INFO 2025-08-08 15:04:18 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 sorted.bam -O sorted.dedup.bam -M picard_dups.log -VALIDATION_STRINGENCY SILENT -REMOVE_DUPLICATES true ********** 15:04:18.713 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/picard-3.4.0-6-g80ca98e2a/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Aug 08 15:04:18 PDT 2025] MarkDuplicates INPUT=[sorted.bam] OUTPUT=sorted.dedup.bam METRICS_FILE=picard_dups.log REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag 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= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Fri Aug 08 15:04:19 PDT 2025] Executing as sam@raven on Linux 5.4.0-144-generic amd64; OpenJDK 64-Bit Server VM 17.0.15+6-Ubuntu-0ubuntu118.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.4.0-6-g80ca98e2a-SNAPSHOT INFO 2025-08-08 15:04:19 MarkDuplicates Start of doWork freeMemory: 377648024; totalMemory: 402653184; maxMemory: 32178700288 INFO 2025-08-08 15:04:19 MarkDuplicates Reading input file and constructing read end information. INFO 2025-08-08 15:04:19 MarkDuplicates Will retain up to 116589493 data points before spilling to disk. INFO 2025-08-08 15:04:22 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: NC_082383.1:595,707 INFO 2025-08-08 15:04:22 MarkDuplicates Tracking 20473 as yet unmatched pairs. 921 records in RAM. INFO 2025-08-08 15:04:24 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: NC_082384.1:4,122,782 INFO 2025-08-08 15:04:24 MarkDuplicates Tracking 37972 as yet unmatched pairs. 1950 records in RAM. INFO 2025-08-08 15:04:27 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: NC_082385.1:4,023,097 INFO 2025-08-08 15:04:27 MarkDuplicates Tracking 55876 as yet unmatched pairs. 3584 records in RAM. INFO 2025-08-08 15:04:29 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: NC_082385.1:31,097,858 INFO 2025-08-08 15:04:29 MarkDuplicates Tracking 68795 as yet unmatched pairs. 862 records in RAM. INFO 2025-08-08 15:04:31 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: NC_082387.1:486,072 INFO 2025-08-08 15:04:31 MarkDuplicates Tracking 80407 as yet unmatched pairs. 6318 records in RAM. INFO 2025-08-08 15:04:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: NC_082387.1:21,916,440 INFO 2025-08-08 15:04:33 MarkDuplicates Tracking 88201 as yet unmatched pairs. 1614 records in RAM. INFO 2025-08-08 15:04:35 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: NC_082388.1:20,242,606 INFO 2025-08-08 15:04:35 MarkDuplicates Tracking 96978 as yet unmatched pairs. 1948 records in RAM. INFO 2025-08-08 15:04:37 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: NC_082389.1:21,761,875 INFO 2025-08-08 15:04:37 MarkDuplicates Tracking 102874 as yet unmatched pairs. 640 records in RAM. INFO 2025-08-08 15:04:39 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: NC_082391.1:2,047,580 INFO 2025-08-08 15:04:39 MarkDuplicates Tracking 106793 as yet unmatched pairs. 8804 records in RAM. INFO 2025-08-08 15:04:40 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: NC_082392.1:6,484,909 INFO 2025-08-08 15:04:40 MarkDuplicates Tracking 108631 as yet unmatched pairs. 7692 records in RAM. INFO 2025-08-08 15:04:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: NC_082393.1:5,528,089 INFO 2025-08-08 15:04:42 MarkDuplicates Tracking 108615 as yet unmatched pairs. 8970 records in RAM. INFO 2025-08-08 15:04:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: NC_082394.1:6,572,698 INFO 2025-08-08 15:04:44 MarkDuplicates Tracking 105286 as yet unmatched pairs. 6942 records in RAM. INFO 2025-08-08 15:04:46 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: NC_082395.1:11,253,272 INFO 2025-08-08 15:04:46 MarkDuplicates Tracking 101218 as yet unmatched pairs. 7205 records in RAM. INFO 2025-08-08 15:04:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: NC_082396.1:9,239,965 INFO 2025-08-08 15:04:48 MarkDuplicates Tracking 95933 as yet unmatched pairs. 8338 records in RAM. INFO 2025-08-08 15:04:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: NC_082397.1:11,382,062 INFO 2025-08-08 15:04:50 MarkDuplicates Tracking 87979 as yet unmatched pairs. 10478 records in RAM. INFO 2025-08-08 15:04:52 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: NC_082398.1:6,655,299 INFO 2025-08-08 15:04:52 MarkDuplicates Tracking 78749 as yet unmatched pairs. 5983 records in RAM. INFO 2025-08-08 15:04:53 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: NC_082399.1:18,643,524 INFO 2025-08-08 15:04:53 MarkDuplicates Tracking 66560 as yet unmatched pairs. 2097 records in RAM. INFO 2025-08-08 15:04:55 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: NC_082401.1:651,384 INFO 2025-08-08 15:04:55 MarkDuplicates Tracking 55143 as yet unmatched pairs. 15293 records in RAM. INFO 2025-08-08 15:04:58 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: NC_082402.1:457,823 INFO 2025-08-08 15:04:58 MarkDuplicates Tracking 41461 as yet unmatched pairs. 13063 records in RAM. INFO 2025-08-08 15:05:00 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: NC_082403.1:7,839,648 INFO 2025-08-08 15:05:00 MarkDuplicates Tracking 23247 as yet unmatched pairs. 8173 records in RAM. INFO 2025-08-08 15:05:02 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_082404.1:16,366,168 INFO 2025-08-08 15:05:02 MarkDuplicates Tracking 3385 as yet unmatched pairs. 3060 records in RAM. INFO 2025-08-08 15:05:03 MarkDuplicates Read 21248842 records. 0 pairs never matched. INFO 2025-08-08 15:05:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 8220444152; totalMemory: 11475615744; maxMemory: 32178700288 INFO 2025-08-08 15:05:04 MarkDuplicates Will retain up to 1005584384 duplicate indices before spilling to disk. INFO 2025-08-08 15:05:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-08-08 15:05:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-08-08 15:05:17 MarkDuplicates Sorting list of duplicate records. INFO 2025-08-08 15:05:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 11425328632; totalMemory: 19511902208; maxMemory: 32178700288 INFO 2025-08-08 15:05:18 MarkDuplicates Marking 2438841 records as duplicates. INFO 2025-08-08 15:05:18 MarkDuplicates Found 140713 optical duplicate clusters. INFO 2025-08-08 15:05:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-08-08 15:06:49 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 90s. Last read position: NC_082393.1:14,447,710 INFO 2025-08-08 15:08:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-08-08 15:08:00 MarkDuplicates Duplicate Index cleanup. INFO 2025-08-08 15:08:00 MarkDuplicates Getting Memory Stats. INFO 2025-08-08 15:08:01 MarkDuplicates Before output close freeMemory: 1308304944; totalMemory: 1342177280; maxMemory: 32178700288 INFO 2025-08-08 15:08:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-08-08 15:08:01 MarkDuplicates After output close freeMemory: 538618168; totalMemory: 570425344; maxMemory: 32178700288 [Fri Aug 08 15:08:01 PDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.71 minutes. Runtime.totalMemory()=570425344