Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/320c77402664fc25775a7c2675bb8d/rna_s1200_S21.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/c85eb9b5ebbc2686a542546f5f63ad/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/c85eb9b5ebbc2686a542546f5f63ad/.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 2026-06-02 14:47:40 RExecutor Executing R script via command: Rscript /tmp/script9958771516596416251.R
ERROR 2026-06-02 14:47:40 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:47:40 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:47:40 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:47:40 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-02 14:47:40 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-02 14:47:40 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-02 14:47:40 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-06-02 14:47:40 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Jun 02, 2026 2:47:40 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
[Tue Jun 02 14:47:40 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
[Tue Jun 02 14:47:40 GMT 2026] Executing as ?@nf-3bc85eb9b5ebbc2686a542546f5f63ad-65102-q4tf5 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 2026-06-02 14:47:42 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 2026-06-02 14:47:43 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 1s. Last read position: chr1:233,139,804
INFO 2026-06-02 14:47:44 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr2:177,215,659
INFO 2026-06-02 14:47:46 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr3:53,864,996
INFO 2026-06-02 14:47:47 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr4:143,538,860
INFO 2026-06-02 14:47:48 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr5:181,237,672
INFO 2026-06-02 14:47:49 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr6:43,499,011
INFO 2026-06-02 14:47:50 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr7:44,696,070
INFO 2026-06-02 14:47:52 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr8:100,706,769
INFO 2026-06-02 14:47:53 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr9:136,454,161
INFO 2026-06-02 14:47:54 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr11:46,547,131
INFO 2026-06-02 14:47:55 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr12:8,605,335
INFO 2026-06-02 14:47:57 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr12:124,911,968
INFO 2026-06-02 14:47:58 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr15:34,904,443
INFO 2026-06-02 14:47:59 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr16:22,513,880
INFO 2026-06-02 14:48:01 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr17:7,311,406
INFO 2026-06-02 14:48:02 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr17:76,047,903
INFO 2026-06-02 14:48:03 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr19:10,689,198
INFO 2026-06-02 14:48:05 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr20:3,755,548
INFO 2026-06-02 14:48:06 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr22:36,518,625
INFO 2026-06-02 14:48:07 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chrX:154,360,515
INFO 2026-06-02 14:48:08 RExecutor Executing R script via command: Rscript /tmp/script7862438462045339800.R /tmp/nxf.XXXXUD8wZf/rna_s1200_S21_collectinsertsize.txt /tmp/nxf.XXXXUD8wZf/rna_s1200_S21_collectinsertsize.pdf rna_s1200_S21.Aligned.sortedByCoord.out.bam
ERROR 2026-06-02 14:48:08 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:48:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:48:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 14:48:08 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-02 14:48:08 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-02 14:48:08 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-02 14:48:08 ProcessExecutor null device
INFO 2026-06-02 14:48:08 ProcessExecutor 1
ERROR 2026-06-02 14:48:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Tue Jun 02 14:48:08 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.46 minutes.
Runtime.totalMemory()=251658240