/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 2026-06-08 19:30:54 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 one.sorted.bam -O one.markdup.bam -M one.markdup_metrics.txt -TMP_DIR /tmp/nxf.bfq8ROwoxh -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 ********** 19:30:54.772 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 [Mon Jun 08 19:30:54 UTC 2026] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[one.sorted.bam] OUTPUT=one.markdup.bam METRICS_FILE=one.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.bfq8ROwoxh] 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 READ_NAME_REGEX= 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 [Mon Jun 08 19:30:54 UTC 2026] Executing as ?@nf-6076a51779eb87e7051cb2eff752360b-b8535-j9624 on Linux 6.12.88 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 2026-06-08 19:30:54 MarkDuplicates Start of doWork freeMemory: 502797072; totalMemory: 514850816; maxMemory: 1908932608 INFO 2026-06-08 19:30:54 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 19:30:54 MarkDuplicates Will retain up to 6916422 data points before spilling to disk. INFO 2026-06-08 19:30:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr3:70,959,020 INFO 2026-06-08 19:30:57 MarkDuplicates Tracking 2651 as yet unmatched pairs. 2650 records in RAM. INFO 2026-06-08 19:30:58 MarkDuplicates Read 1750199 records. 0 pairs never matched. INFO 2026-06-08 19:30:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 715539376; totalMemory: 980418560; maxMemory: 1908932608 INFO 2026-06-08 19:30:59 MarkDuplicates Will retain up to 29827072 duplicate indices before spilling to disk. INFO 2026-06-08 19:30:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 19:31:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-06-08 19:31:01 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 19:31:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 921645392; totalMemory: 1575485440; maxMemory: 1908932608 INFO 2026-06-08 19:31:01 MarkDuplicates Marking 1393144 records as duplicates. INFO 2026-06-08 19:31:01 MarkDuplicates Found 4600 optical duplicate clusters. INFO 2026-06-08 19:31:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 19:31:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 19:31:15 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 19:31:15 MarkDuplicates Representative read Index cleanup. INFO 2026-06-08 19:31:15 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 19:31:15 MarkDuplicates Before output close freeMemory: 1186846400; totalMemory: 1566048256; maxMemory: 1908932608 INFO 2026-06-08 19:31:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 19:31:15 MarkDuplicates After output close freeMemory: 1186860792; totalMemory: 1566048256; maxMemory: 1908932608 [Mon Jun 08 19:31:15 UTC 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.35 minutes. Runtime.totalMemory()=1566048256