Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/ae/3f7d38f45d4f9a07b0620ada7f4269/OP-XX1230_CC-WGSLIB01-gDNA-N.sorted.bam
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/49/e59c3f6de791e38aa45a0a11e209c8/.command.sh
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/49/e59c3f6de791e38aa45a0a11e209c8/.command.run
==> STAGING COMPLETE (3 inputs)
/opt/conda/bin/PicardCommandLine: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up JAVA_TOOL_OPTIONS: -Xmx8g -XX:+UseParallelGC
INFO 2026-05-27 22:28:56 MarkDuplicates
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
**********
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** MarkDuplicates -I OP-XX1230_CC-WGSLIB01-gDNA-N.sorted.bam -O OP-XX1230_CC-WGSLIB01-gDNA-N.markdup.bam -M OP-XX1230_CC-WGSLIB01-gDNA-N.markdup_metrics.txt -TMP_DIR /tmp/nxf.3KtfrNPwzB -VALIDATION_STRINGENCY SILENT -MAX_RECORDS_IN_RAM 250000 -REMOVE_DUPLICATES false -CREATE_INDEX true -TAG_DUPLICATE_SET_MEMBERS true -TAGGING_POLICY All -OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 -READ_NAME_REGEX ^(?:[^:]*:){4}([^:]+):([^:]+):([^:]+)(?::[^:]*)
**********
22:28:56.352 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/picard-3.4.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
WARNING: A restricted method in java.lang.System has been called
WARNING: java.lang.System::load has been called by com.intel.gkl.NativeLibraryLoader in an unnamed module (file:/opt/conda/share/picard-3.4.0-0/picard.jar)
WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
WARNING: Restricted methods will be blocked in a future release unless native access is enabled
[Wed May 27 22:28:56 UTC 2026] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[OP-XX1230_CC-WGSLIB01-gDNA-N.sorted.bam] OUTPUT=OP-XX1230_CC-WGSLIB01-gDNA-N.markdup.bam METRICS_FILE=OP-XX1230_CC-WGSLIB01-gDNA-N.markdup_metrics.txt REMOVE_DUPLICATES=false READ_NAME_REGEX=^(?:[^:]*:){4}([^:]+):([^:]+):([^:]+)(?::[^:]*) OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.3KtfrNPwzB] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_DUP_STRATEGY=FLOW_QUALITY_SUM_STRATEGY FLOW_USE_END_IN_UNPAIRED_READS=false FLOW_USE_UNPAIRED_CLIPPED_END=false FLOW_UNPAIRED_END_UNCERTAINTY=0 FLOW_UNPAIRED_START_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed May 27 22:28:56 UTC 2026] Executing as ?@nf-49e59c3f6de791e38aa45a0a11e209c8-b0892-frk8g on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 25.0.2-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.4.0
INFO 2026-05-27 22:28:56 MarkDuplicates Start of doWork freeMemory: 502793024; totalMemory: 514850816; maxMemory: 1908932608
INFO 2026-05-27 22:28:56 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-27 22:28:56 MarkDuplicates Will retain up to 6916422 data points before spilling to disk.
WARNING 2026-05-27 22:28:56 AbstractOpticalDuplicateFinderCommandLineProgram READ_NAME_REGEX '^(?:[^:]*:){4}([^:]+):([^:]+):([^:]+)(?::[^:]*)' did not match read name 'LH00723:203:23LTG5LT4:1:1102:42688:23490'. Your regex may not be correct. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2026-05-27 22:28:57 MarkDuplicates Read 494455 records. 0 pairs never matched.
INFO 2026-05-27 22:28:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 789880472; totalMemory: 919076864; maxMemory: 1908932608
INFO 2026-05-27 22:28:57 MarkDuplicates Will retain up to 29827072 duplicate indices before spilling to disk.
INFO 2026-05-27 22:28:57 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-27 22:28:57 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-27 22:28:57 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-27 22:28:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 640044008; totalMemory: 1256718336; maxMemory: 1908932608
INFO 2026-05-27 22:28:58 MarkDuplicates Marking 12011 records as duplicates.
INFO 2026-05-27 22:28:58 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2026-05-27 22:28:58 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-27 22:29:02 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-27 22:29:02 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-27 22:29:02 MarkDuplicates Representative read Index cleanup.
INFO 2026-05-27 22:29:02 MarkDuplicates Getting Memory Stats.
INFO 2026-05-27 22:29:02 MarkDuplicates Before output close freeMemory: 995730928; totalMemory: 1375207424; maxMemory: 1908932608
INFO 2026-05-27 22:29:02 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-27 22:29:02 MarkDuplicates After output close freeMemory: 995768072; totalMemory: 1375207424; maxMemory: 1908932608
[Wed May 27 22:29:02 UTC 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=1375207424