Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/e6ad17c8b6b38208f0361b7df7bd3c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/884c42994cf4ec329ed30e2b633151/rna_s1200_S21.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/e6ad17c8b6b38208f0361b7df7bd3c/.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 2026-05-28 16:39:10 RExecutor Executing R script via command: Rscript /tmp/script6122722358294133156.R
ERROR 2026-05-28 16:39:10 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:10 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:10 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:10 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 16:39:10 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 16:39:10 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 16:39:10 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-05-28 16:39:10 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
May 28, 2026 4:39:10 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
[Thu May 28 16:39:11 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 16:39:11 GMT 2026] Executing as ?@nf-eae6ad17c8b6b38208f0361b7df7bd3c-d06c3-62rgl 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 16:39:12 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:00s. Time for last 1,000,000: 0s. Last read position: chr1:111,230,487
INFO 2026-05-28 16:39:12 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 16:39:13 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 16:39:14 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 16:39:15 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 0s. Last read position: chr4:143,538,860
INFO 2026-05-28 16:39:15 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 16:39:16 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 16:39:17 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 16:39:18 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 0s. Last read position: chr8:100,706,769
INFO 2026-05-28 16:39:18 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 0s. Last read position: chr9:136,454,161
INFO 2026-05-28 16:39:19 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 0s. Last read position: chr11:46,547,131
INFO 2026-05-28 16:39:20 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 16:39:21 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 0s. Last read position: chr12:124,911,968
INFO 2026-05-28 16:39:21 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 0s. Last read position: chr15:34,904,443
INFO 2026-05-28 16:39:22 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 0s. Last read position: chr16:22,513,880
INFO 2026-05-28 16:39:23 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 16:39:24 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 16:39:24 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 0s. Last read position: chr19:10,689,198
INFO 2026-05-28 16:39:25 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 0s. Last read position: chr20:3,755,548
INFO 2026-05-28 16:39:26 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 0s. Last read position: chr22:36,518,625
INFO 2026-05-28 16:39:27 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 16:39:27 RExecutor Executing R script via command: Rscript /tmp/script5324998841665562637.R /tmp/nxf.XXXXVb5ppn/rna_s1200_S21_collectinsertsize.txt /tmp/nxf.XXXXVb5ppn/rna_s1200_S21_collectinsertsize.pdf rna_s1200_S21.Aligned.sortedByCoord.out.bam
ERROR 2026-05-28 16:39:27 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:27 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:27 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:39:27 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 16:39:27 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 16:39:27 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 16:39:27 ProcessExecutor null device
INFO 2026-05-28 16:39:27 ProcessExecutor 1
ERROR 2026-05-28 16:39:27 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Thu May 28 16:39:27 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.28 minutes.
Runtime.totalMemory()=341835776