Mercurial > repos > jpayne > snp_pipeline
annotate test-data/samples/sample3/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/sample3/reads.sorted.bam] OUTPUT=samples/sample3/reads.sorted.deduped.bam METRICS_FILE=samples/sample3/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 20:46:32 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 692 9097 0 0 114 2 0 0.006248 20685819 |
| 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 1.99956 |
| jpayne@0 | 14 3.0 2.998681 |
| jpayne@0 | 15 4.0 3.997363 |
| jpayne@0 | 16 5.0 4.995605 |
| jpayne@0 | 17 6.0 5.993409 |
| jpayne@0 | 18 7.0 6.990774 |
| jpayne@0 | 19 8.0 7.9877 |
| jpayne@0 | 20 9.0 8.984188 |
| jpayne@0 | 21 10.0 9.980238 |
| jpayne@0 | 22 11.0 10.97585 |
| jpayne@0 | 23 12.0 11.971024 |
| jpayne@0 | 24 13.0 12.965761 |
| jpayne@0 | 25 14.0 13.96006 |
| jpayne@0 | 26 15.0 14.953922 |
| jpayne@0 | 27 16.0 15.947347 |
| jpayne@0 | 28 17.0 16.940336 |
| jpayne@0 | 29 18.0 17.932887 |
| jpayne@0 | 30 19.0 18.925003 |
| jpayne@0 | 31 20.0 19.916682 |
| jpayne@0 | 32 21.0 20.907925 |
| jpayne@0 | 33 22.0 21.898733 |
| jpayne@0 | 34 23.0 22.889104 |
| jpayne@0 | 35 24.0 23.879041 |
| jpayne@0 | 36 25.0 24.868542 |
| jpayne@0 | 37 26.0 25.857608 |
| jpayne@0 | 38 27.0 26.846239 |
| jpayne@0 | 39 28.0 27.834435 |
| jpayne@0 | 40 29.0 28.822197 |
| jpayne@0 | 41 30.0 29.809525 |
| jpayne@0 | 42 31.0 30.796418 |
| jpayne@0 | 43 32.0 31.782878 |
| jpayne@0 | 44 33.0 32.768904 |
| jpayne@0 | 45 34.0 33.754496 |
| jpayne@0 | 46 35.0 34.739655 |
| jpayne@0 | 47 36.0 35.724381 |
| jpayne@0 | 48 37.0 36.708674 |
| jpayne@0 | 49 38.0 37.692534 |
| jpayne@0 | 50 39.0 38.675962 |
| jpayne@0 | 51 40.0 39.658957 |
| jpayne@0 | 52 41.0 40.64152 |
| jpayne@0 | 53 42.0 41.623651 |
| jpayne@0 | 54 43.0 42.60535 |
| jpayne@0 | 55 44.0 43.586618 |
| jpayne@0 | 56 45.0 44.567454 |
| jpayne@0 | 57 46.0 45.547859 |
| jpayne@0 | 58 47.0 46.527833 |
| jpayne@0 | 59 48.0 47.507376 |
| jpayne@0 | 60 49.0 48.486488 |
| jpayne@0 | 61 50.0 49.46517 |
| jpayne@0 | 62 51.0 50.443421 |
| jpayne@0 | 63 52.0 51.421243 |
| jpayne@0 | 64 53.0 52.398634 |
| jpayne@0 | 65 54.0 53.375596 |
| jpayne@0 | 66 55.0 54.352128 |
| jpayne@0 | 67 56.0 55.328231 |
| jpayne@0 | 68 57.0 56.303904 |
| jpayne@0 | 69 58.0 57.279149 |
| jpayne@0 | 70 59.0 58.253965 |
| jpayne@0 | 71 60.0 59.228352 |
| jpayne@0 | 72 61.0 60.202311 |
| jpayne@0 | 73 62.0 61.175842 |
| jpayne@0 | 74 63.0 62.148945 |
| jpayne@0 | 75 64.0 63.121619 |
| jpayne@0 | 76 65.0 64.093866 |
| jpayne@0 | 77 66.0 65.065686 |
| jpayne@0 | 78 67.0 66.037078 |
| jpayne@0 | 79 68.0 67.008044 |
| jpayne@0 | 80 69.0 67.978582 |
| jpayne@0 | 81 70.0 68.948694 |
| jpayne@0 | 82 71.0 69.918379 |
| jpayne@0 | 83 72.0 70.887638 |
| jpayne@0 | 84 73.0 71.85647 |
| jpayne@0 | 85 74.0 72.824877 |
| jpayne@0 | 86 75.0 73.792858 |
| jpayne@0 | 87 76.0 74.760413 |
| jpayne@0 | 88 77.0 75.727543 |
| jpayne@0 | 89 78.0 76.694247 |
| jpayne@0 | 90 79.0 77.660527 |
| jpayne@0 | 91 80.0 78.626382 |
| jpayne@0 | 92 81.0 79.591812 |
| jpayne@0 | 93 82.0 80.556817 |
| jpayne@0 | 94 83.0 81.521399 |
| jpayne@0 | 95 84.0 82.485556 |
| jpayne@0 | 96 85.0 83.449289 |
| jpayne@0 | 97 86.0 84.412599 |
| jpayne@0 | 98 87.0 85.375485 |
| jpayne@0 | 99 88.0 86.337948 |
| jpayne@0 | 100 89.0 87.299987 |
| jpayne@0 | 101 90.0 88.261604 |
| jpayne@0 | 102 91.0 89.222797 |
| jpayne@0 | 103 92.0 90.183569 |
| jpayne@0 | 104 93.0 91.143917 |
| jpayne@0 | 105 94.0 92.103844 |
| jpayne@0 | 106 95.0 93.063348 |
| jpayne@0 | 107 96.0 94.022431 |
| jpayne@0 | 108 97.0 94.981092 |
| jpayne@0 | 109 98.0 95.939331 |
| jpayne@0 | 110 99.0 96.897149 |
| jpayne@0 | 111 100.0 97.854546 |
| jpayne@0 | 112 |