Program options for daa2rma: SYNOPSIS DAA2RMA [options] DESCRIPTION Computes a MEGAN .rma6 file from a DIAMOND .daa file OPTIONS Input -i, --in [string(s)] Input DAA file. Mandatory option. -mdf, --metaDataFile [string(s)] Files containing metadata to be included in RMA6 files. Output -o, --out [string(s)] Output file(s), one for each input file, or a directory. Mandatory option. -c, --useCompression Compress reads and matches in RMA file (smaller files, longer to generate. Default value: true. Reads -p, --paired Reads are paired. Default value: false. -ps, --pairedSuffixLength [number] Length of name suffix used to distinguish between name (i.e. first word in header) of read and its mate (use 0 if read and mate have same name). Default value: 0. -pof, --pairedReadsInOneFile Are paired reads in one file (usually they are in two). Default value: false. Parameters -lg, --longReads Parse and analyse as long reads. Default value: false. -m, --maxMatchesPerRead [number] Max matches per read. Default value: 100. -class, --classify Run classification algorithm. Default value: true. -ms, --minScore [number] Min score. Default value: 50.0. -me, --maxExpected [number] Max expected. Default value: 0.01. -mpi, --minPercentIdentity [number] Min percent identity. Default value: 0.0. -top, --topPercent [number] Top percent. Default value: 10.0. -supp, --minSupportPercent [number] Min support as percent of assigned reads (0==off). Default value: 0.05. -sup, --minSupport [number] Min support (0==off). Default value: 0. -mrc, --minPercentReadCover [number] Min percent of read length to be covered by alignments. Default value: 0.0. -mrefc, --minPercentReferenceCover [number] Min percent of reference length to be covered by alignments. Default value: 0.0. -alg, --lcaAlgorithm [string] Set the LCA algorithm to use for taxonomic assignment. Default value: naive Legal values: naive, weighted, longReads -lcp, --lcaCoveragePercent [number] Set the percent for the LCA to cover. Default value: 100.0. -ram, --readAssignmentMode [string] Set the read assignment mode. Default value: alignedBases in long read mode, readCount else -cf, --conFile [string] File of contaminant taxa (one Id or name per line). Classification support: -mdb, --mapDB [string] MEGAN mapping db (file megan-map.db). -on, --only [string(s)] Use only named classifications (if not set: use all). Deprecated classification support: -tn, --parseTaxonNames Parse taxon names. Default value: true. -a2t, --acc2taxa [string] Accessopm-to-Taxonomy mapping file. -s2t, --syn2taxa [string] Synonyms-to-Taxonomy mapping file. -t4t, --tags4taxonomy [string] Tags for taxonomy id parsing (must set to activate id parsing). -a2ec, --acc2ec [string] Accession-to-EC mapping file. -s2ec, --syn2ec [string] Synonyms-to-EC mapping file. -t4ec, --tags4ec [string] Tags for EC id parsing (must set to activate id parsing). -a2eggnog, --acc2eggnog [string] Accession-to-EGGNOG mapping file. -s2eggnog, --syn2eggnog [string] Synonyms-to-EGGNOG mapping file. -t4eggnog, --tags4eggnog [string] Tags for EGGNOG id parsing (must set to activate id parsing). -a2gtdb, --acc2gtdb [string] Accession-to-GTDB mapping file. -s2gtdb, --syn2gtdb [string] Synonyms-to-GTDB mapping file. -t4gtdb, --tags4gtdb [string] Tags for GTDB id parsing (must set to activate id parsing). -a2interpro2go, --acc2interpro2go [string] Accession-to-INTERPRO2GO mapping file. -s2interpro2go, --syn2interpro2go [string] Synonyms-to-INTERPRO2GO mapping file. -t4interpro2go, --tags4interpro2go [string] Tags for INTERPRO2GO id parsing (must set to activate id parsing). -a2kegg, --acc2kegg [string] Accession-to-KEGG mapping file. -s2kegg, --syn2kegg [string] Synonyms-to-KEGG mapping file. -t4kegg, --tags4kegg [string] Tags for KEGG id parsing (must set to activate id parsing). -a2seed, --acc2seed [string] Accession-to-SEED mapping file. -s2seed, --syn2seed [string] Synonyms-to-SEED mapping file. -t4seed, --tags4seed [string] Tags for SEED id parsing (must set to activate id parsing). -fwa, --firstWordIsAccession First word in reference header is accession number (set to 'true' for NCBI-nr downloaded Sep 2016 or later). Default value: true. -atags, --accessionTags [string(s)] List of accession tags. Default value(s): 'gb|' ref|. Other: -t, --threads [number] Number of threads. Default value: 8. -v, --verbose Echo commandline options and be verbose. Default value: false. -h, --help Show program usage and quit. AUTHOR(s) Daniel H. Huson. VERSION MEGAN Community Edition (version 6.19.9, built 11 Sep 2020). Copyright (C) 2020 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ----------------------------------------------