Mercurial > repos > jpayne > snp_pipeline
annotate test-data/samples/sample1/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/sample1/reads.sorted.bam] OUTPUT=samples/sample1/reads.sorted.deduped.bam METRICS_FILE=samples/sample1/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 647 9131 0 0 106 2 0 0.005817 20840746 |
| 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 1.999562 |
| jpayne@0 | 14 3.0 2.998686 |
| jpayne@0 | 15 4.0 3.997373 |
| jpayne@0 | 16 5.0 4.995622 |
| jpayne@0 | 17 6.0 5.993433 |
| jpayne@0 | 18 7.0 6.990808 |
| jpayne@0 | 19 8.0 7.987746 |
| jpayne@0 | 20 9.0 8.984247 |
| jpayne@0 | 21 10.0 9.980311 |
| jpayne@0 | 22 11.0 10.97594 |
| jpayne@0 | 23 12.0 11.971132 |
| jpayne@0 | 24 13.0 12.965888 |
| jpayne@0 | 25 14.0 13.960208 |
| jpayne@0 | 26 15.0 14.954093 |
| jpayne@0 | 27 16.0 15.947543 |
| jpayne@0 | 28 17.0 16.940557 |
| jpayne@0 | 29 18.0 17.933137 |
| jpayne@0 | 30 19.0 18.925281 |
| jpayne@0 | 31 20.0 19.916991 |
| jpayne@0 | 32 21.0 20.908267 |
| jpayne@0 | 33 22.0 21.899109 |
| jpayne@0 | 34 23.0 22.889516 |
| jpayne@0 | 35 24.0 23.879489 |
| jpayne@0 | 36 25.0 24.869029 |
| jpayne@0 | 37 26.0 25.858136 |
| jpayne@0 | 38 27.0 26.846809 |
| jpayne@0 | 39 28.0 27.835049 |
| jpayne@0 | 40 29.0 28.822856 |
| jpayne@0 | 41 30.0 29.810231 |
| jpayne@0 | 42 31.0 30.797173 |
| jpayne@0 | 43 32.0 31.783683 |
| jpayne@0 | 44 33.0 32.76976 |
| jpayne@0 | 45 34.0 33.755406 |
| jpayne@0 | 46 35.0 34.74062 |
| jpayne@0 | 47 36.0 35.725402 |
| jpayne@0 | 48 37.0 36.709753 |
| jpayne@0 | 49 38.0 37.693673 |
| jpayne@0 | 50 39.0 38.677162 |
| jpayne@0 | 51 40.0 39.66022 |
| jpayne@0 | 52 41.0 40.642847 |
| jpayne@0 | 53 42.0 41.625044 |
| jpayne@0 | 54 43.0 42.606811 |
| jpayne@0 | 55 44.0 43.588148 |
| jpayne@0 | 56 45.0 44.569054 |
| jpayne@0 | 57 46.0 45.549532 |
| jpayne@0 | 58 47.0 46.529579 |
| jpayne@0 | 59 48.0 47.509198 |
| jpayne@0 | 60 49.0 48.488387 |
| jpayne@0 | 61 50.0 49.467147 |
| jpayne@0 | 62 51.0 50.445479 |
| jpayne@0 | 63 52.0 51.423382 |
| jpayne@0 | 64 53.0 52.400857 |
| jpayne@0 | 65 54.0 53.377903 |
| jpayne@0 | 66 55.0 54.354522 |
| jpayne@0 | 67 56.0 55.330712 |
| jpayne@0 | 68 57.0 56.306476 |
| jpayne@0 | 69 58.0 57.281811 |
| jpayne@0 | 70 59.0 58.25672 |
| jpayne@0 | 71 60.0 59.231201 |
| jpayne@0 | 72 61.0 60.205256 |
| jpayne@0 | 73 62.0 61.178884 |
| jpayne@0 | 74 63.0 62.152085 |
| jpayne@0 | 75 64.0 63.12486 |
| jpayne@0 | 76 65.0 64.097209 |
| jpayne@0 | 77 66.0 65.069132 |
| jpayne@0 | 78 67.0 66.04063 |
| jpayne@0 | 79 68.0 67.011702 |
| jpayne@0 | 80 69.0 67.982348 |
| jpayne@0 | 81 70.0 68.952569 |
| jpayne@0 | 82 71.0 69.922366 |
| jpayne@0 | 83 72.0 70.891737 |
| jpayne@0 | 84 73.0 71.860684 |
| jpayne@0 | 85 74.0 72.829206 |
| jpayne@0 | 86 75.0 73.797305 |
| jpayne@0 | 87 76.0 74.764979 |
| jpayne@0 | 88 77.0 75.732229 |
| jpayne@0 | 89 78.0 76.699055 |
| jpayne@0 | 90 79.0 77.665459 |
| jpayne@0 | 91 80.0 78.631438 |
| jpayne@0 | 92 81.0 79.596995 |
| jpayne@0 | 93 82.0 80.562128 |
| jpayne@0 | 94 83.0 81.526839 |
| jpayne@0 | 95 84.0 82.491128 |
| jpayne@0 | 96 85.0 83.454994 |
| jpayne@0 | 97 86.0 84.418437 |
| jpayne@0 | 98 87.0 85.381459 |
| jpayne@0 | 99 88.0 86.344059 |
| jpayne@0 | 100 89.0 87.306237 |
| jpayne@0 | 101 90.0 88.267994 |
| jpayne@0 | 102 91.0 89.229329 |
| jpayne@0 | 103 92.0 90.190243 |
| jpayne@0 | 104 93.0 91.150737 |
| jpayne@0 | 105 94.0 92.11081 |
| jpayne@0 | 106 95.0 93.070462 |
| jpayne@0 | 107 96.0 94.029693 |
| jpayne@0 | 108 97.0 94.988505 |
| jpayne@0 | 109 98.0 95.946897 |
| jpayne@0 | 110 99.0 96.904868 |
| jpayne@0 | 111 100.0 97.862421 |
| jpayne@0 | 112 |