Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/4914bdd2d85ca7910df5dbb4fadaad/aih-tih-sc-3b436b-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/59/3e379e5e1a78073b72816d4f2f0458/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/3e379e5e1a78073b72816d4f2f0458/.command.run 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/17/ab4cba821fe861f62653a89021cb67/aih-tih-sc-3b436b-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 7:32:22 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 19:32:22 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3b436b-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 19:32:22 GMT 2026] Executing as ?@nf-593e379e5e1a78073b72816d4f2f0458-ea28c-w2fx6 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.XXXX2tQRSh/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai is older than BAM /tmp/nxf.XXXX2tQRSh/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam INFO 2026-06-03 19:32:25 CollectRnaSeqMetrics Loaded 58279 genes. INFO 2026-06-03 19:32:42 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 16s. Last read position: chr1:6,192,969 INFO 2026-06-03 19:32:58 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 16s. Last read position: chr1:11,920,287 INFO 2026-06-03 19:33:11 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 12s. Last read position: chr1:16,585,553 INFO 2026-06-03 19:33:29 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 17s. Last read position: chr1:21,823,299 INFO 2026-06-03 19:33:42 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 12s. Last read position: chr1:23,313,657 INFO 2026-06-03 19:33:57 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 14s. Last read position: chr1:27,261,027 INFO 2026-06-03 19:34:09 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 12s. Last read position: chr1:32,302,664 INFO 2026-06-03 19:34:20 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 10s. Last read position: chr1:37,587,351 INFO 2026-06-03 19:34:59 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 39s. Last read position: chr1:42,831,002 INFO 2026-06-03 19:35:12 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 13s. Last read position: chr1:47,272,097 INFO 2026-06-03 19:35:30 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 17s. Last read position: chr1:63,629,514 INFO 2026-06-03 19:35:47 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 16s. Last read position: chr1:89,262,682 INFO 2026-06-03 19:35:57 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 9s. Last read position: chr1:109,592,124 INFO 2026-06-03 19:36:14 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 17s. Last read position: chr1:116,388,226 INFO 2026-06-03 19:36:22 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 7s. Last read position: chr1:120,454,008 INFO 2026-06-03 19:36:28 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 6s. Last read position: chr1:145,096,860 INFO 2026-06-03 19:36:36 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 8s. Last read position: chr1:146,115,998 INFO 2026-06-03 19:36:48 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 11s. Last read position: chr1:148,126,911 INFO 2026-06-03 19:36:55 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 7s. Last read position: chr1:148,679,302 INFO 2026-06-03 19:37:02 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 6s. Last read position: chr1:149,811,991 INFO 2026-06-03 19:37:03 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr1:150,159,183 INFO 2026-06-03 19:37:11 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 8s. Last read position: chr1:153,932,768 INFO 2026-06-03 19:37:33 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 21s. Last read position: chr1:155,479,602 INFO 2026-06-03 19:37:55 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 22s. Last read position: chr1:158,845,976 INFO 2026-06-03 19:38:06 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 11s. Last read position: chr1:161,544,748 INFO 2026-06-03 19:38:16 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 9s. Last read position: chr1:174,231,269 INFO 2026-06-03 19:38:29 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 12s. Last read position: chr1:186,333,222 INFO 2026-06-03 19:38:41 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 12s. Last read position: chr1:202,741,679 INFO 2026-06-03 19:38:51 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 10s. Last read position: chr1:212,051,489 INFO 2026-06-03 19:39:00 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 8s. Last read position: chr1:226,159,276 INFO 2026-06-03 19:39:17 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 17s. Last read position: chr1:235,791,945 INFO 2026-06-03 19:39:30 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 13s. Last read position: chr2:3,388,015 INFO 2026-06-03 19:39:42 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 12s. Last read position: chr2:25,743,931 INFO 2026-06-03 19:39:51 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 8s. Last read position: chr2:32,916,258 INFO 2026-06-03 19:39:55 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406 INFO 2026-06-03 19:40:04 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 9s. Last read position: chr2:43,995,828 INFO 2026-06-03 19:40:29 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 24s. Last read position: chr2:61,380,336 INFO 2026-06-03 19:40:57 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 28s. Last read position: chr2:73,847,418 INFO 2026-06-03 19:41:07 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 10s. Last read position: chr2:95,108,279 INFO 2026-06-03 19:41:23 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 15s. Last read position: chr2:108,675,941 INFO 2026-06-03 19:41:32 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 8s. Last read position: chr2:119,877,518 INFO 2026-06-03 19:41:51 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 19s. Last read position: chr2:151,464,051 INFO 2026-06-03 19:42:11 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 20s. Last read position: chr2:174,720,378 INFO 2026-06-03 19:43:28 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 76s. Last read position: chr2:188,997,734 INFO 2026-06-03 19:43:56 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 27s. Last read position: chr2:197,494,716 INFO 2026-06-03 19:44:20 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 24s. Last read position: chr2:215,361,997 INFO 2026-06-03 19:45:02 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 41s. Last read position: chr2:215,375,629 INFO 2026-06-03 19:45:53 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 50s. Last read position: chr2:215,386,931 INFO 2026-06-03 19:46:55 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 61s. Last read position: chr2:215,408,187 INFO 2026-06-03 19:48:35 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 100s. Last read position: chr2:215,431,840 INFO 2026-06-03 19:49:17 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 42s. Last read position: chr2:222,634,490 INFO 2026-06-03 19:49:38 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:17:12s. Time for last 1,000,000: 20s. Last read position: chr2:237,346,556 INFO 2026-06-03 19:50:03 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:17:38s. Time for last 1,000,000: 25s. Last read position: chr3:9,840,720 INFO 2026-06-03 19:50:13 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:17:48s. Time for last 1,000,000: 9s. Last read position: chr3:31,626,100 INFO 2026-06-03 19:50:27 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:18:02s. Time for last 1,000,000: 13s. Last read position: chr3:45,225,259 INFO 2026-06-03 19:50:40 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:18:14s. Time for last 1,000,000: 12s. Last read position: chr3:49,101,384 INFO 2026-06-03 19:50:50 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:18:24s. Time for last 1,000,000: 10s. Last read position: chr3:52,510,360 INFO 2026-06-03 19:51:03 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:18:37s. Time for last 1,000,000: 13s. Last read position: chr3:88,150,088 INFO 2026-06-03 19:51:13 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:18:47s. Time for last 1,000,000: 9s. Last read position: chr3:113,659,751 INFO 2026-06-03 19:51:21 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:18:55s. Time for last 1,000,000: 7s. Last read position: chr3:125,560,485 INFO 2026-06-03 19:51:33 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:19:07s. Time for last 1,000,000: 12s. Last read position: chr3:130,964,066 INFO 2026-06-03 19:51:53 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:19:28s. Time for last 1,000,000: 20s. Last read position: chr3:146,102,763 INFO 2026-06-03 19:52:12 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:19:46s. Time for last 1,000,000: 18s. Last read position: chr3:169,116,386 INFO 2026-06-03 19:52:24 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:19:59s. Time for last 1,000,000: 12s. Last read position: chr3:184,304,315 INFO 2026-06-03 19:52:46 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:20:21s. Time for last 1,000,000: 21s. Last read position: chr3:195,725,602 INFO 2026-06-03 19:53:04 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:20:39s. Time for last 1,000,000: 17s. Last read position: chr4:1,930,664 INFO 2026-06-03 19:53:21 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:20:56s. Time for last 1,000,000: 17s. Last read position: chr4:25,383,318 INFO 2026-06-03 19:53:39 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:21:14s. Time for last 1,000,000: 17s. Last read position: chr4:56,931,056 INFO 2026-06-03 19:53:57 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:21:32s. Time for last 1,000,000: 18s. Last read position: chr4:83,273,587 INFO 2026-06-03 19:54:20 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:21:55s. Time for last 1,000,000: 22s. Last read position: chr4:105,190,349 INFO 2026-06-03 19:54:32 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:22:07s. Time for last 1,000,000: 12s. Last read position: chr4:145,064,623 INFO 2026-06-03 19:54:48 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:22:22s. Time for last 1,000,000: 15s. Last read position: chr4:184,728,944 INFO 2026-06-03 19:54:58 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:22:32s. Time for last 1,000,000: 10s. Last read position: chr5:14,336,636 INFO 2026-06-03 19:55:21 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:22:56s. Time for last 1,000,000: 23s. Last read position: chr5:37,153,781 INFO 2026-06-03 19:55:33 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:23:08s. Time for last 1,000,000: 12s. Last read position: chr5:55,267,686 INFO 2026-06-03 19:55:46 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:23:20s. Time for last 1,000,000: 12s. Last read position: chr5:73,498,635 INFO 2026-06-03 19:56:00 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:23:34s. Time for last 1,000,000: 14s. Last read position: chr5:94,470,074 INFO 2026-06-03 19:56:22 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:23:56s. Time for last 1,000,000: 21s. Last read position: chr5:130,184,296 INFO 2026-06-03 19:56:40 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:24:14s. Time for last 1,000,000: 18s. Last read position: chr5:139,836,811 INFO 2026-06-03 19:56:54 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:24:28s. Time for last 1,000,000: 14s. Last read position: chr5:150,119,478 INFO 2026-06-03 19:57:09 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:24:43s. Time for last 1,000,000: 15s. Last read position: chr5:150,407,171 INFO 2026-06-03 19:57:26 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:25:00s. Time for last 1,000,000: 16s. Last read position: chr5:169,588,563 INFO 2026-06-03 19:57:54 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:25:29s. Time for last 1,000,000: 28s. Last read position: chr5:177,459,109 INFO 2026-06-03 19:58:23 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:25:57s. Time for last 1,000,000: 28s. Last read position: chr5:181,257,127 INFO 2026-06-03 19:58:30 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:26:05s. Time for last 1,000,000: 7s. Last read position: chr6:15,522,694 INFO 2026-06-03 19:58:37 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:26:12s. Time for last 1,000,000: 6s. Last read position: chr6:26,045,584 INFO 2026-06-03 19:58:40 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:26:14s. Time for last 1,000,000: 2s. Last read position: chr6:26,285,360 INFO 2026-06-03 19:58:43 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:26:18s. Time for last 1,000,000: 3s. Last read position: chr6:27,837,970 INFO 2026-06-03 19:58:50 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:26:25s. Time for last 1,000,000: 6s. Last read position: chr6:30,628,117 INFO 2026-06-03 19:59:02 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:26:37s. Time for last 1,000,000: 11s. Last read position: chr6:31,637,065 INFO 2026-06-03 19:59:16 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:26:50s. Time for last 1,000,000: 13s. Last read position: chr6:32,119,066 INFO 2026-06-03 19:59:25 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:26:59s. Time for last 1,000,000: 8s. Last read position: chr6:33,293,493 INFO 2026-06-03 19:59:32 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:27:06s. Time for last 1,000,000: 7s. Last read position: chr6:36,596,760 INFO 2026-06-03 19:59:42 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:27:16s. Time for last 1,000,000: 9s. Last read position: chr6:43,502,230 INFO 2026-06-03 19:59:52 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:27:27s. Time for last 1,000,000: 10s. Last read position: chr6:53,013,662 INFO 2026-06-03 20:00:25 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:27:59s. Time for last 1,000,000: 32s. Last read position: chr6:80,022,322 INFO 2026-06-03 20:00:41 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:28:15s. Time for last 1,000,000: 15s. Last read position: chr6:100,540,331 INFO 2026-06-03 20:00:58 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:28:33s. Time for last 1,000,000: 17s. Last read position: chr6:116,279,578 INFO 2026-06-03 20:01:28 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:29:02s. Time for last 1,000,000: 29s. Last read position: chr6:138,334,941 INFO 2026-06-03 20:01:50 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:29:24s. Time for last 1,000,000: 22s. Last read position: chr6:153,282,609 INFO 2026-06-03 20:02:11 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:29:45s. Time for last 1,000,000: 20s. Last read position: chr6:163,563,665 INFO 2026-06-03 20:02:29 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:30:04s. Time for last 1,000,000: 18s. Last read position: chr7:5,378,013 INFO 2026-06-03 20:02:46 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:30:21s. Time for last 1,000,000: 16s. Last read position: chr7:22,727,470 INFO 2026-06-03 20:03:16 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:30:51s. Time for last 1,000,000: 30s. Last read position: chr7:39,987,609 INFO 2026-06-03 20:03:30 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:31:05s. Time for last 1,000,000: 14s. Last read position: chr7:67,067,290 INFO 2026-06-03 20:03:37 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:31:12s. Time for last 1,000,000: 6s. Last read position: chr7:76,978,744 INFO 2026-06-03 20:04:08 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:31:43s. Time for last 1,000,000: 30s. Last read position: chr7:94,427,203 INFO 2026-06-03 20:04:27 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:32:02s. Time for last 1,000,000: 19s. Last read position: chr7:100,881,318 INFO 2026-06-03 20:04:55 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:32:30s. Time for last 1,000,000: 27s. Last read position: chr7:116,210,563 INFO 2026-06-03 20:05:11 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:32:45s. Time for last 1,000,000: 15s. Last read position: chr7:137,928,278 INFO 2026-06-03 20:05:25 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:32:59s. Time for last 1,000,000: 13s. Last read position: chr7:150,793,138 INFO 2026-06-03 20:05:56 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:33:30s. Time for last 1,000,000: 30s. Last read position: chr8:11,845,671 INFO 2026-06-03 20:06:19 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:33:53s. Time for last 1,000,000: 22s. Last read position: chr8:22,615,519 INFO 2026-06-03 20:06:33 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:34:07s. Time for last 1,000,000: 14s. Last read position: chr8:37,840,817 INFO 2026-06-03 20:06:56 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:34:31s. Time for last 1,000,000: 23s. Last read position: chr8:43,103,811 INFO 2026-06-03 20:07:11 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:34:46s. Time for last 1,000,000: 15s. Last read position: chr8:56,073,195 INFO 2026-06-03 20:07:22 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:34:57s. Time for last 1,000,000: 10s. Last read position: chr8:73,292,394 INFO 2026-06-03 20:07:30 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:35:04s. Time for last 1,000,000: 7s. Last read position: chr8:98,150,510 INFO 2026-06-03 20:07:55 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:35:29s. Time for last 1,000,000: 25s. Last read position: chr8:108,203,086 INFO 2026-06-03 20:08:11 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:35:45s. Time for last 1,000,000: 15s. Last read position: chr8:127,736,517 INFO 2026-06-03 20:08:26 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:36:01s. Time for last 1,000,000: 15s. Last read position: chr8:143,691,130 INFO 2026-06-03 20:08:29 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:36:04s. Time for last 1,000,000: 3s. Last read position: chr8:143,862,996 INFO 2026-06-03 20:08:34 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:36:09s. Time for last 1,000,000: 4s. Last read position: chr8:143,992,064 INFO 2026-06-03 20:08:44 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:36:19s. Time for last 1,000,000: 10s. Last read position: chr9:2,039,843 INFO 2026-06-03 20:08:57 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:36:31s. Time for last 1,000,000: 12s. Last read position: chr9:21,815,445 INFO 2026-06-03 20:09:06 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:36:40s. Time for last 1,000,000: 9s. Last read position: chr9:35,699,416 INFO 2026-06-03 20:09:14 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:36:49s. Time for last 1,000,000: 8s. Last read position: chr9:73,158,573 INFO 2026-06-03 20:09:29 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:37:03s. Time for last 1,000,000: 14s. Last read position: chr9:90,843,950 INFO 2026-06-03 20:09:36 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:37:10s. Time for last 1,000,000: 7s. Last read position: chr9:99,132,536 INFO 2026-06-03 20:09:48 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:37:22s. Time for last 1,000,000: 11s. Last read position: chr9:113,267,329 INFO 2026-06-03 20:10:05 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:37:39s. Time for last 1,000,000: 16s. Last read position: chr9:121,301,980 INFO 2026-06-03 20:10:20 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:37:55s. Time for last 1,000,000: 15s. Last read position: chr9:127,093,803 INFO 2026-06-03 20:10:41 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:38:16s. Time for last 1,000,000: 21s. Last read position: chr9:128,983,346 INFO 2026-06-03 20:10:51 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:38:25s. Time for last 1,000,000: 9s. Last read position: chr9:132,912,289 INFO 2026-06-03 20:11:00 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:38:34s. Time for last 1,000,000: 9s. Last read position: chr9:136,476,046 INFO 2026-06-03 20:11:15 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:38:49s. Time for last 1,000,000: 15s. Last read position: chr9:137,811,490 INFO 2026-06-03 20:11:27 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:39:02s. Time for last 1,000,000: 12s. Last read position: chr10:24,524,566 INFO 2026-06-03 20:11:45 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:39:19s. Time for last 1,000,000: 17s. Last read position: chr10:45,374,269 INFO 2026-06-03 20:11:52 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:39:27s. Time for last 1,000,000: 7s. Last read position: chr10:68,742,484 INFO 2026-06-03 20:12:06 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:39:41s. Time for last 1,000,000: 13s. Last read position: chr10:78,035,666 INFO 2026-06-03 20:12:14 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:39:49s. Time for last 1,000,000: 7s. Last read position: chr10:93,663,066 INFO 2026-06-03 20:12:27 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:40:01s. Time for last 1,000,000: 12s. Last read position: chr10:102,473,604 INFO 2026-06-03 20:12:35 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:40:09s. Time for last 1,000,000: 8s. Last read position: chr10:123,160,443 INFO 2026-06-03 20:12:43 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:40:18s. Time for last 1,000,000: 8s. Last read position: chr11:497,969 INFO 2026-06-03 20:12:54 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:40:28s. Time for last 1,000,000: 10s. Last read position: chr11:2,377,495 INFO 2026-06-03 20:13:05 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:40:40s. Time for last 1,000,000: 11s. Last read position: chr11:7,992,089 INFO 2026-06-03 20:13:19 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:40:53s. Time for last 1,000,000: 13s. Last read position: chr11:14,494,418 INFO 2026-06-03 20:13:29 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:41:03s. Time for last 1,000,000: 9s. Last read position: chr11:34,071,746 INFO 2026-06-03 20:13:43 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:41:17s. Time for last 1,000,000: 13s. Last read position: chr11:46,776,344 INFO 2026-06-03 20:13:55 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:41:29s. Time for last 1,000,000: 12s. Last read position: chr11:57,802,048 INFO 2026-06-03 20:14:10 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:41:45s. Time for last 1,000,000: 15s. Last read position: chr11:62,146,788 INFO 2026-06-03 20:14:20 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:41:54s. Time for last 1,000,000: 9s. Last read position: chr11:63,631,082 INFO 2026-06-03 20:14:29 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:42:03s. Time for last 1,000,000: 8s. Last read position: chr11:65,133,539 INFO 2026-06-03 20:14:38 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:42:12s. Time for last 1,000,000: 9s. Last read position: chr11:66,332,226 INFO 2026-06-03 20:14:48 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:42:22s. Time for last 1,000,000: 10s. Last read position: chr11:68,413,906 INFO 2026-06-03 20:15:04 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:42:38s. Time for last 1,000,000: 15s. Last read position: chr11:73,976,680 INFO 2026-06-03 20:15:16 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:42:51s. Time for last 1,000,000: 12s. Last read position: chr11:83,273,816 INFO 2026-06-03 20:15:28 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:43:03s. Time for last 1,000,000: 11s. Last read position: chr11:108,189,252 INFO 2026-06-03 20:15:42 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:43:16s. Time for last 1,000,000: 13s. Last read position: chr11:118,409,023 INFO 2026-06-03 20:15:52 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:43:27s. Time for last 1,000,000: 10s. Last read position: chr11:120,481,395 INFO 2026-06-03 20:16:03 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:43:37s. Time for last 1,000,000: 10s. Last read position: chr11:130,915,013 INFO 2026-06-03 20:16:14 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:43:48s. Time for last 1,000,000: 11s. Last read position: chr12:6,557,510 INFO 2026-06-03 20:16:35 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:44:09s. Time for last 1,000,000: 20s. Last read position: chr12:7,921,500 INFO 2026-06-03 20:16:42 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:44:16s. Time for last 1,000,000: 7s. Last read position: chr12:19,269,780 INFO 2026-06-03 20:16:54 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:44:29s. Time for last 1,000,000: 12s. Last read position: chr12:42,398,932 INFO 2026-06-03 20:17:07 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:44:41s. Time for last 1,000,000: 12s. Last read position: chr12:49,103,782 INFO 2026-06-03 20:17:14 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:44:49s. Time for last 1,000,000: 7s. Last read position: chr12:50,991,649 INFO 2026-06-03 20:17:27 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:45:01s. Time for last 1,000,000: 12s. Last read position: chr12:54,054,969 INFO 2026-06-03 20:17:42 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:45:17s. Time for last 1,000,000: 15s. Last read position: chr12:56,181,524 INFO 2026-06-03 20:17:56 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:45:31s. Time for last 1,000,000: 13s. Last read position: chr12:57,179,414 INFO 2026-06-03 20:18:09 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:45:43s. Time for last 1,000,000: 12s. Last read position: chr12:67,305,647 INFO 2026-06-03 20:18:21 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:45:56s. Time for last 1,000,000: 12s. Last read position: chr12:89,642,188 INFO 2026-06-03 20:18:33 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:46:08s. Time for last 1,000,000: 12s. Last read position: chr12:103,946,685 INFO 2026-06-03 20:18:45 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:46:20s. Time for last 1,000,000: 12s. Last read position: chr12:112,022,355 INFO 2026-06-03 20:19:00 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:46:34s. Time for last 1,000,000: 14s. Last read position: chr12:120,184,230 INFO 2026-06-03 20:19:10 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:46:44s. Time for last 1,000,000: 10s. Last read position: chr12:123,327,749 INFO 2026-06-03 20:19:21 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:46:55s. Time for last 1,000,000: 10s. Last read position: chr12:132,743,190 INFO 2026-06-03 20:19:28 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:47:03s. Time for last 1,000,000: 7s. Last read position: chr13:27,254,225 INFO 2026-06-03 20:19:38 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:47:12s. Time for last 1,000,000: 9s. Last read position: chr13:37,584,060 INFO 2026-06-03 20:19:46 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:47:20s. Time for last 1,000,000: 7s. Last read position: chr13:49,467,795 INFO 2026-06-03 20:19:57 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:47:31s. Time for last 1,000,000: 10s. Last read position: chr13:98,409,495 INFO 2026-06-03 20:20:09 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:47:44s. Time for last 1,000,000: 12s. Last read position: chr13:110,503,133 INFO 2026-06-03 20:20:21 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:47:56s. Time for last 1,000,000: 12s. Last read position: chr14:21,468,644 INFO 2026-06-03 20:20:31 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:48:05s. Time for last 1,000,000: 9s. Last read position: chr14:25,267,114 INFO 2026-06-03 20:20:43 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:48:17s. Time for last 1,000,000: 11s. Last read position: chr14:50,174,374 INFO 2026-06-03 20:20:53 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:48:28s. Time for last 1,000,000: 10s. Last read position: chr14:63,941,777 INFO 2026-06-03 20:21:41 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:49:16s. Time for last 1,000,000: 47s. Last read position: chr14:69,399,273 INFO 2026-06-03 20:21:50 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:49:25s. Time for last 1,000,000: 8s. Last read position: chr14:77,521,550 INFO 2026-06-03 20:22:01 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:49:35s. Time for last 1,000,000: 10s. Last read position: chr14:99,175,929 INFO 2026-06-03 20:22:49 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:50:23s. Time for last 1,000,000: 47s. Last read position: chr14:103,738,687 INFO 2026-06-03 20:23:06 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:50:41s. Time for last 1,000,000: 17s. Last read position: chr15:34,003,157 INFO 2026-06-03 20:23:15 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:50:49s. Time for last 1,000,000: 8s. Last read position: chr15:42,339,805 INFO 2026-06-03 20:23:25 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:50:59s. Time for last 1,000,000: 9s. Last read position: chr15:51,491,726 INFO 2026-06-03 20:23:40 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:51:15s. Time for last 1,000,000: 15s. Last read position: chr15:63,756,618 INFO 2026-06-03 20:23:49 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:51:23s. Time for last 1,000,000: 8s. Last read position: chr15:72,783,270 INFO 2026-06-03 20:23:59 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:51:33s. Time for last 1,000,000: 9s. Last read position: chr15:82,434,326 INFO 2026-06-03 20:24:09 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:51:44s. Time for last 1,000,000: 10s. Last read position: chr15:92,985,546 INFO 2026-06-03 20:24:19 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:51:54s. Time for last 1,000,000: 9s. Last read position: chr16:1,792,328 INFO 2026-06-03 20:24:36 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:52:10s. Time for last 1,000,000: 16s. Last read position: chr16:2,777,000 INFO 2026-06-03 20:24:46 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:52:21s. Time for last 1,000,000: 10s. Last read position: chr16:11,887,662 INFO 2026-06-03 20:24:55 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:52:29s. Time for last 1,000,000: 8s. Last read position: chr16:16,318,533 INFO 2026-06-03 20:24:58 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:52:33s. Time for last 1,000,000: 3s. Last read position: chr16:18,809,528 INFO 2026-06-03 20:25:04 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:52:38s. Time for last 1,000,000: 5s. Last read position: chr16:21,895,663 INFO 2026-06-03 20:25:10 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:52:44s. Time for last 1,000,000: 5s. Last read position: chr16:28,106,110 INFO 2026-06-03 20:25:16 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:52:51s. Time for last 1,000,000: 6s. Last read position: chr16:29,663,891 INFO 2026-06-03 20:25:23 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:52:58s. Time for last 1,000,000: 6s. Last read position: chr16:30,707,610 INFO 2026-06-03 20:25:31 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:53:05s. Time for last 1,000,000: 7s. Last read position: chr16:46,682,161 INFO 2026-06-03 20:25:41 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:53:16s. Time for last 1,000,000: 10s. Last read position: chr16:58,014,316 INFO 2026-06-03 20:25:53 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:53:27s. Time for last 1,000,000: 11s. Last read position: chr16:68,563,976 INFO 2026-06-03 20:26:03 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:53:38s. Time for last 1,000,000: 10s. Last read position: chr16:74,917,950 INFO 2026-06-03 20:26:11 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:53:46s. Time for last 1,000,000: 7s. Last read position: chr16:88,432,344 INFO 2026-06-03 20:26:25 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:53:59s. Time for last 1,000,000: 13s. Last read position: chr17:1,345,467 INFO 2026-06-03 20:26:34 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:54:08s. Time for last 1,000,000: 9s. Last read position: chr17:4,798,331 INFO 2026-06-03 20:26:43 SinglePassSamProgram Processed 214,000,000 records. Elapsed time: 00:54:17s. Time for last 1,000,000: 8s. Last read position: chr17:7,580,217 INFO 2026-06-03 20:26:54 SinglePassSamProgram Processed 215,000,000 records. Elapsed time: 00:54:28s. Time for last 1,000,000: 11s. Last read position: chr17:16,382,432 INFO 2026-06-03 20:27:03 SinglePassSamProgram Processed 216,000,000 records. Elapsed time: 00:54:38s. Time for last 1,000,000: 9s. Last read position: chr17:27,640,546 INFO 2026-06-03 20:27:14 SinglePassSamProgram Processed 217,000,000 records. Elapsed time: 00:54:49s. Time for last 1,000,000: 10s. Last read position: chr17:31,327,781 INFO 2026-06-03 20:27:23 SinglePassSamProgram Processed 218,000,000 records. Elapsed time: 00:54:58s. Time for last 1,000,000: 8s. Last read position: chr17:37,125,714 INFO 2026-06-03 20:27:31 SinglePassSamProgram Processed 219,000,000 records. Elapsed time: 00:55:06s. Time for last 1,000,000: 8s. Last read position: chr17:40,264,966 INFO 2026-06-03 20:27:43 SinglePassSamProgram Processed 220,000,000 records. Elapsed time: 00:55:18s. Time for last 1,000,000: 11s. Last read position: chr17:43,000,042 INFO 2026-06-03 20:27:53 SinglePassSamProgram Processed 221,000,000 records. Elapsed time: 00:55:28s. Time for last 1,000,000: 10s. Last read position: chr17:46,172,067 INFO 2026-06-03 20:28:02 SinglePassSamProgram Processed 222,000,000 records. Elapsed time: 00:55:36s. Time for last 1,000,000: 8s. Last read position: chr17:50,186,835 INFO 2026-06-03 20:28:08 SinglePassSamProgram Processed 223,000,000 records. Elapsed time: 00:55:42s. Time for last 1,000,000: 5s. Last read position: chr17:50,190,893 INFO 2026-06-03 20:28:16 SinglePassSamProgram Processed 224,000,000 records. Elapsed time: 00:55:51s. Time for last 1,000,000: 8s. Last read position: chr17:50,195,924 INFO 2026-06-03 20:28:27 SinglePassSamProgram Processed 225,000,000 records. Elapsed time: 00:56:01s. Time for last 1,000,000: 10s. Last read position: chr17:51,166,444 INFO 2026-06-03 20:28:37 SinglePassSamProgram Processed 226,000,000 records. Elapsed time: 00:56:12s. Time for last 1,000,000: 10s. Last read position: chr17:59,738,842 INFO 2026-06-03 20:28:48 SinglePassSamProgram Processed 227,000,000 records. Elapsed time: 00:56:22s. Time for last 1,000,000: 10s. Last read position: chr17:67,166,564 INFO 2026-06-03 20:28:59 SinglePassSamProgram Processed 228,000,000 records. Elapsed time: 00:56:33s. Time for last 1,000,000: 11s. Last read position: chr17:75,522,151 INFO 2026-06-03 20:29:10 SinglePassSamProgram Processed 229,000,000 records. Elapsed time: 00:56:44s. Time for last 1,000,000: 10s. Last read position: chr17:79,834,510 INFO 2026-06-03 20:29:27 SinglePassSamProgram Processed 230,000,000 records. Elapsed time: 00:57:02s. Time for last 1,000,000: 17s. Last read position: chr17:81,890,803 INFO 2026-06-03 20:29:38 SinglePassSamProgram Processed 231,000,000 records. Elapsed time: 00:57:13s. Time for last 1,000,000: 10s. Last read position: chr18:8,085,677 INFO 2026-06-03 20:29:47 SinglePassSamProgram Processed 232,000,000 records. Elapsed time: 00:57:22s. Time for last 1,000,000: 8s. Last read position: chr18:36,174,508 INFO 2026-06-03 20:30:01 SinglePassSamProgram Processed 233,000,000 records. Elapsed time: 00:57:36s. Time for last 1,000,000: 14s. Last read position: chr18:62,575,484 INFO 2026-06-03 20:30:11 SinglePassSamProgram Processed 234,000,000 records. Elapsed time: 00:57:45s. Time for last 1,000,000: 9s. Last read position: chr19:1,094,031 INFO 2026-06-03 20:30:19 SinglePassSamProgram Processed 235,000,000 records. Elapsed time: 00:57:53s. Time for last 1,000,000: 8s. Last read position: chr19:2,291,447 INFO 2026-06-03 20:30:26 SinglePassSamProgram Processed 236,000,000 records. Elapsed time: 00:58:00s. Time for last 1,000,000: 6s. Last read position: chr19:5,611,417 INFO 2026-06-03 20:30:33 SinglePassSamProgram Processed 237,000,000 records. Elapsed time: 00:58:08s. Time for last 1,000,000: 7s. Last read position: chr19:8,465,432 INFO 2026-06-03 20:30:51 SinglePassSamProgram Processed 238,000,000 records. Elapsed time: 00:58:25s. Time for last 1,000,000: 17s. Last read position: chr19:10,712,218 INFO 2026-06-03 20:31:09 SinglePassSamProgram Processed 239,000,000 records. Elapsed time: 00:58:43s. Time for last 1,000,000: 17s. Last read position: chr19:12,940,348 INFO 2026-06-03 20:31:16 SinglePassSamProgram Processed 240,000,000 records. Elapsed time: 00:58:51s. Time for last 1,000,000: 7s. Last read position: chr19:15,244,443 INFO 2026-06-03 20:31:26 SinglePassSamProgram Processed 241,000,000 records. Elapsed time: 00:59:01s. Time for last 1,000,000: 10s. Last read position: chr19:17,862,932 INFO 2026-06-03 20:31:33 SinglePassSamProgram Processed 242,000,000 records. Elapsed time: 00:59:08s. Time for last 1,000,000: 6s. Last read position: chr19:20,646,379 INFO 2026-06-03 20:31:41 SinglePassSamProgram Processed 243,000,000 records. Elapsed time: 00:59:16s. Time for last 1,000,000: 8s. Last read position: chr19:36,125,664 INFO 2026-06-03 20:31:49 SinglePassSamProgram Processed 244,000,000 records. Elapsed time: 00:59:24s. Time for last 1,000,000: 7s. Last read position: chr19:39,915,193 INFO 2026-06-03 20:32:01 SinglePassSamProgram Processed 245,000,000 records. Elapsed time: 00:59:36s. Time for last 1,000,000: 12s. Last read position: chr19:42,272,881 INFO 2026-06-03 20:32:07 SinglePassSamProgram Processed 246,000,000 records. Elapsed time: 00:59:42s. Time for last 1,000,000: 6s. Last read position: chr19:45,064,464 INFO 2026-06-03 20:32:15 SinglePassSamProgram Processed 247,000,000 records. Elapsed time: 00:59:50s. Time for last 1,000,000: 8s. Last read position: chr19:48,390,444 INFO 2026-06-03 20:32:23 SinglePassSamProgram Processed 248,000,000 records. Elapsed time: 00:59:57s. Time for last 1,000,000: 7s. Last read position: chr19:49,686,699 INFO 2026-06-03 20:32:31 SinglePassSamProgram Processed 249,000,000 records. Elapsed time: 01:00:06s. Time for last 1,000,000: 8s. Last read position: chr19:54,144,116 INFO 2026-06-03 20:32:38 SinglePassSamProgram Processed 250,000,000 records. Elapsed time: 01:00:13s. Time for last 1,000,000: 6s. Last read position: chr19:55,669,130 INFO 2026-06-03 20:32:44 SinglePassSamProgram Processed 251,000,000 records. Elapsed time: 01:00:18s. Time for last 1,000,000: 5s. Last read position: chr20:422,219 INFO 2026-06-03 20:32:51 SinglePassSamProgram Processed 252,000,000 records. Elapsed time: 01:00:25s. Time for last 1,000,000: 7s. Last read position: chr20:5,185,764 INFO 2026-06-03 20:32:59 SinglePassSamProgram Processed 253,000,000 records. Elapsed time: 01:00:34s. Time for last 1,000,000: 8s. Last read position: chr20:31,722,060 INFO 2026-06-03 20:33:09 SinglePassSamProgram Processed 254,000,000 records. Elapsed time: 01:00:44s. Time for last 1,000,000: 10s. Last read position: chr20:35,707,171 INFO 2026-06-03 20:33:19 SinglePassSamProgram Processed 255,000,000 records. Elapsed time: 01:00:53s. Time for last 1,000,000: 9s. Last read position: chr20:43,702,868 INFO 2026-06-03 20:33:31 SinglePassSamProgram Processed 256,000,000 records. Elapsed time: 01:01:05s. Time for last 1,000,000: 11s. Last read position: chr20:49,225,150 INFO 2026-06-03 20:33:44 SinglePassSamProgram Processed 257,000,000 records. Elapsed time: 01:01:19s. Time for last 1,000,000: 13s. Last read position: chr20:59,037,236 INFO 2026-06-03 20:33:50 SinglePassSamProgram Processed 258,000,000 records. Elapsed time: 01:01:25s. Time for last 1,000,000: 5s. Last read position: chr21:6,484,637 INFO 2026-06-03 20:33:54 SinglePassSamProgram Processed 259,000,000 records. Elapsed time: 01:01:29s. Time for last 1,000,000: 4s. Last read position: chr21:31,663,830 INFO 2026-06-03 20:34:07 SinglePassSamProgram Processed 260,000,000 records. Elapsed time: 01:01:42s. Time for last 1,000,000: 12s. Last read position: chr21:39,898,514 INFO 2026-06-03 20:34:18 SinglePassSamProgram Processed 261,000,000 records. Elapsed time: 01:01:53s. Time for last 1,000,000: 11s. Last read position: chr21:46,002,587 INFO 2026-06-03 20:34:29 SinglePassSamProgram Processed 262,000,000 records. Elapsed time: 01:02:04s. Time for last 1,000,000: 10s. Last read position: chr22:21,799,038 INFO 2026-06-03 20:34:40 SinglePassSamProgram Processed 263,000,000 records. Elapsed time: 01:02:15s. Time for last 1,000,000: 10s. Last read position: chr22:29,528,084 INFO 2026-06-03 20:34:49 SinglePassSamProgram Processed 264,000,000 records. Elapsed time: 01:02:24s. Time for last 1,000,000: 9s. Last read position: chr22:36,490,031 INFO 2026-06-03 20:34:57 SinglePassSamProgram Processed 265,000,000 records. Elapsed time: 01:02:31s. Time for last 1,000,000: 7s. Last read position: chr22:40,856,451 INFO 2026-06-03 20:35:04 SinglePassSamProgram Processed 266,000,000 records. Elapsed time: 01:02:39s. Time for last 1,000,000: 7s. Last read position: chr22:50,210,779 INFO 2026-06-03 20:35:10 SinglePassSamProgram Processed 267,000,000 records. Elapsed time: 01:02:45s. Time for last 1,000,000: 6s. Last read position: chrX:11,759,855 INFO 2026-06-03 20:35:18 SinglePassSamProgram Processed 268,000,000 records. Elapsed time: 01:02:53s. Time for last 1,000,000: 7s. Last read position: chrX:37,840,521 INFO 2026-06-03 20:35:37 SinglePassSamProgram Processed 269,000,000 records. Elapsed time: 01:03:11s. Time for last 1,000,000: 18s. Last read position: chrX:47,584,956 INFO 2026-06-03 20:35:47 SinglePassSamProgram Processed 270,000,000 records. Elapsed time: 01:03:21s. Time for last 1,000,000: 9s. Last read position: chrX:53,568,730 INFO 2026-06-03 20:36:02 SinglePassSamProgram Processed 271,000,000 records. Elapsed time: 01:03:36s. Time for last 1,000,000: 14s. Last read position: chrX:71,298,743 INFO 2026-06-03 20:36:13 SinglePassSamProgram Processed 272,000,000 records. Elapsed time: 01:03:48s. Time for last 1,000,000: 11s. Last read position: chrX:97,141,741 INFO 2026-06-03 20:36:22 SinglePassSamProgram Processed 273,000,000 records. Elapsed time: 01:03:56s. Time for last 1,000,000: 8s. Last read position: chrX:120,604,232 INFO 2026-06-03 20:36:30 SinglePassSamProgram Processed 274,000,000 records. Elapsed time: 01:04:05s. Time for last 1,000,000: 8s. Last read position: chrX:153,505,267 INFO 2026-06-03 20:36:46 SinglePassSamProgram Processed 275,000,000 records. Elapsed time: 01:04:21s. Time for last 1,000,000: 15s. Last read position: chrX:154,466,731 INFO 2026-06-03 20:36:51 SinglePassSamProgram Processed 276,000,000 records. Elapsed time: 01:04:25s. Time for last 1,000,000: 4s. Last read position: KI270711.1:6,094 INFO 2026-06-03 20:36:51 SinglePassSamProgram Processed 277,000,000 records. Elapsed time: 01:04:26s. Time for last 1,000,000: 0s. Last read position: */* INFO 2026-06-03 20:36:52 SinglePassSamProgram Processed 278,000,000 records. Elapsed time: 01:04:27s. Time for last 1,000,000: 0s. Last read position: */* [Wed Jun 03 20:36:54 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 64.53 minutes. Runtime.totalMemory()=3392143360