Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e545aefcf807c43a0eace781e83888/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ab4cba821fe861f62653a89021cb67/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e545aefcf807c43a0eace781e83888/.command.run ==> STAGING COMPLETE (3 inputs) /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory INFO 2026-06-03 19:30:33 RExecutor Executing R script via command: Rscript /tmp/script5447706927414062808.R ERROR 2026-06-03 19:30:33 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:30:33 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:30:33 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:30:33 ProcessExecutor During startup - Warning messages: ERROR 2026-06-03 19:30:33 ProcessExecutor 1: Setting LC_CTYPE failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 2: Setting LC_COLLATE failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 3: Setting LC_TIME failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 5: Setting LC_MONETARY failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 6: Setting LC_PAPER failed, using "C" ERROR 2026-06-03 19:30:33 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C" INFO 2026-06-03 19:30:33 ProcessExecutor [1] "Checking if R is installed" ERROR 2026-06-03 19:30:33 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) Jun 03, 2026 7:30:33 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 19:30:33 GMT 2026] CollectInsertSizeMetrics --Histogram_FILE aih-tih-sc-3b436b-R1_A23YTGFLT4_1_collectinsertsize.pdf --INPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1_collectinsertsize.txt --DEVIATIONS 10.0 --MINIMUM_PCT 0.05 --METRIC_ACCUMULATION_LEVEL ALL_READS --INCLUDE_DUPLICATES false --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 19:30:34 GMT 2026] Executing as ?@nf-40e545aefcf807c43a0eace781e83888-d3bd1-t8d6h on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 20-internal-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.0 INFO 2026-06-03 19:30:35 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: chr1:6,192,969 INFO 2026-06-03 19:30:37 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:11,920,287 INFO 2026-06-03 19:30:38 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:16,585,553 INFO 2026-06-03 19:30:39 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr1:21,823,299 INFO 2026-06-03 19:30:40 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:23,313,657 INFO 2026-06-03 19:30:42 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:27,261,027 INFO 2026-06-03 19:30:43 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:32,302,664 INFO 2026-06-03 19:30:44 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:37,587,351 INFO 2026-06-03 19:30:45 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:42,831,002 INFO 2026-06-03 19:30:47 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:47,272,097 INFO 2026-06-03 19:30:48 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:63,629,514 INFO 2026-06-03 19:30:50 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:89,262,682 INFO 2026-06-03 19:30:51 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:109,592,124 INFO 2026-06-03 19:30:52 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:116,388,226 INFO 2026-06-03 19:30:54 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:120,454,008 INFO 2026-06-03 19:30:55 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:145,096,860 INFO 2026-06-03 19:30:57 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:146,115,998 INFO 2026-06-03 19:30:58 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:148,126,911 INFO 2026-06-03 19:31:00 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:148,679,302 INFO 2026-06-03 19:31:01 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:149,811,991 INFO 2026-06-03 19:31:02 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:150,159,183 INFO 2026-06-03 19:31:04 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:153,932,768 INFO 2026-06-03 19:31:05 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:155,479,602 INFO 2026-06-03 19:31:06 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:158,845,976 INFO 2026-06-03 19:31:07 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:161,544,748 INFO 2026-06-03 19:31:09 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:174,231,269 INFO 2026-06-03 19:31:10 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:186,333,222 INFO 2026-06-03 19:31:12 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:202,741,679 INFO 2026-06-03 19:31:13 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:212,051,489 INFO 2026-06-03 19:31:14 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:226,159,276 INFO 2026-06-03 19:31:16 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:235,791,945 INFO 2026-06-03 19:31:17 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr2:3,388,015 INFO 2026-06-03 19:31:19 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr2:25,743,931 INFO 2026-06-03 19:31:20 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,258 INFO 2026-06-03 19:31:21 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-03 19:31:23 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr2:43,995,828 INFO 2026-06-03 19:31:24 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:61,380,336 INFO 2026-06-03 19:31:25 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr2:73,847,418 INFO 2026-06-03 19:31:26 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr2:95,108,279 INFO 2026-06-03 19:31:28 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr2:108,675,941 INFO 2026-06-03 19:31:29 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr2:119,877,518 INFO 2026-06-03 19:31:30 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr2:151,464,051 INFO 2026-06-03 19:31:32 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:174,720,378 INFO 2026-06-03 19:31:33 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr2:188,997,734 INFO 2026-06-03 19:31:34 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:197,494,716 INFO 2026-06-03 19:31:35 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,997 INFO 2026-06-03 19:31:37 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr2:215,375,629 INFO 2026-06-03 19:31:38 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr2:215,386,931 INFO 2026-06-03 19:31:39 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr2:215,408,187 INFO 2026-06-03 19:31:41 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr2:215,431,840 INFO 2026-06-03 19:31:42 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:222,634,490 INFO 2026-06-03 19:31:43 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr2:237,346,556 INFO 2026-06-03 19:31:44 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr3:9,840,720 INFO 2026-06-03 19:31:46 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr3:31,626,100 INFO 2026-06-03 19:31:47 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr3:45,225,259 INFO 2026-06-03 19:31:48 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr3:49,101,384 INFO 2026-06-03 19:31:50 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr3:52,510,360 INFO 2026-06-03 19:31:51 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr3:88,150,088 INFO 2026-06-03 19:31:52 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr3:113,659,751 INFO 2026-06-03 19:31:54 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr3:125,560,485 INFO 2026-06-03 19:31:55 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr3:130,964,066 INFO 2026-06-03 19:31:56 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr3:146,102,763 INFO 2026-06-03 19:31:58 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr3:169,116,386 INFO 2026-06-03 19:31:59 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr3:184,304,315 INFO 2026-06-03 19:32:01 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr3:195,725,602 INFO 2026-06-03 19:32:02 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr4:1,930,664 INFO 2026-06-03 19:32:03 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr4:25,383,318 INFO 2026-06-03 19:32:05 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr4:56,931,056 INFO 2026-06-03 19:32:06 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr4:83,273,587 INFO 2026-06-03 19:32:07 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr4:105,190,349 INFO 2026-06-03 19:32:08 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr4:145,064,623 INFO 2026-06-03 19:32:10 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr4:184,728,944 INFO 2026-06-03 19:32:11 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr5:14,336,636 INFO 2026-06-03 19:32:12 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr5:37,153,781 INFO 2026-06-03 19:32:14 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr5:55,267,686 INFO 2026-06-03 19:32:15 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr5:73,498,635 INFO 2026-06-03 19:32:16 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr5:94,470,074 INFO 2026-06-03 19:32:18 SinglePassSamProgram Processed 78,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr5:130,184,296 INFO 2026-06-03 19:32:19 SinglePassSamProgram Processed 79,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr5:139,836,811 INFO 2026-06-03 19:32:20 SinglePassSamProgram Processed 80,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr5:150,119,478 INFO 2026-06-03 19:32:22 SinglePassSamProgram Processed 81,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,171 INFO 2026-06-03 19:32:23 SinglePassSamProgram Processed 82,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr5:169,588,563 INFO 2026-06-03 19:32:24 SinglePassSamProgram Processed 83,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr5:177,459,109 INFO 2026-06-03 19:32:26 SinglePassSamProgram Processed 84,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr5:181,257,127 INFO 2026-06-03 19:32:27 SinglePassSamProgram Processed 85,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr6:15,522,694 INFO 2026-06-03 19:32:28 SinglePassSamProgram Processed 86,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr6:26,045,584 INFO 2026-06-03 19:32:29 SinglePassSamProgram Processed 87,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr6:26,285,360 INFO 2026-06-03 19:32:30 SinglePassSamProgram Processed 88,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr6:27,837,970 INFO 2026-06-03 19:32:32 SinglePassSamProgram Processed 89,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr6:30,628,117 INFO 2026-06-03 19:32:33 SinglePassSamProgram Processed 90,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr6:31,637,065 INFO 2026-06-03 19:32:34 SinglePassSamProgram Processed 91,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr6:32,119,066 INFO 2026-06-03 19:32:35 SinglePassSamProgram Processed 92,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr6:33,293,493 INFO 2026-06-03 19:32:37 SinglePassSamProgram Processed 93,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr6:36,596,760 INFO 2026-06-03 19:32:38 SinglePassSamProgram Processed 94,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr6:43,502,230 INFO 2026-06-03 19:32:39 SinglePassSamProgram Processed 95,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr6:53,013,662 INFO 2026-06-03 19:32:40 SinglePassSamProgram Processed 96,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr6:80,022,322 INFO 2026-06-03 19:32:42 SinglePassSamProgram Processed 97,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr6:100,540,331 INFO 2026-06-03 19:32:43 SinglePassSamProgram Processed 98,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr6:116,279,578 INFO 2026-06-03 19:32:44 SinglePassSamProgram Processed 99,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr6:138,334,941 INFO 2026-06-03 19:32:45 SinglePassSamProgram Processed 100,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr6:153,282,609 INFO 2026-06-03 19:32:47 SinglePassSamProgram Processed 101,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr6:163,563,665 INFO 2026-06-03 19:32:48 SinglePassSamProgram Processed 102,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr7:5,378,013 INFO 2026-06-03 19:32:49 SinglePassSamProgram Processed 103,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr7:22,727,470 INFO 2026-06-03 19:32:51 SinglePassSamProgram Processed 104,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr7:39,987,609 INFO 2026-06-03 19:32:52 SinglePassSamProgram Processed 105,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:67,067,290 INFO 2026-06-03 19:32:53 SinglePassSamProgram Processed 106,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr7:76,978,744 INFO 2026-06-03 19:32:55 SinglePassSamProgram Processed 107,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr7:94,427,203 INFO 2026-06-03 19:32:56 SinglePassSamProgram Processed 108,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,881,318 INFO 2026-06-03 19:32:57 SinglePassSamProgram Processed 109,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr7:116,210,563 INFO 2026-06-03 19:32:58 SinglePassSamProgram Processed 110,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr7:137,928,278 INFO 2026-06-03 19:33:00 SinglePassSamProgram Processed 111,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr7:150,793,138 INFO 2026-06-03 19:33:01 SinglePassSamProgram Processed 112,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr8:11,845,671 INFO 2026-06-03 19:33:02 SinglePassSamProgram Processed 113,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr8:22,615,519 INFO 2026-06-03 19:33:03 SinglePassSamProgram Processed 114,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr8:37,840,817 INFO 2026-06-03 19:33:05 SinglePassSamProgram Processed 115,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr8:43,103,811 INFO 2026-06-03 19:33:06 SinglePassSamProgram Processed 116,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr8:56,073,195 INFO 2026-06-03 19:33:08 SinglePassSamProgram Processed 117,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr8:73,292,394 INFO 2026-06-03 19:33:09 SinglePassSamProgram Processed 118,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr8:98,150,510 INFO 2026-06-03 19:33:10 SinglePassSamProgram Processed 119,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr8:108,203,086 INFO 2026-06-03 19:33:12 SinglePassSamProgram Processed 120,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr8:127,736,517 INFO 2026-06-03 19:33:13 SinglePassSamProgram Processed 121,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,691,130 INFO 2026-06-03 19:33:14 SinglePassSamProgram Processed 122,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,996 INFO 2026-06-03 19:33:16 SinglePassSamProgram Processed 123,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,992,064 INFO 2026-06-03 19:33:17 SinglePassSamProgram Processed 124,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr9:2,039,843 INFO 2026-06-03 19:33:18 SinglePassSamProgram Processed 125,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr9:21,815,445 INFO 2026-06-03 19:33:20 SinglePassSamProgram Processed 126,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr9:35,699,416 INFO 2026-06-03 19:33:21 SinglePassSamProgram Processed 127,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr9:73,158,573 INFO 2026-06-03 19:33:22 SinglePassSamProgram Processed 128,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr9:90,843,950 INFO 2026-06-03 19:33:23 SinglePassSamProgram Processed 129,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr9:99,132,536 INFO 2026-06-03 19:33:25 SinglePassSamProgram Processed 130,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr9:113,267,329 INFO 2026-06-03 19:33:26 SinglePassSamProgram Processed 131,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr9:121,301,980 INFO 2026-06-03 19:33:27 SinglePassSamProgram Processed 132,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr9:127,093,803 INFO 2026-06-03 19:33:29 SinglePassSamProgram Processed 133,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr9:128,983,346 INFO 2026-06-03 19:33:30 SinglePassSamProgram Processed 134,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr9:132,912,289 INFO 2026-06-03 19:33:31 SinglePassSamProgram Processed 135,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr9:136,476,046 INFO 2026-06-03 19:33:33 SinglePassSamProgram Processed 136,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr9:137,811,490 INFO 2026-06-03 19:33:34 SinglePassSamProgram Processed 137,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr10:24,524,566 INFO 2026-06-03 19:33:35 SinglePassSamProgram Processed 138,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr10:45,374,269 INFO 2026-06-03 19:33:37 SinglePassSamProgram Processed 139,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr10:68,742,484 INFO 2026-06-03 19:33:38 SinglePassSamProgram Processed 140,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr10:78,035,666 INFO 2026-06-03 19:33:39 SinglePassSamProgram Processed 141,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr10:93,663,066 INFO 2026-06-03 19:33:41 SinglePassSamProgram Processed 142,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr10:102,473,604 INFO 2026-06-03 19:33:42 SinglePassSamProgram Processed 143,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr10:123,160,443 INFO 2026-06-03 19:33:43 SinglePassSamProgram Processed 144,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr11:497,969 INFO 2026-06-03 19:33:45 SinglePassSamProgram Processed 145,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr11:2,377,495 INFO 2026-06-03 19:33:46 SinglePassSamProgram Processed 146,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr11:7,992,089 INFO 2026-06-03 19:33:47 SinglePassSamProgram Processed 147,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr11:14,494,418 INFO 2026-06-03 19:33:48 SinglePassSamProgram Processed 148,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr11:34,071,746 INFO 2026-06-03 19:33:50 SinglePassSamProgram Processed 149,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr11:46,776,344 INFO 2026-06-03 19:33:51 SinglePassSamProgram Processed 150,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr11:57,802,048 INFO 2026-06-03 19:33:52 SinglePassSamProgram Processed 151,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr11:62,146,788 INFO 2026-06-03 19:33:54 SinglePassSamProgram Processed 152,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr11:63,631,082 INFO 2026-06-03 19:33:55 SinglePassSamProgram Processed 153,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr11:65,133,539 INFO 2026-06-03 19:33:56 SinglePassSamProgram Processed 154,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr11:66,332,226 INFO 2026-06-03 19:33:57 SinglePassSamProgram Processed 155,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr11:68,413,906 INFO 2026-06-03 19:33:59 SinglePassSamProgram Processed 156,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr11:73,976,680 INFO 2026-06-03 19:34:00 SinglePassSamProgram Processed 157,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr11:83,273,816 INFO 2026-06-03 19:34:01 SinglePassSamProgram Processed 158,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr11:108,189,252 INFO 2026-06-03 19:34:02 SinglePassSamProgram Processed 159,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr11:118,409,023 INFO 2026-06-03 19:34:04 SinglePassSamProgram Processed 160,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr11:120,481,395 INFO 2026-06-03 19:34:05 SinglePassSamProgram Processed 161,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr11:130,915,013 INFO 2026-06-03 19:34:06 SinglePassSamProgram Processed 162,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr12:6,557,510 INFO 2026-06-03 19:34:08 SinglePassSamProgram Processed 163,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr12:7,921,500 INFO 2026-06-03 19:34:09 SinglePassSamProgram Processed 164,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr12:19,269,780 INFO 2026-06-03 19:34:10 SinglePassSamProgram Processed 165,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr12:42,398,932 INFO 2026-06-03 19:34:11 SinglePassSamProgram Processed 166,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr12:49,103,782 INFO 2026-06-03 19:34:13 SinglePassSamProgram Processed 167,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr12:50,991,649 INFO 2026-06-03 19:34:14 SinglePassSamProgram Processed 168,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr12:54,054,969 INFO 2026-06-03 19:34:15 SinglePassSamProgram Processed 169,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr12:56,181,524 INFO 2026-06-03 19:34:17 SinglePassSamProgram Processed 170,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr12:57,179,414 INFO 2026-06-03 19:34:18 SinglePassSamProgram Processed 171,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr12:67,305,647 INFO 2026-06-03 19:34:19 SinglePassSamProgram Processed 172,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr12:89,642,188 INFO 2026-06-03 19:34:20 SinglePassSamProgram Processed 173,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr12:103,946,685 INFO 2026-06-03 19:34:22 SinglePassSamProgram Processed 174,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr12:112,022,355 INFO 2026-06-03 19:34:23 SinglePassSamProgram Processed 175,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr12:120,184,230 INFO 2026-06-03 19:34:24 SinglePassSamProgram Processed 176,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr12:123,327,749 INFO 2026-06-03 19:34:26 SinglePassSamProgram Processed 177,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr12:132,743,190 INFO 2026-06-03 19:34:27 SinglePassSamProgram Processed 178,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr13:27,254,225 INFO 2026-06-03 19:34:28 SinglePassSamProgram Processed 179,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr13:37,584,060 INFO 2026-06-03 19:34:29 SinglePassSamProgram Processed 180,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr13:49,467,795 INFO 2026-06-03 19:34:31 SinglePassSamProgram Processed 181,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr13:98,409,495 INFO 2026-06-03 19:34:32 SinglePassSamProgram Processed 182,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr13:110,503,133 INFO 2026-06-03 19:34:33 SinglePassSamProgram Processed 183,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr14:21,468,644 INFO 2026-06-03 19:34:34 SinglePassSamProgram Processed 184,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr14:25,267,114 INFO 2026-06-03 19:34:36 SinglePassSamProgram Processed 185,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr14:50,174,374 INFO 2026-06-03 19:34:37 SinglePassSamProgram Processed 186,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr14:63,941,777 INFO 2026-06-03 19:34:38 SinglePassSamProgram Processed 187,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr14:69,399,273 INFO 2026-06-03 19:34:40 SinglePassSamProgram Processed 188,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr14:77,521,550 INFO 2026-06-03 19:34:41 SinglePassSamProgram Processed 189,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr14:99,175,929 INFO 2026-06-03 19:34:42 SinglePassSamProgram Processed 190,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr14:103,738,687 INFO 2026-06-03 19:34:43 SinglePassSamProgram Processed 191,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr15:34,003,157 INFO 2026-06-03 19:34:45 SinglePassSamProgram Processed 192,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr15:42,339,805 INFO 2026-06-03 19:34:46 SinglePassSamProgram Processed 193,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr15:51,491,726 INFO 2026-06-03 19:34:47 SinglePassSamProgram Processed 194,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr15:63,756,618 INFO 2026-06-03 19:34:48 SinglePassSamProgram Processed 195,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr15:72,783,270 INFO 2026-06-03 19:34:50 SinglePassSamProgram Processed 196,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr15:82,434,326 INFO 2026-06-03 19:34:51 SinglePassSamProgram Processed 197,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr15:92,985,546 INFO 2026-06-03 19:34:52 SinglePassSamProgram Processed 198,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr16:1,792,328 INFO 2026-06-03 19:34:54 SinglePassSamProgram Processed 199,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr16:2,777,000 INFO 2026-06-03 19:34:55 SinglePassSamProgram Processed 200,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr16:11,887,662 INFO 2026-06-03 19:34:56 SinglePassSamProgram Processed 201,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr16:16,318,533 INFO 2026-06-03 19:34:57 SinglePassSamProgram Processed 202,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr16:18,809,528 INFO 2026-06-03 19:34:58 SinglePassSamProgram Processed 203,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr16:21,895,663 INFO 2026-06-03 19:35:00 SinglePassSamProgram Processed 204,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr16:28,106,110 INFO 2026-06-03 19:35:01 SinglePassSamProgram Processed 205,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr16:29,663,891 INFO 2026-06-03 19:35:02 SinglePassSamProgram Processed 206,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr16:30,707,610 INFO 2026-06-03 19:35:03 SinglePassSamProgram Processed 207,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr16:46,682,161 INFO 2026-06-03 19:35:05 SinglePassSamProgram Processed 208,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr16:58,014,316 INFO 2026-06-03 19:35:06 SinglePassSamProgram Processed 209,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr16:68,563,976 INFO 2026-06-03 19:35:07 SinglePassSamProgram Processed 210,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr16:74,917,950 INFO 2026-06-03 19:35:09 SinglePassSamProgram Processed 211,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr16:88,432,344 INFO 2026-06-03 19:35:10 SinglePassSamProgram Processed 212,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr17:1,345,467 INFO 2026-06-03 19:35:11 SinglePassSamProgram Processed 213,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr17:4,798,331 INFO 2026-06-03 19:35:12 SinglePassSamProgram Processed 214,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr17:7,580,217 INFO 2026-06-03 19:35:14 SinglePassSamProgram Processed 215,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,432 INFO 2026-06-03 19:35:15 SinglePassSamProgram Processed 216,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr17:27,640,546 INFO 2026-06-03 19:35:16 SinglePassSamProgram Processed 217,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr17:31,327,781 INFO 2026-06-03 19:35:17 SinglePassSamProgram Processed 218,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr17:37,125,714 INFO 2026-06-03 19:35:19 SinglePassSamProgram Processed 219,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr17:40,264,966 INFO 2026-06-03 19:35:20 SinglePassSamProgram Processed 220,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr17:43,000,042 INFO 2026-06-03 19:35:21 SinglePassSamProgram Processed 221,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr17:46,172,067 INFO 2026-06-03 19:35:22 SinglePassSamProgram Processed 222,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,835 INFO 2026-06-03 19:35:24 SinglePassSamProgram Processed 223,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,893 INFO 2026-06-03 19:35:25 SinglePassSamProgram Processed 224,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,924 INFO 2026-06-03 19:35:26 SinglePassSamProgram Processed 225,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr17:51,166,444 INFO 2026-06-03 19:35:28 SinglePassSamProgram Processed 226,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr17:59,738,842 INFO 2026-06-03 19:35:29 SinglePassSamProgram Processed 227,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr17:67,166,564 INFO 2026-06-03 19:35:30 SinglePassSamProgram Processed 228,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr17:75,522,151 INFO 2026-06-03 19:35:31 SinglePassSamProgram Processed 229,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr17:79,834,510 INFO 2026-06-03 19:35:33 SinglePassSamProgram Processed 230,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr17:81,890,803 INFO 2026-06-03 19:35:34 SinglePassSamProgram Processed 231,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr18:8,085,677 INFO 2026-06-03 19:35:35 SinglePassSamProgram Processed 232,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr18:36,174,508 INFO 2026-06-03 19:35:37 SinglePassSamProgram Processed 233,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr18:62,575,484 INFO 2026-06-03 19:35:38 SinglePassSamProgram Processed 234,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr19:1,094,031 INFO 2026-06-03 19:35:39 SinglePassSamProgram Processed 235,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr19:2,291,447 INFO 2026-06-03 19:35:40 SinglePassSamProgram Processed 236,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr19:5,611,417 INFO 2026-06-03 19:35:42 SinglePassSamProgram Processed 237,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr19:8,465,432 INFO 2026-06-03 19:35:43 SinglePassSamProgram Processed 238,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr19:10,712,218 INFO 2026-06-03 19:35:44 SinglePassSamProgram Processed 239,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr19:12,940,348 INFO 2026-06-03 19:35:45 SinglePassSamProgram Processed 240,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr19:15,244,443 INFO 2026-06-03 19:35:47 SinglePassSamProgram Processed 241,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr19:17,862,932 INFO 2026-06-03 19:35:48 SinglePassSamProgram Processed 242,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr19:20,646,379 INFO 2026-06-03 19:35:49 SinglePassSamProgram Processed 243,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr19:36,125,664 INFO 2026-06-03 19:35:51 SinglePassSamProgram Processed 244,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr19:39,915,193 INFO 2026-06-03 19:35:52 SinglePassSamProgram Processed 245,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr19:42,272,881 INFO 2026-06-03 19:35:53 SinglePassSamProgram Processed 246,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr19:45,064,464 INFO 2026-06-03 19:35:54 SinglePassSamProgram Processed 247,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr19:48,390,444 INFO 2026-06-03 19:35:56 SinglePassSamProgram Processed 248,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr19:49,686,699 INFO 2026-06-03 19:35:57 SinglePassSamProgram Processed 249,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr19:54,144,116 INFO 2026-06-03 19:35:58 SinglePassSamProgram Processed 250,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr19:55,669,130 INFO 2026-06-03 19:35:59 SinglePassSamProgram Processed 251,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr20:422,219 INFO 2026-06-03 19:36:01 SinglePassSamProgram Processed 252,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr20:5,185,764 INFO 2026-06-03 19:36:02 SinglePassSamProgram Processed 253,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr20:31,722,060 INFO 2026-06-03 19:36:03 SinglePassSamProgram Processed 254,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr20:35,707,171 INFO 2026-06-03 19:36:05 SinglePassSamProgram Processed 255,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr20:43,702,868 INFO 2026-06-03 19:36:06 SinglePassSamProgram Processed 256,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr20:49,225,150 INFO 2026-06-03 19:36:07 SinglePassSamProgram Processed 257,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr20:59,037,236 INFO 2026-06-03 19:36:08 SinglePassSamProgram Processed 258,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr21:6,484,637 INFO 2026-06-03 19:36:10 SinglePassSamProgram Processed 259,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr21:31,663,830 INFO 2026-06-03 19:36:11 SinglePassSamProgram Processed 260,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr21:39,898,514 INFO 2026-06-03 19:36:12 SinglePassSamProgram Processed 261,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr21:46,002,587 INFO 2026-06-03 19:36:13 SinglePassSamProgram Processed 262,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr22:21,799,038 INFO 2026-06-03 19:36:15 SinglePassSamProgram Processed 263,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr22:29,528,084 INFO 2026-06-03 19:36:16 SinglePassSamProgram Processed 264,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr22:36,490,031 INFO 2026-06-03 19:36:17 SinglePassSamProgram Processed 265,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr22:40,856,451 INFO 2026-06-03 19:36:18 SinglePassSamProgram Processed 266,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr22:50,210,779 INFO 2026-06-03 19:36:20 SinglePassSamProgram Processed 267,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chrX:11,759,855 INFO 2026-06-03 19:36:21 SinglePassSamProgram Processed 268,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chrX:37,840,521 INFO 2026-06-03 19:36:22 SinglePassSamProgram Processed 269,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chrX:47,584,956 INFO 2026-06-03 19:36:23 SinglePassSamProgram Processed 270,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chrX:53,568,730 INFO 2026-06-03 19:36:25 SinglePassSamProgram Processed 271,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chrX:71,298,743 INFO 2026-06-03 19:36:26 SinglePassSamProgram Processed 272,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chrX:97,141,741 INFO 2026-06-03 19:36:27 SinglePassSamProgram Processed 273,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chrX:120,604,232 INFO 2026-06-03 19:36:29 SinglePassSamProgram Processed 274,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chrX:153,505,267 INFO 2026-06-03 19:36:30 SinglePassSamProgram Processed 275,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chrX:154,466,731 INFO 2026-06-03 19:36:31 SinglePassSamProgram Processed 276,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: KI270711.1:6,094 INFO 2026-06-03 19:36:32 RExecutor Executing R script via command: Rscript /tmp/script18314133913407833899.R /tmp/nxf.XXXXV42xo3/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_collectinsertsize.txt /tmp/nxf.XXXXV42xo3/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_collectinsertsize.pdf aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam ERROR 2026-06-03 19:36:32 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:36:32 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:36:32 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-06-03 19:36:32 ProcessExecutor During startup - Warning messages: ERROR 2026-06-03 19:36:32 ProcessExecutor 1: Setting LC_CTYPE failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 2: Setting LC_COLLATE failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 3: Setting LC_TIME failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 5: Setting LC_MONETARY failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 6: Setting LC_PAPER failed, using "C" ERROR 2026-06-03 19:36:32 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C" INFO 2026-06-03 19:36:32 ProcessExecutor null device INFO 2026-06-03 19:36:32 ProcessExecutor 1 ERROR 2026-06-03 19:36:32 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) [Wed Jun 03 19:36:32 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 5.98 minutes. Runtime.totalMemory()=251658240