## 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-GSM919930.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919930.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919930.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 15:53:34 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 9101322 1481534 0 0 1513660 0 0.166312 24235906 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 6820282 6820282 2.0 1.686925 540627 540627 3.0 2.15879 110723 110723 4.0 2.482927 43889 43889 5.0 2.705584 22352 22352 6.0 2.858532 13192 13192 7.0 2.963597 8455 8455 8.0 3.035768 5852 5852 9.0 3.085344 4215 4215 10.0 3.119399 3026 3026 11.0 3.142793 2332 2332 12.0 3.158862 1908 1908 13.0 3.169901 1432 1432 14.0 3.177483 1166 1166 15.0 3.182692 947 947 16.0 3.18627 788 788 17.0 3.188728 696 696 18.0 3.190416 540 540 19.0 3.191576 484 484 20.0 3.192372 432 432 21.0 3.19292 371 371 22.0 3.193296 319 319 23.0 3.193554 285 285 24.0 3.193731 261 261 25.0 3.193853 228 228 26.0 3.193937 216 216 27.0 3.193994 193 193 28.0 3.194034 170 170 29.0 3.194061 150 150 30.0 3.19408 137 137 31.0 3.194092 123 123 32.0 3.194101 115 115 33.0 3.194107 102 102 34.0 3.194111 93 93 35.0 3.194114 98 98 36.0 3.194116 87 87 37.0 3.194117 71 71 38.0 3.194118 63 63 39.0 3.194119 63 63 40.0 3.194119 73 73 41.0 3.19412 53 53 42.0 3.19412 48 48 43.0 3.19412 41 41 44.0 3.19412 46 46 45.0 3.19412 32 32 46.0 3.19412 55 55 47.0 3.19412 35 35 48.0 3.19412 30 30 49.0 3.19412 32 32 50.0 3.19412 33 33 51.0 3.19412 27 27 52.0 3.19412 35 35 53.0 3.19412 19 19 54.0 3.19412 30 30 55.0 3.19412 18 18 56.0 3.19412 18 18 57.0 3.19412 16 16 58.0 3.19412 14 14 59.0 3.19412 17 17 60.0 3.19412 17 17 61.0 3.19412 12 12 62.0 3.19412 14 14 63.0 3.19412 12 12 64.0 3.19412 15 15 65.0 3.19412 11 11 66.0 3.19412 7 7 67.0 3.19412 12 12 68.0 3.19412 15 15 69.0 3.19412 12 12 70.0 3.19412 11 11 71.0 3.19412 10 10 72.0 3.19412 10 10 73.0 3.19412 10 10 74.0 3.19412 11 11 75.0 3.19412 6 6 76.0 3.19412 10 10 77.0 3.19412 7 7 78.0 3.19412 6 6 79.0 3.19412 6 6 80.0 3.19412 7 7 81.0 3.19412 7 7 82.0 3.19412 4 4 83.0 3.19412 4 4 84.0 3.19412 10 10 85.0 3.19412 6 6 86.0 3.19412 4 4 87.0 3.19412 5 5 88.0 3.19412 7 7 89.0 3.19412 1 1 90.0 3.19412 11 11 91.0 3.19412 2 2 92.0 3.19412 4 4 93.0 3.19412 3 3 94.0 3.19412 8 8 95.0 3.19412 2 2 96.0 3.19412 9 9 97.0 3.19412 3 3 98.0 3.19412 3 3 99.0 3.19412 4 4 100.0 3.19412 7 7 101.0 0 4 4 102.0 0 4 4 103.0 0 2 2 104.0 0 2 2 105.0 0 2 2 106.0 0 5 5 107.0 0 2 2 108.0 0 4 4 109.0 0 5 5 110.0 0 3 3 111.0 0 2 2 112.0 0 1 1 114.0 0 5 5 115.0 0 4 4 116.0 0 2 2 117.0 0 2 2 118.0 0 1 1 119.0 0 2 2 120.0 0 2 2 121.0 0 1 1 122.0 0 2 2 123.0 0 1 1 124.0 0 4 4 125.0 0 3 3 126.0 0 4 4 127.0 0 1 1 128.0 0 3 3 129.0 0 1 1 130.0 0 3 3 131.0 0 2 2 134.0 0 1 1 136.0 0 2 2 138.0 0 2 2 140.0 0 2 2 141.0 0 1 1 143.0 0 2 2 145.0 0 3 3 146.0 0 3 3 147.0 0 3 3 148.0 0 1 1 149.0 0 1 1 150.0 0 1 1 152.0 0 1 1 154.0 0 2 2 158.0 0 2 2 159.0 0 2 2 160.0 0 2 2 163.0 0 1 1 165.0 0 1 1 166.0 0 1 1 168.0 0 1 1 170.0 0 2 2 171.0 0 1 1 172.0 0 1 1 173.0 0 1 1 174.0 0 1 1 175.0 0 1 1 178.0 0 1 1 181.0 0 2 2 182.0 0 1 1 183.0 0 1 1 184.0 0 1 1 185.0 0 1 1 187.0 0 1 1 189.0 0 1 1 191.0 0 1 1 192.0 0 2 2 194.0 0 3 3 195.0 0 2 2 197.0 0 1 1 201.0 0 1 1 202.0 0 1 1 203.0 0 1 1 204.0 0 1 1 210.0 0 1 1 217.0 0 1 1 219.0 0 1 1 233.0 0 1 1 249.0 0 1 1 252.0 0 1 1 255.0 0 1 1 259.0 0 1 1 262.0 0 1 1 272.0 0 1 1 274.0 0 1 1 278.0 0 1 1 282.0 0 2 2 284.0 0 3 3 286.0 0 1 1 313.0 0 2 2 320.0 0 1 1 356.0 0 1 1 363.0 0 2 2 366.0 0 1 1 372.0 0 1 1 389.0 0 2 2 409.0 0 1 1 441.0 0 1 1 451.0 0 1 1 458.0 0 1 1 472.0 0 1 1 505.0 0 1 1 513.0 0 1 1 549.0 0 1 1 1068.0 0 1 1 1096.0 0 1 1 1692.0 0 1 1