## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-09-17/ES_Ciu_Tom_1_2015-09-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-09-17/ES_Ciu_Tom_1_2015-09-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-09-17/ES_Ciu_Tom_1_2015-09-17.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 08:52:12 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 6851704 35666849 0 0 2775439 3591472 0 0.127369 165003475 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 28526967 28526967 2.0 1.805608 2899795 2899795 3.0 2.454612 264893 264893 4.0 2.977455 24194 24194 5.0 3.398661 2796 2796 6.0 3.737988 747 747 7.0 4.011353 414 414 8.0 4.231577 308 308 9.0 4.408992 249 249 10.0 4.551919 175 175 11.0 4.667061 170 170 12.0 4.759821 146 146 13.0 4.83455 157 157 14.0 4.894751 142 142 15.0 4.94325 127 127 16.0 4.982321 109 109 17.0 5.013797 90 90 18.0 5.039154 76 76 19.0 5.059582 76 76 20.0 5.076039 75 75 21.0 5.089297 86 86 22.0 5.099978 53 53 23.0 5.108582 62 62 24.0 5.115514 40 40 25.0 5.121098 46 46 26.0 5.125597 30 30 27.0 5.129221 37 37 28.0 5.132141 52 52 29.0 5.134493 28 28 30.0 5.136388 36 36 31.0 5.137915 34 34 32.0 5.139145 42 42 33.0 5.140135 37 37 34.0 5.140933 22 22 35.0 5.141576 23 23 36.0 5.142094 15 15 37.0 5.142512 17 17 38.0 5.142848 29 29 39.0 5.143119 17 17 40.0 5.143337 17 17 41.0 5.143513 16 16 42.0 5.143654 15 15 43.0 5.143768 11 11 44.0 5.14386 17 17 45.0 5.143934 18 18 46.0 5.143994 16 16 47.0 5.144042 14 14 48.0 5.144081 10 10 49.0 5.144112 6 6 50.0 5.144137 16 16 51.0 5.144157 14 14 52.0 5.144174 8 8 53.0 5.144187 8 8 54.0 5.144197 17 17 55.0 5.144206 8 8 56.0 5.144213 4 4 57.0 5.144218 9 9 58.0 5.144223 9 9 59.0 5.144226 8 8 60.0 5.144229 14 14 61.0 5.144232 5 5 62.0 5.144233 11 11 63.0 5.144235 3 3 64.0 5.144236 9 9 65.0 5.144237 7 7 66.0 5.144238 4 4 67.0 5.144239 5 5 68.0 5.144239 8 8 69.0 5.144239 3 3 70.0 5.14424 2 2 71.0 5.14424 5 5 72.0 5.14424 6 6 73.0 5.14424 1 1 74.0 5.144241 4 4 75.0 5.144241 4 4 76.0 5.144241 4 4 77.0 5.144241 6 6 78.0 5.144241 9 9 79.0 5.144241 0 0 80.0 5.144241 5 5 81.0 5.144241 3 3 82.0 5.144241 3 3 83.0 5.144241 3 3 84.0 5.144241 2 2 85.0 5.144241 4 4 86.0 5.144241 1 1 87.0 5.144241 3 3 88.0 5.144241 3 3 89.0 5.144241 4 4 90.0 5.144241 1 1 91.0 5.144241 2 2 92.0 5.144241 3 3 93.0 5.144241 1 1 94.0 5.144241 0 0 95.0 5.144241 3 3 96.0 5.144241 2 2 97.0 5.144241 3 3 98.0 5.144241 0 0 99.0 5.144241 1 1 100.0 5.144241 2 2 101.0 0 1 1 102.0 0 2 2 105.0 0 4 4 107.0 0 1 1 108.0 0 1 1 109.0 0 2 2 110.0 0 1 1 111.0 0 2 2 113.0 0 4 4 114.0 0 1 1 115.0 0 1 1 116.0 0 1 1 117.0 0 1 1 118.0 0 2 2 121.0 0 2 2 123.0 0 1 1 124.0 0 1 1 126.0 0 1 1 128.0 0 1 1 129.0 0 2 2 130.0 0 1 1 134.0 0 2 2 137.0 0 1 1 138.0 0 1 1 139.0 0 1 1 140.0 0 3 3 144.0 0 1 1 148.0 0 2 2 151.0 0 1 1 153.0 0 1 1 157.0 0 1 1 159.0 0 1 1 173.0 0 1 1 174.0 0 2 2 178.0 0 1 1 179.0 0 1 1 180.0 0 2 2 199.0 0 1 1 200.0 0 1 1 212.0 0 1 1 227.0 0 1 1 235.0 0 1 1