/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2026-05-28 04:38:02 RExecutor Executing R script via command: Rscript /tmp/script12455804902731680887.R
ERROR 2026-05-28 04:38:02 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:02 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:02 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:02 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 04:38:02 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 04:38:02 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 04:38:02 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-05-28 04:38:02 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
May 28, 2026 4:38:02 AM 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
[Thu May 28 04:38:02 GMT 2026] CollectInsertSizeMetrics --Histogram_FILE rna_s1200_S21_collectinsertsize.pdf --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_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
[Thu May 28 04:38:02 GMT 2026] Executing as ?@nf-2c800bf4d6b4e57cb38e48e50686233c-be5d5-mqq8j 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 2026-05-28 04:38:03 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: chr1:111,230,487
INFO 2026-05-28 04:38:04 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 0s. Last read position: chr1:233,139,804
INFO 2026-05-28 04:38:05 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 0s. Last read position: chr2:177,215,659
INFO 2026-05-28 04:38:06 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr3:53,864,996
INFO 2026-05-28 04:38:06 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 0s. Last read position: chr4:143,538,860
INFO 2026-05-28 04:38:07 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 0s. Last read position: chr5:181,237,672
INFO 2026-05-28 04:38:08 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 0s. Last read position: chr6:43,499,011
INFO 2026-05-28 04:38:09 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr7:44,696,070
INFO 2026-05-28 04:38:10 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 0s. Last read position: chr8:100,706,769
INFO 2026-05-28 04:38:10 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 0s. Last read position: chr9:136,454,161
INFO 2026-05-28 04:38:11 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr11:46,547,131
INFO 2026-05-28 04:38:12 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr12:8,605,335
INFO 2026-05-28 04:38:13 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 0s. Last read position: chr12:124,911,968
INFO 2026-05-28 04:38:14 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 0s. Last read position: chr15:34,904,443
INFO 2026-05-28 04:38:14 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 0s. Last read position: chr16:22,513,880
INFO 2026-05-28 04:38:15 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 0s. Last read position: chr17:7,311,406
INFO 2026-05-28 04:38:16 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 0s. Last read position: chr17:76,047,903
INFO 2026-05-28 04:38:17 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 0s. Last read position: chr19:10,689,198
INFO 2026-05-28 04:38:17 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 0s. Last read position: chr20:3,755,548
INFO 2026-05-28 04:38:18 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 0s. Last read position: chr22:36,518,625
INFO 2026-05-28 04:38:19 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 0s. Last read position: chrX:154,360,515
INFO 2026-05-28 04:38:19 RExecutor Executing R script via command: Rscript /tmp/script11906833454263939082.R /tmp/nxf.XXXXRCeLiD/rna_s1200_S21_collectinsertsize.txt /tmp/nxf.XXXXRCeLiD/rna_s1200_S21_collectinsertsize.pdf rna_s1200_S21.Aligned.sortedByCoord.out.bam
ERROR 2026-05-28 04:38:19 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:19 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:19 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 04:38:19 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 04:38:19 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 04:38:19 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 04:38:20 ProcessExecutor null device
INFO 2026-05-28 04:38:20 ProcessExecutor 1
ERROR 2026-05-28 04:38:20 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Thu May 28 04:38:20 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=373293056