Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/9a59678e42cbec632bf3d4427dc496/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/8c51e677048cb72c10a987d74941dc/rna_s1221_S42.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/9a59678e42cbec632bf3d4427dc496/.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 2026-05-27 16:04:08 RExecutor Executing R script via command: Rscript /tmp/script10104699580602582674.R ERROR 2026-05-27 16:04:08 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:08 ProcessExecutor During startup - Warning messages: ERROR 2026-05-27 16:04:08 ProcessExecutor 1: Setting LC_CTYPE failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 2: Setting LC_COLLATE failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 3: Setting LC_TIME failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 5: Setting LC_MONETARY failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 6: Setting LC_PAPER failed, using "C" ERROR 2026-05-27 16:04:08 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C" INFO 2026-05-27 16:04:08 ProcessExecutor [1] "Checking if R is installed" ERROR 2026-05-27 16:04:08 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) May 27, 2026 4:04:08 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 May 27 16:04:08 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 [Wed May 27 16:04:08 GMT 2026] Executing as ?@nf-879a59678e42cbec632bf3d4427dc496-3e582-2br6j 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 2026-05-27 16:04:10 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: chr1:109,668,493 INFO 2026-05-27 16:04:11 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 1s. Last read position: chr1:228,097,688 INFO 2026-05-27 16:04:13 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr2:159,748,300 INFO 2026-05-27 16:04:14 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr3:51,969,471 INFO 2026-05-27 16:04:15 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr4:102,578,927 INFO 2026-05-27 16:04:17 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr5:175,965,027 INFO 2026-05-27 16:04:18 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr6:34,417,468 INFO 2026-05-27 16:04:19 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr7:26,196,874 INFO 2026-05-27 16:04:21 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr8:85,477,248 INFO 2026-05-27 16:04:22 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr9:133,348,921 INFO 2026-05-27 16:04:23 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr11:32,934,959 INFO 2026-05-27 16:04:25 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr12:6,934,175 INFO 2026-05-27 16:04:26 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr12:122,361,130 INFO 2026-05-27 16:04:27 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr15:22,577,157 INFO 2026-05-27 16:04:28 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr16:21,456,352 INFO 2026-05-27 16:04:30 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr17:7,252,517 INFO 2026-05-27 16:04:31 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr17:75,834,458 INFO 2026-05-27 16:04:32 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr19:12,666,543 INFO 2026-05-27 16:04:33 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr20:34,540,578 INFO 2026-05-27 16:04:35 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,807 INFO 2026-05-27 16:04:36 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr22:38,230,583 INFO 2026-05-27 16:04:37 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chrY:12,912,799 INFO 2026-05-27 16:04:38 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,680 INFO 2026-05-27 16:04:39 RExecutor Executing R script via command: Rscript /tmp/script9066302340971177779.R /tmp/nxf.XXXXIyB5Ve/rna_s1221_S42_collectinsertsize.txt /tmp/nxf.XXXXIyB5Ve/rna_s1221_S42_collectinsertsize.pdf rna_s1221_S42.Aligned.sortedByCoord.out.bam ERROR 2026-05-27 16:04:39 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:39 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:39 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) ERROR 2026-05-27 16:04:39 ProcessExecutor During startup - Warning messages: ERROR 2026-05-27 16:04:39 ProcessExecutor 1: Setting LC_CTYPE failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 2: Setting LC_COLLATE failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 3: Setting LC_TIME failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 5: Setting LC_MONETARY failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 6: Setting LC_PAPER failed, using "C" ERROR 2026-05-27 16:04:39 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C" INFO 2026-05-27 16:04:40 ProcessExecutor null device INFO 2026-05-27 16:04:40 ProcessExecutor 1 ERROR 2026-05-27 16:04:40 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) [Wed May 27 16:04:40 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.52 minutes. Runtime.totalMemory()=255852544