## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/bwa-mem2/hg38-PKC19_ATAC_2.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-PKC19_ATAC_2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-PKC19_ATAC_2.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/GZnl] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Feb 18 16:51:12 CET 2021 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 57194 25208640 0 0 42716 17282784 3416 0.685659 8330005 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000021 2202230 0 2202614 2.0 1.048519 1650627 3406 1650788 3.0 1.050871 1270959 5 1270983 4.0 1.050985 935816 0 935759 5.0 1.050991 658713 0 658642 6.0 1.050991 444082 0 443959 7.0 1.050991 288557 0 288464 8.0 1.050991 180913 0 180849 9.0 1.050991 110429 0 110381 10.0 1.050991 65847 0 65795 11.0 1.050991 37784 0 37765 12.0 1.050991 21421 0 21404 13.0 1.050991 11777 0 11759 14.0 1.050991 6555 0 6549 15.0 1.050991 3470 0 3472 16.0 1.050991 1876 0 1877 17.0 1.050991 1007 0 1006 18.0 1.050991 522 0 521 19.0 1.050991 263 0 261 20.0 1.050991 149 0 149 21.0 1.050991 74 0 74 22.0 1.050991 49 0 49 23.0 1.050991 29 0 29 24.0 1.050991 18 0 18 25.0 1.050991 8 0 8 26.0 1.050991 6 0 6 27.0 1.050991 6 0 6 28.0 1.050991 5 0 5 29.0 1.050991 5 0 5 30.0 1.050991 2 0 2 31.0 1.050991 1 0 1 32.0 1.050991 0 0 0 33.0 1.050991 0 0 0 34.0 1.050991 0 0 0 35.0 1.050991 0 0 0 36.0 1.050991 0 0 0 37.0 1.050991 0 0 0 38.0 1.050991 0 0 0 39.0 1.050991 1 0 1 40.0 1.050991 0 0 0 41.0 1.050991 0 0 0 42.0 1.050991 0 0 0 43.0 1.050991 0 0 0 44.0 1.050991 0 0 0 45.0 1.050991 0 0 0 46.0 1.050991 0 0 0 47.0 1.050991 0 0 0 48.0 1.050991 0 0 0 49.0 1.050991 0 0 0 50.0 1.050991 0 0 0 51.0 1.050991 0 0 0 52.0 1.050991 0 0 0 53.0 1.050991 0 0 0 54.0 1.050991 0 0 0 55.0 1.050991 0 0 0 56.0 1.050991 0 0 0 57.0 1.050991 0 0 0 58.0 1.050991 0 0 0 59.0 1.050991 0 0 0 60.0 1.050991 0 0 0 61.0 1.050991 0 0 0 62.0 1.050991 0 0 0 63.0 1.050991 0 0 0 64.0 1.050991 0 0 0 65.0 1.050991 0 0 0 66.0 1.050991 0 0 0 67.0 1.050991 0 0 0 68.0 1.050991 0 0 0 69.0 1.050991 0 0 0 70.0 1.050991 0 0 0 71.0 1.050991 0 0 0 72.0 1.050991 0 0 0 73.0 1.050991 0 0 0 74.0 1.050991 0 0 0 75.0 1.050991 0 0 0 76.0 1.050991 0 0 0 77.0 1.050991 0 0 0 78.0 1.050991 0 0 0 79.0 1.050991 0 0 0 80.0 1.050991 0 0 0 81.0 1.050991 0 0 0 82.0 1.050991 0 0 0 83.0 1.050991 0 0 0 84.0 1.050991 0 0 0 85.0 1.050991 0 0 0 86.0 1.050991 0 0 0 87.0 1.050991 0 0 0 88.0 1.050991 0 0 0 89.0 1.050991 0 0 0 90.0 1.050991 0 0 0 91.0 1.050991 0 0 0 92.0 1.050991 0 0 0 93.0 1.050991 0 0 0 94.0 1.050991 0 0 0 95.0 1.050991 0 0 0 96.0 1.050991 0 0 0 97.0 1.050991 0 0 0 98.0 1.050991 0 0 0 99.0 1.050991 0 0 0 100.0 1.050991 0 0 0