## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-06-15/UA_Kie_Cho_1_2015-06-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-06-15/UA_Kie_Cho_1_2015-06-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-06-15/UA_Kie_Cho_1_2015-06-15.mark_duplicates_report.txt 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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 08:36:59 UTC 2023 ## 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 lib1 9109747 30598701 0 0 3468569 3090394 0 0.137246 141101207 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 24471398 24471398 2.0 1.805046 2502013 2502013 3.0 2.453144 223839 223839 4.0 2.974893 19939 19939 5.0 3.394924 2262 2262 6.0 3.733069 533 533 7.0 4.00529 302 302 8.0 4.224441 260 260 9.0 4.400868 202 202 10.0 4.542899 169 169 11.0 4.657241 177 177 12.0 4.749291 150 150 13.0 4.823395 149 149 14.0 4.883053 117 117 15.0 4.93108 97 97 16.0 4.969744 108 108 17.0 5.000871 100 100 18.0 5.025929 91 91 19.0 5.046102 58 58 20.0 5.062342 71 71 21.0 5.075416 63 63 22.0 5.085941 58 58 23.0 5.094414 55 55 24.0 5.101235 37 37 25.0 5.106727 53 53 26.0 5.111148 35 35 27.0 5.114707 48 48 28.0 5.117572 41 41 29.0 5.119879 26 26 30.0 5.121736 31 31 31.0 5.12323 34 34 32.0 5.124434 34 34 33.0 5.125403 31 31 34.0 5.126183 25 25 35.0 5.126811 17 17 36.0 5.127316 15 15 37.0 5.127723 22 22 38.0 5.128051 21 21 39.0 5.128314 18 18 40.0 5.128527 22 22 41.0 5.128698 21 21 42.0 5.128835 18 18 43.0 5.128946 18 18 44.0 5.129035 19 19 45.0 5.129107 14 14 46.0 5.129165 10 10 47.0 5.129211 10 10 48.0 5.129249 7 7 49.0 5.129279 13 13 50.0 5.129303 14 14 51.0 5.129323 13 13 52.0 5.129339 3 3 53.0 5.129351 15 15 54.0 5.129361 12 12 55.0 5.12937 6 6 56.0 5.129376 9 9 57.0 5.129382 7 7 58.0 5.129386 4 4 59.0 5.129389 6 6 60.0 5.129392 9 9 61.0 5.129394 4 4 62.0 5.129396 10 10 63.0 5.129398 3 3 64.0 5.129399 5 5 65.0 5.1294 3 3 66.0 5.1294 3 3 67.0 5.129401 5 5 68.0 5.129402 3 3 69.0 5.129402 3 3 70.0 5.129402 5 5 71.0 5.129402 7 7 72.0 5.129403 3 3 73.0 5.129403 5 5 74.0 5.129403 6 6 75.0 5.129403 7 7 76.0 5.129403 4 4 77.0 5.129403 2 2 78.0 5.129403 2 2 79.0 5.129403 2 2 80.0 5.129403 2 2 81.0 5.129403 2 2 82.0 5.129403 3 3 83.0 5.129403 5 5 84.0 5.129403 4 4 85.0 5.129403 2 2 86.0 5.129403 1 1 87.0 5.129403 2 2 88.0 5.129404 3 3 89.0 5.129404 0 0 90.0 5.129404 2 2 91.0 5.129404 6 6 92.0 5.129404 3 3 93.0 5.129404 4 4 94.0 5.129404 0 0 95.0 5.129404 4 4 96.0 5.129404 1 1 97.0 5.129404 4 4 98.0 5.129404 1 1 99.0 5.129404 3 3 100.0 5.129404 2 2 102.0 0 1 1 103.0 0 3 3 104.0 0 1 1 105.0 0 1 1 107.0 0 1 1 108.0 0 3 3 109.0 0 1 1 111.0 0 2 2 112.0 0 3 3 113.0 0 1 1 114.0 0 1 1 115.0 0 1 1 118.0 0 1 1 122.0 0 3 3 123.0 0 1 1 124.0 0 2 2 127.0 0 1 1 129.0 0 1 1 130.0 0 1 1 131.0 0 2 2 138.0 0 1 1 140.0 0 2 2 143.0 0 2 2 147.0 0 1 1 150.0 0 2 2 157.0 0 2 2 161.0 0 1 1 164.0 0 1 1 168.0 0 1 1 171.0 0 1 1 172.0 0 1 1 185.0 0 1 1 204.0 0 1 1 208.0 0 1 1 230.0 0 1 1 236.0 0 1 1 265.0 0 1 1