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. -mrl, --minReadLength [number] Minimum read length. Default value: 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. -tsm, --tempStoreInMemory Temporary storage in memory for SQLITE. Default value: false. -tsd, --tempStoreDir [string] Temporary storage directory for SQLITE (if not in-memory). -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 6.21.5, built 5 May 2021). Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ---------------------------------------------- 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. -mrl, --minReadLength [number] Minimum read length. Default value: 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. -tsm, --tempStoreInMemory Temporary storage in memory for SQLITE. Default value: false. -tsd, --tempStoreDir [string] Temporary storage directory for SQLITE (if not in-memory). -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 6.21.5, built 5 May 2021). Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ---------------------------------------------- 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. -mrl, --minReadLength [number] Minimum read length. Default value: 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. -tsm, --tempStoreInMemory Temporary storage in memory for SQLITE. Default value: false. -tsd, --tempStoreDir [string] Temporary storage directory for SQLITE (if not in-memory). -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 6.21.5, built 5 May 2021). Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ---------------------------------------------- Program options for daa2rma: SYNOPSIS Meganizer [options] DESCRIPTION Prepares ('meganizes') a DIAMOND .daa file for use with MEGAN OPTIONS Files -i, --in [string(s)] Input DAA file(s). Each is meganized separately. Mandatory option. -mdf, --metaDataFile [string(s)] Files containing metadata to be included in files. Mode -lg, --longReads Parse and analyse as long reads. Default value: false. Parameters -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. -mrl, --minReadLength [number] Minimum read length. Default value: 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] Accession-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. -tsm, --tempStoreInMemory Temporary storage in memory for SQLITE. Default value: false. -tsd, --tempStoreDir [string] Temporary storage directory for SQLITE (if not in-memory). -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 6.21.5, built 5 May 2021). Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ---------------------------------------------- Program options for daa2rma: SYNOPSIS Meganizer [options] DESCRIPTION Prepares ('meganizes') a DIAMOND .daa file for use with MEGAN OPTIONS Files -i, --in [string(s)] Input DAA file(s). Each is meganized separately. Mandatory option. -mdf, --metaDataFile [string(s)] Files containing metadata to be included in files. Mode -lg, --longReads Parse and analyse as long reads. Default value: false. Parameters -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. -mrl, --minReadLength [number] Minimum read length. Default value: 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] Accession-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. -tsm, --tempStoreInMemory Temporary storage in memory for SQLITE. Default value: false. -tsd, --tempStoreDir [string] Temporary storage directory for SQLITE (if not in-memory). -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 6.21.5, built 5 May 2021). Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.. ----------------------------------------------