## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606340.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606340.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606340.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp] 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 REMOVE_DUPLICATES=false 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: Tue Nov 02 22:36:23 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 0 28811928 4155070 0 0 5376703 0 0.186614 67259969 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 20704751 20704751 2.0 1.651572 1874951 1874951 3.0 2.076119 421492 421492 4.0 2.352742 166497 166497 5.0 2.532982 84709 84709 6.0 2.650421 49462 49462 7.0 2.726942 31575 31575 8.0 2.7768 21485 21485 9.0 2.809286 15193 15193 10.0 2.830454 11453 11453 11.0 2.844246 8566 8566 12.0 2.853232 6696 6696 13.0 2.859088 5443 5443 14.0 2.862903 4451 4451 15.0 2.865389 3561 3561 16.0 2.867008 2990 2990 17.0 2.868064 2543 2543 18.0 2.868751 2046 2046 19.0 2.869199 1792 1792 20.0 2.869491 1499 1499 21.0 2.869682 1371 1371 22.0 2.869805 1118 1118 23.0 2.869886 1023 1023 24.0 2.869939 901 901 25.0 2.869973 797 797 26.0 2.869995 691 691 27.0 2.87001 608 608 28.0 2.87002 589 589 29.0 2.870026 515 515 30.0 2.87003 461 461 31.0 2.870032 407 407 32.0 2.870034 415 415 33.0 2.870035 321 321 34.0 2.870036 311 311 35.0 2.870036 284 284 36.0 2.870037 283 283 37.0 2.870037 241 241 38.0 2.870037 229 229 39.0 2.870037 214 214 40.0 2.870037 196 196 41.0 2.870037 177 177 42.0 2.870037 156 156 43.0 2.870037 166 166 44.0 2.870037 140 140 45.0 2.870037 127 127 46.0 2.870037 142 142 47.0 2.870037 112 112 48.0 2.870037 98 98 49.0 2.870037 79 79 50.0 2.870037 85 85 51.0 2.870037 102 102 52.0 2.870037 80 80 53.0 2.870037 79 79 54.0 2.870037 66 66 55.0 2.870037 53 53 56.0 2.870037 69 69 57.0 2.870037 62 62 58.0 2.870037 44 44 59.0 2.870037 56 56 60.0 2.870037 44 44 61.0 2.870037 50 50 62.0 2.870037 54 54 63.0 2.870037 39 39 64.0 2.870037 45 45 65.0 2.870037 40 40 66.0 2.870037 32 32 67.0 2.870037 34 34 68.0 2.870037 34 34 69.0 2.870037 28 28 70.0 2.870037 29 29 71.0 2.870037 25 25 72.0 2.870037 33 33 73.0 2.870037 30 30 74.0 2.870037 27 27 75.0 2.870037 22 22 76.0 2.870037 22 22 77.0 2.870037 16 16 78.0 2.870037 30 30 79.0 2.870037 15 15 80.0 2.870037 19 19 81.0 2.870037 17 17 82.0 2.870037 12 12 83.0 2.870037 22 22 84.0 2.870037 19 19 85.0 2.870037 10 10 86.0 2.870037 17 17 87.0 2.870037 7 7 88.0 2.870037 9 9 89.0 2.870037 11 11 90.0 2.870037 12 12 91.0 2.870037 8 8 92.0 2.870037 7 7 93.0 2.870037 10 10 94.0 2.870037 5 5 95.0 2.870037 9 9 96.0 2.870037 9 9 97.0 2.870037 13 13 98.0 2.870037 5 5 99.0 2.870037 13 13 100.0 2.870037 9 9 101.0 0 10 10 102.0 0 7 7 103.0 0 6 6 104.0 0 12 12 105.0 0 5 5 106.0 0 8 8 107.0 0 10 10 108.0 0 12 12 109.0 0 7 7 110.0 0 3 3 111.0 0 6 6 112.0 0 4 4 113.0 0 5 5 114.0 0 3 3 115.0 0 4 4 116.0 0 5 5 117.0 0 8 8 118.0 0 10 10 119.0 0 5 5 120.0 0 2 2 121.0 0 5 5 122.0 0 5 5 123.0 0 3 3 124.0 0 9 9 125.0 0 6 6 126.0 0 3 3 127.0 0 1 1 128.0 0 4 4 129.0 0 4 4 130.0 0 4 4 131.0 0 3 3 132.0 0 3 3 133.0 0 2 2 134.0 0 2 2 135.0 0 3 3 136.0 0 8 8 137.0 0 2 2 138.0 0 4 4 139.0 0 4 4 140.0 0 1 1 141.0 0 2 2 142.0 0 2 2 143.0 0 1 1 144.0 0 4 4 146.0 0 1 1 147.0 0 2 2 148.0 0 4 4 150.0 0 1 1 151.0 0 3 3 153.0 0 1 1 154.0 0 3 3 155.0 0 1 1 157.0 0 2 2 158.0 0 1 1 159.0 0 1 1 160.0 0 1 1 161.0 0 3 3 162.0 0 2 2 163.0 0 1 1 167.0 0 1 1 168.0 0 2 2 171.0 0 1 1 172.0 0 1 1 173.0 0 3 3 174.0 0 1 1 175.0 0 1 1 176.0 0 1 1 178.0 0 1 1 179.0 0 3 3 181.0 0 1 1 182.0 0 1 1 183.0 0 1 1 185.0 0 2 2 187.0 0 1 1 189.0 0 2 2 191.0 0 1 1 192.0 0 1 1 193.0 0 2 2 197.0 0 1 1 198.0 0 1 1 200.0 0 1 1 201.0 0 1 1 202.0 0 1 1 206.0 0 1 1 209.0 0 1 1 211.0 0 1 1 216.0 0 1 1 218.0 0 1 1 219.0 0 2 2 221.0 0 2 2 222.0 0 1 1 223.0 0 1 1 226.0 0 1 1 236.0 0 1 1 238.0 0 1 1 245.0 0 2 2 246.0 0 1 1 250.0 0 1 1 260.0 0 2 2 265.0 0 1 1 268.0 0 1 1 275.0 0 1 1 289.0 0 1 1 303.0 0 1 1 314.0 0 1 1 345.0 0 1 1 358.0 0 1 1 387.0 0 1 1 394.0 0 1 1 444.0 0 1 1 464.0 0 1 1 483.0 0 1 1 9183.0 0 1 1