/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 19:04:58 RExecutor Executing R script via command: Rscript /tmp/script1833418717872937188.R
ERROR 2026-06-03 19:04:58 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:04:58 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:04:58 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:04:58 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 19:04:58 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 19:04:58 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 19:04:58 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-06-03 19:04:58 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Jun 03, 2026 7:04:58 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 19:04:58 GMT 2026] CollectInsertSizeMetrics --Histogram_FILE aih-tih-sc-0754d2-R1_A23YTGFLT4_1_collectinsertsize.pdf --INPUT aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0754d2-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 19:04:58 GMT 2026] Executing as ?@nf-8ac29efd8e394bdfb8b1347d60042781-c4438-7wfnk 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
INFO 2026-06-03 19:04:59 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:00s. Time for last 1,000,000: 0s. Last read position: chr1:18,916,969
INFO 2026-06-03 19:05:00 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 0s. Last read position: chr1:35,192,740
INFO 2026-06-03 19:05:01 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 0s. Last read position: chr1:58,577,046
INFO 2026-06-03 19:05:01 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr1:149,842,639
INFO 2026-06-03 19:05:02 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr1:161,072,695
INFO 2026-06-03 19:05:03 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 0s. Last read position: chr1:222,844,852
INFO 2026-06-03 19:05:03 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 0s. Last read position: chr2:28,778,918
INFO 2026-06-03 19:05:04 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr2:74,482,441
INFO 2026-06-03 19:05:05 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr2:177,212,771
INFO 2026-06-03 19:05:06 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 0s. Last read position: chr3:12,600,178
INFO 2026-06-03 19:05:06 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 0s. Last read position: chr3:52,492,122
INFO 2026-06-03 19:05:07 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr3:149,657,225
INFO 2026-06-03 19:05:08 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr3:188,866,335
INFO 2026-06-03 19:05:09 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 0s. Last read position: chr4:55,396,195
INFO 2026-06-03 19:05:09 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 0s. Last read position: chr5:14,358,246
INFO 2026-06-03 19:05:10 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 0s. Last read position: chr5:140,700,829
INFO 2026-06-03 19:05:11 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 0s. Last read position: chr6:3,015,538
INFO 2026-06-03 19:05:11 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 0s. Last read position: chr6:29,829,566
INFO 2026-06-03 19:05:12 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 0s. Last read position: chr6:31,816,768
INFO 2026-06-03 19:05:13 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 0s. Last read position: chr6:31,829,132
INFO 2026-06-03 19:05:13 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 0s. Last read position: chr6:43,770,792
INFO 2026-06-03 19:05:14 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 0s. Last read position: chr6:158,771,281
INFO 2026-06-03 19:05:15 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 0s. Last read position: chr7:44,884,635
INFO 2026-06-03 19:05:16 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 0s. Last read position: chr7:76,302,838
INFO 2026-06-03 19:05:16 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 0s. Last read position: chr7:128,947,818
INFO 2026-06-03 19:05:17 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 0s. Last read position: chr8:60,781,301
INFO 2026-06-03 19:05:18 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 0s. Last read position: chr8:133,262,118
INFO 2026-06-03 19:05:18 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 0s. Last read position: chr8:143,859,923
INFO 2026-06-03 19:05:19 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 0s. Last read position: chr8:143,863,064
INFO 2026-06-03 19:05:20 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 0s. Last read position: chr8:143,866,317
INFO 2026-06-03 19:05:20 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 0s. Last read position: chr8:144,095,079
INFO 2026-06-03 19:05:21 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 0s. Last read position: chr9:84,670,440
INFO 2026-06-03 19:05:22 SinglePassSamProgram Processed 33,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 0s. Last read position: chr9:128,166,267
INFO 2026-06-03 19:05:22 SinglePassSamProgram Processed 34,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 0s. Last read position: chr9:137,301,761
INFO 2026-06-03 19:05:23 SinglePassSamProgram Processed 35,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 0s. Last read position: chr10:79,296,576
INFO 2026-06-03 19:05:24 SinglePassSamProgram Processed 36,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 0s. Last read position: chr11:561,839
INFO 2026-06-03 19:05:25 SinglePassSamProgram Processed 37,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 0s. Last read position: chr11:46,397,744
INFO 2026-06-03 19:05:25 SinglePassSamProgram Processed 38,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 0s. Last read position: chr11:65,038,798
INFO 2026-06-03 19:05:26 SinglePassSamProgram Processed 39,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 0s. Last read position: chr11:117,392,494
INFO 2026-06-03 19:05:27 SinglePassSamProgram Processed 40,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 0s. Last read position: chr12:49,484,613
INFO 2026-06-03 19:05:28 SinglePassSamProgram Processed 41,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 0s. Last read position: chr12:57,156,093
INFO 2026-06-03 19:05:28 SinglePassSamProgram Processed 42,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 0s. Last read position: chr12:122,341,053
INFO 2026-06-03 19:05:29 SinglePassSamProgram Processed 43,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 0s. Last read position: chr14:20,343,235
INFO 2026-06-03 19:05:30 SinglePassSamProgram Processed 44,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 0s. Last read position: chr14:76,154,522
INFO 2026-06-03 19:05:30 SinglePassSamProgram Processed 45,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 0s. Last read position: chr14:104,948,580
INFO 2026-06-03 19:05:31 SinglePassSamProgram Processed 46,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 0s. Last read position: chr15:64,681,359
INFO 2026-06-03 19:05:32 SinglePassSamProgram Processed 47,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 0s. Last read position: chr16:2,208,547
INFO 2026-06-03 19:05:32 SinglePassSamProgram Processed 48,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 0s. Last read position: chr16:18,343,617
INFO 2026-06-03 19:05:33 SinglePassSamProgram Processed 49,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 0s. Last read position: chr16:30,225,615
INFO 2026-06-03 19:05:34 SinglePassSamProgram Processed 50,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 0s. Last read position: chr16:81,445,261
INFO 2026-06-03 19:05:35 SinglePassSamProgram Processed 51,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 0s. Last read position: chr17:7,587,190
INFO 2026-06-03 19:05:35 SinglePassSamProgram Processed 52,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 0s. Last read position: chr17:38,850,129
INFO 2026-06-03 19:05:36 SinglePassSamProgram Processed 53,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 0s. Last read position: chr17:47,531,262
INFO 2026-06-03 19:05:37 SinglePassSamProgram Processed 54,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 0s. Last read position: chr17:78,121,032
INFO 2026-06-03 19:05:37 SinglePassSamProgram Processed 55,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 0s. Last read position: chr18:49,992,348
INFO 2026-06-03 19:05:38 SinglePassSamProgram Processed 56,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 0s. Last read position: chr19:4,123,802
INFO 2026-06-03 19:05:39 SinglePassSamProgram Processed 57,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 0s. Last read position: chr19:13,993,690
INFO 2026-06-03 19:05:39 SinglePassSamProgram Processed 58,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 0s. Last read position: chr19:34,399,962
INFO 2026-06-03 19:05:40 SinglePassSamProgram Processed 59,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 0s. Last read position: chr19:40,367,709
INFO 2026-06-03 19:05:41 SinglePassSamProgram Processed 60,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 0s. Last read position: chr19:49,090,293
INFO 2026-06-03 19:05:42 SinglePassSamProgram Processed 61,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 0s. Last read position: chr20:17,570,142
INFO 2026-06-03 19:05:42 SinglePassSamProgram Processed 62,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 0s. Last read position: chr20:62,813,465
INFO 2026-06-03 19:05:43 SinglePassSamProgram Processed 63,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 0s. Last read position: chr21:8,217,372
INFO 2026-06-03 19:05:44 SinglePassSamProgram Processed 64,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 0s. Last read position: chr21:8,400,314
INFO 2026-06-03 19:05:44 SinglePassSamProgram Processed 65,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 0s. Last read position: chr21:29,327,296
INFO 2026-06-03 19:05:45 SinglePassSamProgram Processed 66,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 0s. Last read position: chr22:29,288,659
INFO 2026-06-03 19:05:46 SinglePassSamProgram Processed 67,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 0s. Last read position: chr22:46,263,083
INFO 2026-06-03 19:05:46 SinglePassSamProgram Processed 68,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 0s. Last read position: chrX:53,085,841
INFO 2026-06-03 19:05:47 SinglePassSamProgram Processed 69,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 0s. Last read position: GL000220.1:112,697
INFO 2026-06-03 19:05:48 SinglePassSamProgram Processed 70,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,559
INFO 2026-06-03 19:05:48 SinglePassSamProgram Processed 71,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,598
INFO 2026-06-03 19:05:49 RExecutor Executing R script via command: Rscript /tmp/script2752361950742108570.R /tmp/nxf.XXXXXpsK9J/aih-tih-sc-0754d2-R1_A23YTGFLT4_1_collectinsertsize.txt /tmp/nxf.XXXXXpsK9J/aih-tih-sc-0754d2-R1_A23YTGFLT4_1_collectinsertsize.pdf aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
ERROR 2026-06-03 19:05:49 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:05:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:05:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 19:05:49 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 19:05:49 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 19:05:49 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 19:05:49 ProcessExecutor null device
INFO 2026-06-03 19:05:49 ProcessExecutor 1
ERROR 2026-06-03 19:05:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Wed Jun 03 19:05:49 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.86 minutes.
Runtime.totalMemory()=322961408