Mercurial > repos > jpayne > snp_pipeline
annotate test-data/samples/sample2/duplicate_reads_metrics.txt @ 58:d53281e6edae
planemo upload
| author | jpayne |
|---|---|
| date | Mon, 17 Jun 2024 02:57:10 -0400 |
| parents | eefdd97a6749 |
| children |
| rev | line source |
|---|---|
| jpayne@0 | 1 ## htsjdk.samtools.metrics.StringHeader |
| jpayne@0 | 2 # MarkDuplicates INPUT=[samples/sample2/reads.sorted.bam] OUTPUT=samples/sample2/reads.sorted.deduped.bam METRICS_FILE=samples/sample2/duplicate_reads_metrics.txt VERBOSITY=WARNING 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 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=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 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 |
| jpayne@0 | 3 ## htsjdk.samtools.metrics.StringHeader |
| jpayne@0 | 4 # Started on: Wed Jan 03 20:46:11 UTC 2018 |
| jpayne@0 | 5 |
| jpayne@0 | 6 ## METRICS CLASS picard.sam.DuplicationMetrics |
| jpayne@0 | 7 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 |
| jpayne@0 | 8 Unknown Library 614 9171 0 0 92 3 0 0.00517 14014816 |
| jpayne@0 | 9 |
| jpayne@0 | 10 ## HISTOGRAM java.lang.Double |
| jpayne@0 | 11 BIN VALUE |
| jpayne@0 | 12 1.0 1 |
| jpayne@0 | 13 2.0 1.999346 |
| jpayne@0 | 14 3.0 2.998038 |
| jpayne@0 | 15 4.0 3.996077 |
| jpayne@0 | 16 5.0 4.993463 |
| jpayne@0 | 17 6.0 5.990196 |
| jpayne@0 | 18 7.0 6.986278 |
| jpayne@0 | 19 8.0 7.981707 |
| jpayne@0 | 20 9.0 8.976486 |
| jpayne@0 | 21 10.0 9.970614 |
| jpayne@0 | 22 11.0 10.964091 |
| jpayne@0 | 23 12.0 11.956919 |
| jpayne@0 | 24 13.0 12.949097 |
| jpayne@0 | 25 14.0 13.940626 |
| jpayne@0 | 26 15.0 14.931507 |
| jpayne@0 | 27 16.0 15.921739 |
| jpayne@0 | 28 17.0 16.911324 |
| jpayne@0 | 29 18.0 17.900261 |
| jpayne@0 | 30 19.0 18.888551 |
| jpayne@0 | 31 20.0 19.876195 |
| jpayne@0 | 32 21.0 20.863193 |
| jpayne@0 | 33 22.0 21.849545 |
| jpayne@0 | 34 23.0 22.835252 |
| jpayne@0 | 35 24.0 23.820314 |
| jpayne@0 | 36 25.0 24.804731 |
| jpayne@0 | 37 26.0 25.788505 |
| jpayne@0 | 38 27.0 26.771635 |
| jpayne@0 | 39 28.0 27.754122 |
| jpayne@0 | 40 29.0 28.735966 |
| jpayne@0 | 41 30.0 29.717168 |
| jpayne@0 | 42 31.0 30.697728 |
| jpayne@0 | 43 32.0 31.677647 |
| jpayne@0 | 44 33.0 32.656924 |
| jpayne@0 | 45 34.0 33.635561 |
| jpayne@0 | 46 35.0 34.613558 |
| jpayne@0 | 47 36.0 35.590915 |
| jpayne@0 | 48 37.0 36.567633 |
| jpayne@0 | 49 38.0 37.543712 |
| jpayne@0 | 50 39.0 38.519152 |
| jpayne@0 | 51 40.0 39.493954 |
| jpayne@0 | 52 41.0 40.468118 |
| jpayne@0 | 53 42.0 41.441646 |
| jpayne@0 | 54 43.0 42.414536 |
| jpayne@0 | 55 44.0 43.38679 |
| jpayne@0 | 56 45.0 44.358408 |
| jpayne@0 | 57 46.0 45.32939 |
| jpayne@0 | 58 47.0 46.299737 |
| jpayne@0 | 59 48.0 47.269449 |
| jpayne@0 | 60 49.0 48.238527 |
| jpayne@0 | 61 50.0 49.206971 |
| jpayne@0 | 62 51.0 50.174782 |
| jpayne@0 | 63 52.0 51.141959 |
| jpayne@0 | 64 53.0 52.108504 |
| jpayne@0 | 65 54.0 53.074417 |
| jpayne@0 | 66 55.0 54.039697 |
| jpayne@0 | 67 56.0 55.004346 |
| jpayne@0 | 68 57.0 55.968364 |
| jpayne@0 | 69 58.0 56.931752 |
| jpayne@0 | 70 59.0 57.894509 |
| jpayne@0 | 71 60.0 58.856637 |
| jpayne@0 | 72 61.0 59.818135 |
| jpayne@0 | 73 62.0 60.779004 |
| jpayne@0 | 74 63.0 61.739244 |
| jpayne@0 | 75 64.0 62.698857 |
| jpayne@0 | 76 65.0 63.657841 |
| jpayne@0 | 77 66.0 64.616198 |
| jpayne@0 | 78 67.0 65.573929 |
| jpayne@0 | 79 68.0 66.531033 |
| jpayne@0 | 80 69.0 67.48751 |
| jpayne@0 | 81 70.0 68.443362 |
| jpayne@0 | 82 71.0 69.398589 |
| jpayne@0 | 83 72.0 70.353191 |
| jpayne@0 | 84 73.0 71.307168 |
| jpayne@0 | 85 74.0 72.260522 |
| jpayne@0 | 86 75.0 73.213252 |
| jpayne@0 | 87 76.0 74.165358 |
| jpayne@0 | 88 77.0 75.116842 |
| jpayne@0 | 89 78.0 76.067703 |
| jpayne@0 | 90 79.0 77.017942 |
| jpayne@0 | 91 80.0 77.96756 |
| jpayne@0 | 92 81.0 78.916556 |
| jpayne@0 | 93 82.0 79.864931 |
| jpayne@0 | 94 83.0 80.812687 |
| jpayne@0 | 95 84.0 81.759822 |
| jpayne@0 | 96 85.0 82.706337 |
| jpayne@0 | 97 86.0 83.652234 |
| jpayne@0 | 98 87.0 84.597512 |
| jpayne@0 | 99 88.0 85.542171 |
| jpayne@0 | 100 89.0 86.486212 |
| jpayne@0 | 101 90.0 87.429636 |
| jpayne@0 | 102 91.0 88.372442 |
| jpayne@0 | 103 92.0 89.314632 |
| jpayne@0 | 104 93.0 90.256206 |
| jpayne@0 | 105 94.0 91.197163 |
| jpayne@0 | 106 95.0 92.137505 |
| jpayne@0 | 107 96.0 93.077232 |
| jpayne@0 | 108 97.0 94.016344 |
| jpayne@0 | 109 98.0 94.954842 |
| jpayne@0 | 110 99.0 95.892726 |
| jpayne@0 | 111 100.0 96.829996 |
| jpayne@0 | 112 |