Processed 346,000,000 records. Elapsed time: 01:03:23s. Time for last 1,000,000: 19s. Last read position: chr17:1,013,113 INFO 2026-06-03 20:49:16 SinglePassSamProgram Processed 347,000,000 records. Elapsed time: 01:03:35s. Time for last 1,000,000: 12s. Last read position: chr17:2,387,057 INFO 2026-06-03 20:49:26 SinglePassSamProgram Processed 348,000,000 records. Elapsed time: 01:03:46s. Time for last 1,000,000: 10s. Last read position: chr17:4,720,463 INFO 2026-06-03 20:49:37 SinglePassSamProgram Processed 349,000,000 records. Elapsed time: 01:03:56s. Time for last 1,000,000: 10s. Last read position: chr17:7,221,294 INFO 2026-06-03 20:49:47 SinglePassSamProgram Processed 350,000,000 records. Elapsed time: 01:04:07s. Time for last 1,000,000: 10s. Last read position: chr17:7,513,977 INFO 2026-06-03 20:49:57 SinglePassSamProgram Processed 351,000,000 records. Elapsed time: 01:04:17s. Time for last 1,000,000: 10s. Last read position: chr17:9,022,326 INFO 2026-06-03 20:50:11 SinglePassSamProgram Processed 352,000,000 records. Elapsed time: 01:04:30s. Time for last 1,000,000: 13s. Last read position: chr17:17,793,184 INFO 2026-06-03 20:50:24 SinglePassSamProgram Processed 353,000,000 records. Elapsed time: 01:04:43s. Time for last 1,000,000: 13s. Last read position: chr17:21,198,788 INFO 2026-06-03 20:50:36 SinglePassSamProgram Processed 354,000,000 records. Elapsed time: 01:04:55s. Time for last 1,000,000: 11s. Last read position: chr17:29,166,299 INFO 2026-06-03 20:50:47 SinglePassSamProgram Processed 355,000,000 records. Elapsed time: 01:05:07s. Time for last 1,000,000: 11s. Last read position: chr17:35,710,262 INFO 2026-06-03 20:50:54 SinglePassSamProgram Processed 356,000,000 records. Elapsed time: 01:05:14s. Time for last 1,000,000: 6s. Last read position: chr17:38,463,364 INFO 2026-06-03 20:51:03 SinglePassSamProgram Processed 357,000,000 records. Elapsed time: 01:05:23s. Time for last 1,000,000: 9s. Last read position: chr17:39,716,537 INFO 2026-06-03 20:51:17 SinglePassSamProgram Processed 358,000,000 records. Elapsed time: 01:05:37s. Time for last 1,000,000: 13s. Last read position: chr17:40,878,145 INFO 2026-06-03 20:51:28 SinglePassSamProgram Processed 359,000,000 records. Elapsed time: 01:05:48s. Time for last 1,000,000: 11s. Last read position: chr17:42,793,638 INFO 2026-06-03 20:51:38 SinglePassSamProgram Processed 360,000,000 records. Elapsed time: 01:05:57s. Time for last 1,000,000: 9s. Last read position: chr17:45,136,697 INFO 2026-06-03 20:51:47 SinglePassSamProgram Processed 361,000,000 records. Elapsed time: 01:06:07s. Time for last 1,000,000: 9s. Last read position: chr17:47,676,418 INFO 2026-06-03 20:51:55 SinglePassSamProgram Processed 362,000,000 records. Elapsed time: 01:06:15s. Time for last 1,000,000: 8s. Last read position: chr17:50,185,419 INFO 2026-06-03 20:52:01 SinglePassSamProgram Processed 363,000,000 records. Elapsed time: 01:06:20s. Time for last 1,000,000: 5s. Last read position: chr17:50,190,547 INFO 2026-06-03 20:52:11 SinglePassSamProgram Processed 364,000,000 records. Elapsed time: 01:06:30s. Time for last 1,000,000: 10s. Last read position: chr17:50,196,616 INFO 2026-06-03 20:52:23 SinglePassSamProgram Processed 365,000,000 records. Elapsed time: 01:06:43s. Time for last 1,000,000: 12s. Last read position: chr17:50,863,485 INFO 2026-06-03 20:52:32 SinglePassSamProgram Processed 366,000,000 records. Elapsed time: 01:06:52s. Time for last 1,000,000: 8s. Last read position: chr17:59,663,842 INFO 2026-06-03 20:52:44 SinglePassSamProgram Processed 367,000,000 records. Elapsed time: 01:07:03s. Time for last 1,000,000: 11s. Last read position: chr17:64,499,948 INFO 2026-06-03 20:52:56 SinglePassSamProgram Processed 368,000,000 records. Elapsed time: 01:07:16s. Time for last 1,000,000: 12s. Last read position: chr17:68,877,558 INFO 2026-06-03 20:53:07 SinglePassSamProgram Processed 369,000,000 records. Elapsed time: 01:07:27s. Time for last 1,000,000: 11s. Last read position: chr17:75,573,136 INFO 2026-06-03 20:53:42 SinglePassSamProgram Processed 370,000,000 records. Elapsed time: 01:08:02s. Time for last 1,000,000: 34s. Last read position: chr17:75,847,665 INFO 2026-06-03 20:53:52 SinglePassSamProgram Processed 371,000,000 records. Elapsed time: 01:08:11s. Time for last 1,000,000: 9s. Last read position: chr17:78,120,679 INFO 2026-06-03 20:54:03 SinglePassSamProgram Processed 372,000,000 records. Elapsed time: 01:08:23s. Time for last 1,000,000: 11s. Last read position: chr17:80,363,258 INFO 2026-06-03 20:54:24 SinglePassSamProgram Processed 373,000,000 records. Elapsed time: 01:08:44s. Time for last 1,000,000: 21s. Last read position: chr17:81,868,776 INFO 2026-06-03 20:54:36 SinglePassSamProgram Processed 374,000,000 records. Elapsed time: 01:08:55s. Time for last 1,000,000: 11s. Last read position: chr18:657,745 INFO 2026-06-03 20:54:44 SinglePassSamProgram Processed 375,000,000 records. Elapsed time: 01:09:04s. Time for last 1,000,000: 8s. Last read position: chr18:23,545,027 INFO 2026-06-03 20:54:54 SinglePassSamProgram Processed 376,000,000 records. Elapsed time: 01:09:14s. Time for last 1,000,000: 9s. Last read position: chr18:50,040,282 INFO 2026-06-03 20:55:13 SinglePassSamProgram Processed 377,000,000 records. Elapsed time: 01:09:33s. Time for last 1,000,000: 19s. Last read position: chr18:74,633,427 INFO 2026-06-03 20:55:20 SinglePassSamProgram Processed 378,000,000 records. Elapsed time: 01:09:40s. Time for last 1,000,000: 7s. Last read position: chr19:901,452 INFO 2026-06-03 20:55:31 SinglePassSamProgram Processed 379,000,000 records. Elapsed time: 01:09:50s. Time for last 1,000,000: 10s. Last read position: chr19:1,300,368 INFO 2026-06-03 20:55:38 SinglePassSamProgram Processed 380,000,000 records. Elapsed time: 01:09:58s. Time for last 1,000,000: 7s. Last read position: chr19:2,129,105 INFO 2026-06-03 20:55:45 SinglePassSamProgram Processed 381,000,000 records. Elapsed time: 01:10:05s. Time for last 1,000,000: 7s. Last read position: chr19:3,708,492 INFO 2026-06-03 20:55:52 SinglePassSamProgram Processed 382,000,000 records. Elapsed time: 01:10:11s. Time for last 1,000,000: 6s. Last read position: chr19:5,090,613 INFO 2026-06-03 20:55:58 SinglePassSamProgram Processed 383,000,000 records. Elapsed time: 01:10:18s. Time for last 1,000,000: 6s. Last read position: chr19:6,420,422 INFO 2026-06-03 20:56:07 SinglePassSamProgram Processed 384,000,000 records. Elapsed time: 01:10:27s. Time for last 1,000,000: 9s. Last read position: chr19:8,335,509 INFO 2026-06-03 20:56:21 SinglePassSamProgram Processed 385,000,000 records. Elapsed time: 01:10:41s. Time for last 1,000,000: 13s. Last read position: chr19:10,637,680 INFO 2026-06-03 20:56:51 SinglePassSamProgram Processed 386,000,000 records. Elapsed time: 01:11:11s. Time for last 1,000,000: 30s. Last read position: chr19:11,436,065 INFO 2026-06-03 20:57:00 SinglePassSamProgram Processed 387,000,000 records. Elapsed time: 01:11:19s. Time for last 1,000,000: 8s. Last read position: chr19:13,153,392 INFO 2026-06-03 20:57:08 SinglePassSamProgram Processed 388,000,000 records. Elapsed time: 01:11:28s. Time for last 1,000,000: 8s. Last read position: chr19:15,110,630 INFO 2026-06-03 20:57:17 SinglePassSamProgram Processed 389,000,000 records. Elapsed time: 01:11:37s. Time for last 1,000,000: 8s. Last read position: chr19:15,424,364 INFO 2026-06-03 20:57:28 SinglePassSamProgram Processed 390,000,000 records. Elapsed time: 01:11:48s. Time for last 1,000,000: 10s. Last read position: chr19:17,511,809 INFO 2026-06-03 20:57:34 SinglePassSamProgram Processed 391,000,000 records. Elapsed time: 01:11:53s. Time for last 1,000,000: 5s. Last read position: chr19:18,541,774 INFO 2026-06-03 20:57:40 SinglePassSamProgram Processed 392,000,000 records. Elapsed time: 01:12:00s. Time for last 1,000,000: 6s. Last read position: chr19:32,598,178 INFO 2026-06-03 20:57:49 SinglePassSamProgram Processed 393,000,000 records. Elapsed time: 01:12:08s. Time for last 1,000,000: 8s. Last read position: chr19:35,721,048 INFO 2026-06-03 20:57:58 SinglePassSamProgram Processed 394,000,000 records. Elapsed time: 01:12:17s. Time for last 1,000,000: 9s. Last read position: chr19:38,641,570 INFO 2026-06-03 20:58:04 SinglePassSamProgram Processed 395,000,000 records. Elapsed time: 01:12:24s. Time for last 1,000,000: 6s. Last read position: chr19:39,408,584 INFO 2026-06-03 20:58:10 SinglePassSamProgram Processed 396,000,000 records. Elapsed time: 01:12:30s. Time for last 1,000,000: 5s. Last read position: chr19:39,875,887 INFO 2026-06-03 20:58:12 SinglePassSamProgram Processed 397,000,000 records. Elapsed time: 01:12:32s. Time for last 1,000,000: 2s. Last read position: chr19:39,886,501 INFO 2026-06-03 20:58:15 SinglePassSamProgram Processed 398,000,000 records. Elapsed time: 01:12:35s. Time for last 1,000,000: 3s. Last read position: chr19:39,893,440 INFO 2026-06-03 20:58:20 SinglePassSamProgram Processed 399,000,000 records. Elapsed time: 01:12:39s. Time for last 1,000,000: 4s. Last read position: chr19:39,913,978 INFO 2026-06-03 20:58:26 SinglePassSamProgram Processed 400,000,000 records. Elapsed time: 01:12:46s. Time for last 1,000,000: 6s. Last read position: chr19:40,242,663 INFO 2026-06-03 20:58:41 SinglePassSamProgram Processed 401,000,000 records. Elapsed time: 01:13:01s. Time for last 1,000,000: 15s. Last read position: chr19:41,687,142 INFO 2026-06-03 20:58:49 SinglePassSamProgram Processed 402,000,000 records. Elapsed time: 01:13:09s. Time for last 1,000,000: 7s. Last read position: chr19:42,090,198 INFO 2026-06-03 20:58:58 SinglePassSamProgram Processed 403,000,000 records. Elapsed time: 01:13:17s. Time for last 1,000,000: 8s. Last read position: chr19:42,527,350 INFO 2026-06-03 20:59:03 SinglePassSamProgram Processed 404,000,000 records. Elapsed time: 01:13:23s. Time for last 1,000,000: 5s. Last read position: chr19:45,178,146 INFO 2026-06-03 20:59:11 SinglePassSamProgram Processed 405,000,000 records. Elapsed time: 01:13:31s. Time for last 1,000,000: 8s. Last read position: chr19:46,720,599 INFO 2026-06-03 20:59:18 SinglePassSamProgram Processed 406,000,000 records. Elapsed time: 01:13:38s. Time for last 1,000,000: 6s. Last read position: chr19:48,603,610 INFO 2026-06-03 20:59:26 SinglePassSamProgram Processed 407,000,000 records. Elapsed time: 01:13:45s. Time for last 1,000,000: 7s. Last read position: chr19:49,200,771 INFO 2026-06-03 20:59:33 SinglePassSamProgram Processed 408,000,000 records. Elapsed time: 01:13:52s. Time for last 1,000,000: 7s. Last read position: chr19:49,801,023 INFO 2026-06-03 20:59:56 SinglePassSamProgram Processed 409,000,000 records. Elapsed time: 01:14:15s. Time for last 1,000,000: 22s. Last read position: chr19:50,480,639 INFO 2026-06-03 21:00:02 SinglePassSamProgram Processed 410,000,000 records. Elapsed time: 01:14:22s. Time for last 1,000,000: 6s. Last read position: chr19:54,454,545 INFO 2026-06-03 21:00:09 SinglePassSamProgram Processed 411,000,000 records. Elapsed time: 01:14:29s. Time for last 1,000,000: 6s. Last read position: chr19:55,455,883 INFO 2026-06-03 21:00:13 SinglePassSamProgram Processed 412,000,000 records. Elapsed time: 01:14:33s. Time for last 1,000,000: 3s. Last read position: chr19:58,085,087 INFO 2026-06-03 21:00:21 SinglePassSamProgram Processed 413,000,000 records. Elapsed time: 01:14:40s. Time for last 1,000,000: 7s. Last read position: chr20:3,164,672 INFO 2026-06-03 21:00:29 SinglePassSamProgram Processed 414,000,000 records. Elapsed time: 01:14:49s. Time for last 1,000,000: 8s. Last read position: chr20:17,614,736 INFO 2026-06-03 21:00:42 SinglePassSamProgram Processed 415,000,000 records. Elapsed time: 01:15:01s. Time for last 1,000,000: 12s. Last read position: chr20:23,637,682 INFO 2026-06-03 21:00:49 SinglePassSamProgram Processed 416,000,000 records. Elapsed time: 01:15:09s. Time for last 1,000,000: 7s. Last read position: chr20:34,393,816 INFO 2026-06-03 21:01:03 SinglePassSamProgram Processed 417,000,000 records. Elapsed time: 01:15:23s. Time for last 1,000,000: 13s. Last read position: chr20:36,793,420 INFO 2026-06-03 21:01:11 SinglePassSamProgram Processed 418,000,000 records. Elapsed time: 01:15:31s. Time for last 1,000,000: 8s. Last read position: chr20:44,715,230 INFO 2026-06-03 21:01:26 SinglePassSamProgram Processed 419,000,000 records. Elapsed time: 01:15:46s. Time for last 1,000,000: 15s. Last read position: chr20:49,905,965 INFO 2026-06-03 21:01:31 SinglePassSamProgram Processed 420,000,000 records. Elapsed time: 01:15:51s. Time for last 1,000,000: 4s. Last read position: chr20:58,713,993 INFO 2026-06-03 21:01:45 SinglePassSamProgram Processed 421,000,000 records. Elapsed time: 01:16:05s. Time for last 1,000,000: 13s. Last read position: chr20:62,861,680 INFO 2026-06-03 21:01:52 SinglePassSamProgram Processed 422,000,000 records. Elapsed time: 01:16:12s. Time for last 1,000,000: 7s. Last read position: chr21:5,033,727 INFO 2026-06-03 21:01:53 SinglePassSamProgram Processed 423,000,000 records. Elapsed time: 01:16:13s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,841 INFO 2026-06-03 21:01:54 SinglePassSamProgram Processed 424,000,000 records. Elapsed time: 01:16:14s. Time for last 1,000,000: 0s. Last read position: chr21:8,258,912 INFO 2026-06-03 21:01:55 SinglePassSamProgram Processed 425,000,000 records. Elapsed time: 01:16:15s. Time for last 1,000,000: 0s. Last read position: chr21:8,258,961 INFO 2026-06-03 21:01:56 SinglePassSamProgram Processed 426,000,000 records. Elapsed time: 01:16:15s. Time for last 1,000,000: 0s. Last read position: chr21:8,399,124 INFO 2026-06-03 21:01:57 SinglePassSamProgram Processed 427,000,000 records. Elapsed time: 01:16:17s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,913 INFO 2026-06-03 21:01:58 SinglePassSamProgram Processed 428,000,000 records. Elapsed time: 01:16:18s. Time for last 1,000,000: 0s. Last read position: chr21:8,441,987 INFO 2026-06-03 21:01:59 SinglePassSamProgram Processed 429,000,000 records. Elapsed time: 01:16:18s. Time for last 1,000,000: 0s. Last read position: chr21:8,444,562 INFO 2026-06-03 21:02:06 SinglePassSamProgram Processed 430,000,000 records. Elapsed time: 01:16:25s. Time for last 1,000,000: 7s. Last read position: chr21:33,549,921 INFO 2026-06-03 21:02:21 SinglePassSamProgram Processed 431,000,000 records. Elapsed time: 01:16:40s. Time for last 1,000,000: 15s. Last read position: chr21:39,661,297 INFO 2026-06-03 21:02:42 SinglePassSamProgram Processed 432,000,000 records. Elapsed time: 01:17:01s. Time for last 1,000,000: 20s. Last read position: chr21:44,227,465 INFO 2026-06-03 21:02:53 SinglePassSamProgram Processed 433,000,000 records. Elapsed time: 01:17:13s. Time for last 1,000,000: 11s. Last read position: chr21:46,115,880 INFO 2026-06-03 21:03:05 SinglePassSamProgram Processed 434,000,000 records. Elapsed time: 01:17:25s. Time for last 1,000,000: 12s. Last read position: chr22:19,064,946 INFO 2026-06-03 21:03:17 SinglePassSamProgram Processed 435,000,000 records. Elapsed time: 01:17:37s. Time for last 1,000,000: 12s. Last read position: chr22:22,906,510 INFO 2026-06-03 21:03:26 SinglePassSamProgram Processed 436,000,000 records. Elapsed time: 01:17:45s. Time for last 1,000,000: 8s. Last read position: chr22:25,028,322 INFO 2026-06-03 21:03:38 SinglePassSamProgram Processed 437,000,000 records. Elapsed time: 01:17:57s. Time for last 1,000,000: 12s. Last read position: chr22:29,299,687 INFO 2026-06-03 21:03:50 SinglePassSamProgram Processed 438,000,000 records. Elapsed time: 01:18:09s. Time for last 1,000,000: 12s. Last read position: chr22:31,754,128 INFO 2026-06-03 21:04:01 SinglePassSamProgram Processed 439,000,000 records. Elapsed time: 01:18:21s. Time for last 1,000,000: 11s. Last read position: chr22:36,326,567 INFO 2026-06-03 21:04:09 SinglePassSamProgram Processed 440,000,000 records. Elapsed time: 01:18:28s. Time for last 1,000,000: 7s. Last read position: chr22:37,944,191 INFO 2026-06-03 21:04:15 SinglePassSamProgram Processed 441,000,000 records. Elapsed time: 01:18:35s. Time for last 1,000,000: 6s. Last read position: chr22:40,265,649 INFO 2026-06-03 21:04:25 SinglePassSamProgram Processed 442,000,000 records. Elapsed time: 01:18:45s. Time for last 1,000,000: 10s. Last read position: chr22:42,214,871 INFO 2026-06-03 21:04:32 SinglePassSamProgram Processed 443,000,000 records. Elapsed time: 01:18:52s. Time for last 1,000,000: 6s. Last read position: chr22:50,220,226 INFO 2026-06-03 21:04:45 SinglePassSamProgram Processed 444,000,000 records. Elapsed time: 01:19:05s. Time for last 1,000,000: 12s. Last read position: chr22:50,720,897 INFO 2026-06-03 21:04:50 SinglePassSamProgram Processed 445,000,000 records. Elapsed time: 01:19:10s. Time for last 1,000,000: 5s. Last read position: chrX:17,732,241 INFO 2026-06-03 21:05:10 SinglePassSamProgram Processed 446,000,000 records. Elapsed time: 01:19:30s. Time for last 1,000,000: 19s. Last read position: chrX:43,728,292 INFO 2026-06-03 21:05:21 SinglePassSamProgram Processed 447,000,000 records. Elapsed time: 01:19:41s. Time for last 1,000,000: 11s. Last read position: chrX:50,085,995 INFO 2026-06-03 21:05:35 SinglePassSamProgram Processed 448,000,000 records. Elapsed time: 01:19:55s. Time for last 1,000,000: 13s. Last read position: chrX:65,737,317 INFO 2026-06-03 21:05:49 SinglePassSamProgram Processed 449,000,000 records. Elapsed time: 01:20:08s. Time for last 1,000,000: 13s. Last read position: chrX:77,684,152 INFO 2026-06-03 21:05:56 SinglePassSamProgram Processed 450,000,000 records. Elapsed time: 01:20:16s. Time for last 1,000,000: 7s. Last read position: chrX:120,163,717 INFO 2026-06-03 21:06:04 SinglePassSamProgram Processed 451,000,000 records. Elapsed time: 01:20:24s. Time for last 1,000,000: 8s. Last read position: chrX:153,693,309 INFO 2026-06-03 21:06:26 SinglePassSamProgram Processed 452,000,000 records. Elapsed time: 01:20:45s. Time for last 1,000,000: 21s. Last read position: chrX:154,441,132 INFO 2026-06-03 21:06:29 SinglePassSamProgram Processed 453,000,000 records. Elapsed time: 01:20:48s. Time for last 1,000,000: 2s. Last read position: GL000220.1:114,135 INFO 2026-06-03 21:06:29 SinglePassSamProgram Processed 454,000,000 records. Elapsed time: 01:20:49s. Time for last 1,000,000: 0s. Last read position: GL000220.1:114,193 INFO 2026-06-03 21:06:30 SinglePassSamProgram Processed 455,000,000 records. Elapsed time: 01:20:49s. Time for last 1,000,000: 0s. Last read position: GL000220.1:116,771 INFO 2026-06-03 21:06:30 SinglePassSamProgram Processed 456,000,000 records. Elapsed time: 01:20:50s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,134 INFO 2026-06-03 21:06:31 SinglePassSamProgram Processed 457,000,000 records. Elapsed time: 01:20:51s. Time for last 1,000,000: 0s. Last read position: GL000220.1:159,553 INFO 2026-06-03 21:06:32 SinglePassSamProgram Processed 458,000,000 records. Elapsed time: 01:20:51s. Time for last 1,000,000: 0s. Last read position: KI270733.1:130,774 INFO 2026-06-03 21:06:33 SinglePassSamProgram Processed 459,000,000 records. Elapsed time: 01:20:52s. Time for last 1,000,000: 0s. Last read position: KI270733.1:131,040 INFO 2026-06-03 21:06:33 SinglePassSamProgram Processed 460,000,000 records. Elapsed time: 01:20:53s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,640 INFO 2026-06-03 21:06:34 SinglePassSamProgram Processed 461,000,000 records. Elapsed time: 01:20:54s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,094 INFO 2026-06-03 21:06:35 SinglePassSamProgram Processed 462,000,000 records. Elapsed time: 01:20:54s. Time for last 1,000,000: 0s. Last read position: KI270733.1:178,243 INFO 2026-06-03 21:06:35 SinglePassSamProgram Processed 463,000,000 records. Elapsed time: 01:20:55s. Time for last 1,000,000: 0s. Last read position: */* INFO 2026-06-03 21:06:36 SinglePassSamProgram Processed 464,000,000 records. Elapsed time: 01:20:56s. Time for last 1,000,000: 0s. Last read position: */* INFO 2026-06-03 21:06:37 SinglePassSamProgram Processed 465,000,000 records. Elapsed time: 01:20:56s. Time for last 1,000,000: 0s. Last read position: */* [Wed Jun 03 21:06:39 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 81.04 minutes. Runtime.totalMemory()=3400007680