sherrillmix/taxonomizr

Issues

• Download failed with error: "FTP response timeout".

  #67 opened a month ago
  1

• Error in prepareDatabase('accessionTaxa.sql'), change in url?

  #66 opened 5 months ago
  3

• error in prepareDatabase

  #65 opened 6 months ago
  3

• Exclude species with no rank

  #64 opened 7 months ago
  1

• Does this tool do LCA?

  #63 opened 9 months ago
  1

• Unable to query SQL database when built with `getAccessions=FALSE`

  #62 opened a year ago
  2

• Pointing R to an already prepared database

  #61 opened a year ago
  4

• Cannot get taxonomizr to work

  #60 opened a year ago
  4

• Error:database is locked with prepareDatabase

  #59 opened a year ago
  3

• prepareDatabase('accessionTaxa.sql') downloading names and nodes with getnamesandnodes() error:

  #58 opened a year ago
  9

• Error in downloading database using prepareDatabase

  #57 opened 2 years ago
  9

• accessionToTaxa returns a single NA when the input contains too many accession ID

  #56 opened 2 years ago
  3

• Error: disk I/O error In addition: Warning message: Couldn't set synchronous mode: disk I/O error

  #55 opened 2 years ago
  5

• Questions for the issue of taxonomizr package being terminated during operation

  #54 opened 2 years ago
  1

• Get all bacterial species

  #53 opened 2 years ago
  2

• Error in preparing accessionTaxa.sql with prepareDatabase()

  #52 opened 2 years ago
  10

• Manual preparation of database

  #51 opened 2 years ago
  1

• error: no such column: tmp.query.accession

  #50 opened 2 years ago
  1

• Assignment of taxonomy to blast hits

  #49 opened 2 years ago
  1

• read.names.sql for common names

  #48 opened 2 years ago
  2

• FR: set a variable with default path for the databases

  #47 opened 2 years ago
  5

• Preparing SQL for only specific taxa

  #46 opened 2 years ago
  7

• `accessionToTaxa` function not converting accession numbers to taxIDs?

  #45 opened 2 years ago
  7

• error: 'Query and SQL mismatch'

  #44 opened 2 years ago
  6

• get taxID for a huge list of accesion numbers

  #43 opened 2 years ago
  1

• sql 4 protein accession: "Error in connection_import_file"

  #42 opened 2 years ago
  4

• Disk is full (and moving tmp location doesn't solve it)

  #41 opened 2 years ago
  10

• Kingdom bacteria only

  #40 opened 2 years ago
  2

• AccessionToTaxa error in file.remove(tmp)

  #39 opened 2 years ago
  4

• accession2taxid ftp

  #38 opened 3 years ago
  4

• I can't match the accession number with taxa ID

  #37 opened 3 years ago
  5

• Error: no such table: main.names

  #36 opened 3 years ago
  4

• getAccession2taxid(types='prot') download old files

  #35 opened 3 years ago
  5

• Problem with Convert names, nodes and accessions to database

  #34 opened 3 years ago
  8

• prepareDatabase() and getAccession2taxid() curl error - server did not report OK, got 450

  #33 opened 3 years ago
  9

• Error in readBin while reading .gz files

  #31 opened 3 years ago
  9

• All taxonomic levels

  #30 opened 3 years ago
  3

• Error in accesion to taxa

  #29 opened 3 years ago
  3

• read.accession not working; preparedatabase failed

  #28 opened 3 years ago
  3

• prepareDatabase('accessionTaxa.sql') - Error in utils::download.file(url, tarFile, mode = "wb") : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz'

  #27 opened 3 years ago
  11

• read.accession2taxid failing

  #26 opened 4 years ago
  3

• Error Reading in prot.accession2taxid.gz file

  #25 opened 4 years ago
  6

• accessionToTaxa error

  #24 opened 4 years ago
  2

• Error in utils::download.file(url, tarFile, mode = "wb") : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz'

  #23 opened 4 years ago
  1

• Error in connection_import_file(conn@ptr, name, value, sep, eol, skip) : RS_sqlite_import: disk I/O error Error: no such savepoint: dbWriteTable

  #22 opened 4 years ago
  3

• Can't find nodes table?

  #21 opened 4 years ago
  2

• Error with prepareDatabase: RS_sqlite_import: expected 3 columns but found 4

  #20 opened 4 years ago
  1

• Database or disk is full error

  #19 opened 4 years ago
  3

• Input and output vector have different lengths, and vectors can't have named values

  #18 opened 4 years ago
  4

• Convert taxon structure to newick format

  #17 opened 4 years ago
  22