Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/6abe212ba92b3ca8a2fa0d47eb8aed/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/58c681ed7b8e293ceeff5d315d0678/rna_s1221_S42.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/6abe212ba92b3ca8a2fa0d47eb8aed/.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 16:38:23 RExecutor Executing R script via command: Rscript /tmp/script11357364569544421466.R
ERROR 2026-05-28 16:38:23 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:23 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:23 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:24 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 16:38:24 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 16:38:24 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 16:38:24 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-05-28 16:38:24 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
May 28, 2026 4:38:24 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 16:38:24 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
[Thu May 28 16:38:24 GMT 2026] Executing as ?@nf-bf6abe212ba92b3ca8a2fa0d47eb8aed-125b0-cq7b5 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 16:38:25 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 2026-05-28 16:38:26 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 2026-05-28 16:38:27 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr2:159,748,300
INFO 2026-05-28 16:38:28 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr3:51,969,471
INFO 2026-05-28 16:38:29 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr4:102,578,927
INFO 2026-05-28 16:38:30 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr5:175,965,027
INFO 2026-05-28 16:38:31 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr6:34,417,468
INFO 2026-05-28 16:38:32 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr7:26,196,874
INFO 2026-05-28 16:38:33 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr8:85,477,248
INFO 2026-05-28 16:38:34 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr9:133,348,921
INFO 2026-05-28 16:38:36 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr11:32,934,959
INFO 2026-05-28 16:38:37 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr12:6,934,175
INFO 2026-05-28 16:38:38 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr12:122,361,130
INFO 2026-05-28 16:38:39 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr15:22,577,157
INFO 2026-05-28 16:38:40 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr16:21,456,352
INFO 2026-05-28 16:38:41 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr17:7,252,517
INFO 2026-05-28 16:38:42 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr17:75,834,458
INFO 2026-05-28 16:38:43 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr19:12,666,543
INFO 2026-05-28 16:38:44 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr20:34,540,578
INFO 2026-05-28 16:38:45 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,807
INFO 2026-05-28 16:38:46 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 0s. Last read position: chr22:38,230,583
INFO 2026-05-28 16:38:47 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chrY:12,912,799
INFO 2026-05-28 16:38:48 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,680
INFO 2026-05-28 16:38:48 RExecutor Executing R script via command: Rscript /tmp/script724493542685687620.R /tmp/nxf.XXXXJjhbMY/rna_s1221_S42_collectinsertsize.txt /tmp/nxf.XXXXJjhbMY/rna_s1221_S42_collectinsertsize.pdf rna_s1221_S42.Aligned.sortedByCoord.out.bam
ERROR 2026-05-28 16:38:49 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-05-28 16:38:49 ProcessExecutor During startup - Warning messages:
ERROR 2026-05-28 16:38:49 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-05-28 16:38:49 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-05-28 16:38:49 ProcessExecutor null device
INFO 2026-05-28 16:38:49 ProcessExecutor 1
ERROR 2026-05-28 16:38:49 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Thu May 28 16:38:49 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.42 minutes.
Runtime.totalMemory()=218103808