Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/3bd69399c453f24e7dec10206ce319/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/4d40ad7538894f3daef343612a34d4/rna_s1221_S42.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/3bd69399c453f24e7dec10206ce319/.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 2026-06-03 21:55:38 RExecutor Executing R script via command: Rscript /tmp/script4605513281638631808.R
ERROR 2026-06-03 21:55:38 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:55:38 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:55:38 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:55:38 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 21:55:38 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 21:55:38 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 21:55:38 ProcessExecutor [1] "Checking if R is installed"
ERROR 2026-06-03 21:55:38 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Jun 03, 2026 9:55:38 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 Jun 03 21:55:38 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 Jun 03 21:55:38 GMT 2026] Executing as ?@nf-4e3bd69399c453f24e7dec10206ce319-1cfd4-jn6sm on Linux 6.12.88 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 2026-06-03 21:55:40 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 2026-06-03 21:55:41 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 2026-06-03 21:55:42 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 2026-06-03 21:55:43 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 2026-06-03 21:55:45 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 2026-06-03 21:55:46 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr5:175,965,027
INFO 2026-06-03 21:55:47 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr6:34,417,468
INFO 2026-06-03 21:55:48 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr7:26,196,874
INFO 2026-06-03 21:55:49 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr8:85,477,248
INFO 2026-06-03 21:55:51 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr9:133,348,921
INFO 2026-06-03 21:55:52 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr11:32,934,959
INFO 2026-06-03 21:55:53 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr12:6,934,175
INFO 2026-06-03 21:55:54 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr12:122,361,130
INFO 2026-06-03 21:55:55 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr15:22,577,157
INFO 2026-06-03 21:55:56 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr16:21,456,352
INFO 2026-06-03 21:55:58 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr17:7,252,517
INFO 2026-06-03 21:55:59 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr17:75,834,458
INFO 2026-06-03 21:56:00 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr19:12,666,543
INFO 2026-06-03 21:56:01 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr20:34,540,578
INFO 2026-06-03 21:56:02 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,807
INFO 2026-06-03 21:56:03 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr22:38,230,583
INFO 2026-06-03 21:56:04 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chrY:12,912,799
INFO 2026-06-03 21:56:05 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,680
INFO 2026-06-03 21:56:06 RExecutor Executing R script via command: Rscript /tmp/script3710283269918137928.R /tmp/nxf.XXXXA1slkS/rna_s1221_S42_collectinsertsize.txt /tmp/nxf.XXXXA1slkS/rna_s1221_S42_collectinsertsize.pdf rna_s1221_S42.Aligned.sortedByCoord.out.bam
ERROR 2026-06-03 21:56:06 ProcessExecutor /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:56:06 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:56:06 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
ERROR 2026-06-03 21:56:06 ProcessExecutor During startup - Warning messages:
ERROR 2026-06-03 21:56:06 ProcessExecutor 1: Setting LC_CTYPE failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 2: Setting LC_COLLATE failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 3: Setting LC_TIME failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 4: Setting LC_MESSAGES failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 5: Setting LC_MONETARY failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 6: Setting LC_PAPER failed, using "C"
ERROR 2026-06-03 21:56:06 ProcessExecutor 7: Setting LC_MEASUREMENT failed, using "C"
INFO 2026-06-03 21:56:06 ProcessExecutor null device
INFO 2026-06-03 21:56:06 ProcessExecutor 1
ERROR 2026-06-03 21:56:06 ProcessExecutor sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Wed Jun 03 21:56:06 GMT 2026] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.47 minutes.
Runtime.totalMemory()=218103808