Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/33d1144efae2fc796b3994700f3756/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/77f6521aa147bd4bf2fd365c3f16aa/rna_s1221_S42.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/33d1144efae2fc796b3994700f3756/.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 15:28:16 RExecutor Executing R script via command: Rscript /tmp/script11847390356110220267.R
ERROR 2026-06-02 15:28:16 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:16 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-02 15:28:16 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-02 15:28:16 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-02 15:28:16 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-06-02 15:28:16 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Jun 02, 2026 3:28:16 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 15:28:16 GMT 2026] CollectInsertSizeMetrics --Histogram_FILE rna_s1221_S42_collectinsertsize.pdf --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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 15:28:17 GMT 2026] Executing as ?@nf-b733d1144efae2fc796b3994700f3756-2f6ad-fcf6p 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 15:28:17 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:00s. Time for last 1,000,000: 0s. Last read position: chr1:110,018,371
INFO 2026-06-02 15:28:18 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 0s. Last read position: chr1:228,146,888
INFO 2026-06-02 15:28:19 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 0s. Last read position: chr2:159,759,241
INFO 2026-06-02 15:28:20 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr3:51,993,725
INFO 2026-06-02 15:28:20 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr4:102,597,542
INFO 2026-06-02 15:28:21 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 0s. Last read position: chr5:176,506,768
INFO 2026-06-02 15:28:22 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 0s. Last read position: chr6:34,421,771
INFO 2026-06-02 15:28:23 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr7:26,197,277
INFO 2026-06-02 15:28:23 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr8:89,914,196
INFO 2026-06-02 15:28:24 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 0s. Last read position: chr9:133,349,561
INFO 2026-06-02 15:28:25 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 0s. Last read position: chr11:33,068,720
INFO 2026-06-02 15:28:26 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr12:6,945,786
INFO 2026-06-02 15:28:26 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr12:122,752,900
INFO 2026-06-02 15:28:27 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 0s. Last read position: chr15:28,076,562
INFO 2026-06-02 15:28:28 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 0s. Last read position: chr16:21,834,735
INFO 2026-06-02 15:28:29 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 0s. Last read position: chr17:7,318,111
INFO 2026-06-02 15:28:29 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 0s. Last read position: chr17:76,039,898
INFO 2026-06-02 15:28:30 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 0s. Last read position: chr19:12,734,557
INFO 2026-06-02 15:28:31 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 0s. Last read position: chr20:35,277,516
INFO 2026-06-02 15:28:32 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 0s. Last read position: chr21:8,398,054
INFO 2026-06-02 15:28:32 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 0s. Last read position: chr22:38,495,046
INFO 2026-06-02 15:28:33 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 0s. Last read position: chrY:19,721,298
INFO 2026-06-02 15:28:34 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 0s. Last read position: KI270733.1:134,152
INFO 2026-06-02 15:28:34 RExecutor Executing R script via command: Rscript /tmp/script6189632727837732047.R /tmp/nxf.XXXXxmpfMU/rna_s1221_S42_collectinsertsize.txt /tmp/nxf.XXXXxmpfMU/rna_s1221_S42_collectinsertsize.pdf rna_s1221_S42.Aligned.sortedByCoord.out.bam
ERROR 2026-06-02 15:28:34 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:34 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:34 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-02 15:28:34 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-02 15:28:34 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-02 15:28:34 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-02 15:28:34 ProcessExecutor null device
INFO 2026-06-02 15:28:34 ProcessExecutor 1
ERROR 2026-06-02 15:28:34 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Tue Jun 02 15:28:34 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=352321536