Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/63c000507fe4de01dead0e5fbca422/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/1df1663baebbd37ee71760bb555a15/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/63c000507fe4de01dead0e5fbca422/.command.sh
==> 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 19:06:01 RExecutor Executing R script via command: Rscript /tmp/script8568159337350904676.R
ERROR 2026-06-03 19:06:01 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:06:01 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:06:01 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:06:01 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 19:06:01 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 19:06:01 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 19:06:01 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-06-03 19:06:01 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Jun 03, 2026 7:06:01 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 19:06:03 GMT 2026] CollectInsertSizeMetrics --Histogram_FILE aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_collectinsertsize.pdf --INPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-24ecfe-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 19:06:03 GMT 2026] Executing as ?@nf-7263c000507fe4de01dead0e5fbca422-1b031-chg4g 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 19:06:05 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:20,661,311
INFO 2026-06-03 19:06:07 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:35,883,358
INFO 2026-06-03 19:06:08 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr1:112,525,377
INFO 2026-06-03 19:06:10 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr1:155,060,725
INFO 2026-06-03 19:06:12 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:201,817,087
INFO 2026-06-03 19:06:13 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr2:17,931,676
INFO 2026-06-03 19:06:15 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr2:47,005,991
INFO 2026-06-03 19:06:17 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr2:108,534,554
INFO 2026-06-03 19:06:18 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr2:190,999,626
INFO 2026-06-03 19:06:20 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr2:219,418,482
INFO 2026-06-03 19:06:22 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr3:12,901,128
INFO 2026-06-03 19:06:24 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr3:52,516,735
INFO 2026-06-03 19:06:25 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr3:170,129,354
INFO 2026-06-03 19:06:27 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr4:10,098,990
INFO 2026-06-03 19:06:28 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr4:154,540,889
INFO 2026-06-03 19:06:30 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr5:122,775,099
INFO 2026-06-03 19:06:32 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,152
INFO 2026-06-03 19:06:33 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr6:495,294
INFO 2026-06-03 19:06:35 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr6:31,645,003
INFO 2026-06-03 19:06:37 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr6:43,051,419
INFO 2026-06-03 19:06:38 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr6:152,352,241
INFO 2026-06-03 19:06:40 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr7:6,501,816
INFO 2026-06-03 19:06:42 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr7:76,048,144
INFO 2026-06-03 19:06:43 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,326
INFO 2026-06-03 19:06:45 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr7:102,642,629
INFO 2026-06-03 19:06:46 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr7:151,079,853
INFO 2026-06-03 19:06:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr8:64,580,836
INFO 2026-06-03 19:06:50 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,590
INFO 2026-06-03 19:06:52 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr9:32,550,876
INFO 2026-06-03 19:06:53 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr9:115,086,604
INFO 2026-06-03 19:06:55 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr9:136,497,027
INFO 2026-06-03 19:06:57 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr10:69,415,941
INFO 2026-06-03 19:06:59 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr10:119,651,679
INFO 2026-06-03 19:07:00 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr11:2,928,915
INFO 2026-06-03 19:07:02 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr11:62,519,717
INFO 2026-06-03 19:07:04 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr11:66,599,243
INFO 2026-06-03 19:07:06 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr11:114,254,573
INFO 2026-06-03 19:07:08 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr12:7,921,550
INFO 2026-06-03 19:07:09 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr12:54,283,815
INFO 2026-06-03 19:07:11 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr12:108,591,851
INFO 2026-06-03 19:07:13 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr13:20,002,894
INFO 2026-06-03 19:07:14 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr14:22,998,445
INFO 2026-06-03 19:07:16 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr14:77,025,941
INFO 2026-06-03 19:07:18 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr14:105,643,216
INFO 2026-06-03 19:07:20 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,074
INFO 2026-06-03 19:07:21 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr15:39,581,196
INFO 2026-06-03 19:07:23 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr15:75,208,378
INFO 2026-06-03 19:07:25 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr16:1,777,287
INFO 2026-06-03 19:07:26 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr16:15,718,349
INFO 2026-06-03 19:07:28 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,866
INFO 2026-06-03 19:07:30 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr16:30,729,063
INFO 2026-06-03 19:07:32 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr16:79,599,116
INFO 2026-06-03 19:07:33 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr17:7,015,082
INFO 2026-06-03 19:07:35 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr17:35,441,773
INFO 2026-06-03 19:07:37 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr17:48,058,939
INFO 2026-06-03 19:07:39 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,266
INFO 2026-06-03 19:07:40 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,796
INFO 2026-06-03 19:07:42 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,185
INFO 2026-06-03 19:07:44 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr17:63,681,782
INFO 2026-06-03 19:07:46 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr17:81,846,475
INFO 2026-06-03 19:07:48 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr19:1,272,088
INFO 2026-06-03 19:07:49 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr19:10,713,167
INFO 2026-06-03 19:07:51 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr19:18,427,775
INFO 2026-06-03 19:07:53 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr19:39,913,812
INFO 2026-06-03 19:07:54 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr19:47,745,724
INFO 2026-06-03 19:07:56 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr19:57,280,724
INFO 2026-06-03 19:07:58 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr20:43,460,774
INFO 2026-06-03 19:08:00 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr21:5,163,565
INFO 2026-06-03 19:08:01 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,739
INFO 2026-06-03 19:08:03 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,618
INFO 2026-06-03 19:08:05 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr22:18,517,172
INFO 2026-06-03 19:08:06 SinglePassSamProgram Processed 72,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr22:37,128,650
INFO 2026-06-03 19:08:08 SinglePassSamProgram Processed 73,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chrX:9,684,079
INFO 2026-06-03 19:08:10 SinglePassSamProgram Processed 74,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chrX:136,207,097
INFO 2026-06-03 19:08:11 SinglePassSamProgram Processed 75,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,146
INFO 2026-06-03 19:08:13 SinglePassSamProgram Processed 76,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,719
INFO 2026-06-03 19:08:15 SinglePassSamProgram Processed 77,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,463
INFO 2026-06-03 19:08:16 RExecutor Executing R script via command: Rscript /tmp/script13988642854844796919.R /tmp/nxf.XXXXEvCkCO/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_collectinsertsize.txt /tmp/nxf.XXXXEvCkCO/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_collectinsertsize.pdf aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
ERROR 2026-06-03 19:08:16 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:08:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:08:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:08:16 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 19:08:16 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 19:08:16 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 19:08:16 ProcessExecutor null device
INFO 2026-06-03 19:08:16 ProcessExecutor 1
ERROR 2026-06-03 19:08:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Wed Jun 03 19:08:16 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 2.25 minutes.
Runtime.totalMemory()=390070272