sherrillmix/taxonomizr issues and pull requests

#68 - sql table failed to generate and I can't delete it to try again

Issue - State: open - Opened by maxfarrell 26 days ago - 2 comments

#67 - Download failed with error: "FTP response timeout".

Issue - State: closed - Opened by castle-ah 2 months ago - 1 comment

#66 - Error in prepareDatabase('accessionTaxa.sql'), change in url?

Issue - State: closed - Opened by mgpapadaki 7 months ago - 3 comments

#64 - Exclude species with no rank

Issue - State: open - Opened by mweberr 8 months ago - 1 comment

#63 - Does this tool do LCA?

Issue - State: closed - Opened by NeginValizadegan 10 months ago - 1 comment

#62 - Unable to query SQL database when built with `getAccessions=FALSE`

Issue - State: closed - Opened by silvia-s over 1 year ago - 2 comments

#61 - Pointing R to an already prepared database

Issue - State: closed - Opened by jkimsis over 1 year ago - 4 comments

#60 - Cannot get taxonomizr to work

Issue - State: closed - Opened by RBuesink over 1 year ago - 4 comments

#59 - Error:database is locked with prepareDatabase

Issue - State: closed - Opened by sarah-buddle over 1 year ago - 3 comments

#58 - prepareDatabase('accessionTaxa.sql') downloading names and nodes with getnamesandnodes() error:

Issue - State: closed - Opened by xuxia10 over 1 year ago - 9 comments

#57 - Error in downloading database using prepareDatabase

Issue - State: closed - Opened by sxh1136 over 1 year ago - 9 comments

#56 - accessionToTaxa returns a single NA when the input contains too many accession ID

Issue - State: closed - Opened by Ilaria-Pirona over 1 year ago - 3 comments

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

Issue - State: closed - Opened by Ilaria-Pirona over 1 year ago - 5 comments

#54 - Questions for the issue of taxonomizr package being terminated during operation

Issue - State: closed - Opened by kejsh1320 over 1 year ago - 1 comment

#53 - Get all bacterial species

Issue - State: closed - Opened by mweberr almost 2 years ago - 2 comments

#52 - Error in preparing accessionTaxa.sql with prepareDatabase()

Issue - State: closed - Opened by sbresnahan almost 2 years ago - 10 comments

#51 - Manual preparation of database

Issue - State: closed - Opened by sankadinesh almost 2 years ago - 1 comment

#50 - error: no such column: tmp.query.accession

Issue - State: closed - Opened by ewelinarubin almost 2 years ago - 1 comment

#49 - Assignment of taxonomy to blast hits

Issue - State: closed - Opened by simang5c almost 2 years ago - 1 comment

#48 - read.names.sql for common names

Issue - State: closed - Opened by meixilin about 2 years ago - 2 comments

#47 - FR: set a variable with default path for the databases

Issue - State: closed - Opened by splaisan about 2 years ago - 5 comments

#46 - Preparing SQL for only specific taxa

Issue - State: closed - Opened by NenBarto about 2 years ago - 7 comments

#45 - `accessionToTaxa` function not converting accession numbers to taxIDs?

Issue - State: closed - Opened by jiwoonp about 2 years ago - 7 comments

#44 - error: 'Query and SQL mismatch'

Issue - State: closed - Opened by sumitra20 over 2 years ago - 6 comments

#43 - get taxID for a huge list of accesion numbers

Issue - State: closed - Opened by sumitra20 over 2 years ago - 1 comment

#42 - sql 4 protein accession: "Error in connection_import_file"

Issue - State: closed - Opened by ferreirafm over 2 years ago - 4 comments

#41 - Disk is full (and moving tmp location doesn't solve it)

Issue - State: closed - Opened by Aron-github over 2 years ago - 10 comments

#40 - Kingdom bacteria only

Issue - State: closed - Opened by mweberr over 2 years ago - 2 comments

#39 - AccessionToTaxa error in file.remove(tmp)

Issue - State: closed - Opened by pollingmarcel over 2 years ago - 4 comments

#38 - accession2taxid ftp

Issue - State: closed - Opened by mweberr over 2 years ago - 4 comments

#37 - I can't match the accession number with taxa ID

Issue - State: closed - Opened by vini8cs over 2 years ago - 5 comments

#36 - Error: no such table: main.names

Issue - State: closed - Opened by showteeth over 2 years ago - 4 comments

#35 - getAccession2taxid(types='prot') download old files

Issue - State: closed - Opened by ZexuanZhao almost 3 years ago - 5 comments

#34 - Problem with Convert names, nodes and accessions to database

Issue - State: closed - Opened by SergeyBaikal over 3 years ago - 8 comments

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

Issue - State: closed - Opened by elaine-shen over 3 years ago - 9 comments

#32 - shift ncbi urls from ftp to https protocol

Pull Request - State: closed - Opened by wanjauk over 3 years ago - 5 comments

#31 - Error in readBin while reading .gz files

Issue - State: closed - Opened by Eliot-RUIZ over 3 years ago - 9 comments

#30 - All taxonomic levels

Issue - State: closed - Opened by dleopold over 3 years ago - 3 comments

#29 - Error in accesion to taxa

Issue - State: closed - Opened by lcamVz over 3 years ago - 3 comments

#28 - read.accession not working; preparedatabase failed

Issue - State: closed - Opened by lcamVz over 3 years ago - 3 comments

#27 - 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'

Issue - State: closed - Opened by David-Madrigal over 3 years ago - 11 comments

#26 - read.accession2taxid failing

Issue - State: closed - Opened by dleopold over 3 years ago - 3 comments

#25 - Error Reading in prot.accession2taxid.gz file

Issue - State: closed - Opened by jnicholls01 over 3 years ago - 6 comments

#24 - accessionToTaxa error

Issue - State: closed - Opened by RaulLanda over 3 years ago - 2 comments

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

Issue - State: closed - Opened by catcatzilla almost 4 years ago - 1 comment

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

Issue - State: closed - Opened by wjj666 almost 4 years ago - 3 comments

#21 - Can't find nodes table?

Issue - State: closed - Opened by aminards almost 4 years ago - 2 comments

#20 - Error with prepareDatabase: RS_sqlite_import: expected 3 columns but found 4

Issue - State: closed - Opened by MaikeHu almost 4 years ago - 1 comment

#19 - Database or disk is full error

Issue - State: closed - Opened by ptskidmore almost 4 years ago - 3 comments

#18 - Input and output vector have different lengths, and vectors can't have named values

Issue - State: closed - Opened by shiraz-shah about 4 years ago - 4 comments

#17 - Convert taxon structure to newick format

Issue - State: closed - Opened by mweberr over 4 years ago - 22 comments

#16 - Function distance between taxons

Issue - State: closed - Opened by mweberr over 4 years ago - 5 comments

#15 - Unable to covert genbank IDs to lineage

Issue - State: closed - Opened by sankadinesh almost 5 years ago - 7 comments

#14 - Error from read.names.sql

Issue - State: closed - Opened by kgun12 about 5 years ago - 3 comments

#13 - Error in result_create(conn@ptr, statement) : no such table: ...

Issue - State: closed - Opened by raerickson over 5 years ago - 2 comments

#12 - nucl_est.accession2taxid.gz unavailable

Issue - State: closed - Opened by swuyts over 5 years ago - 17 comments

#11 - Error prepareDatabase

Issue - State: closed - Opened by cgandini almost 6 years ago - 2 comments

#10 - accession number not matching with taxa ID

Issue - State: closed - Opened by ngeraldi almost 6 years ago - 9 comments

#9 - Merge sqlite branch into main

Pull Request - State: closed - Opened by sherrillmix about 6 years ago - 2 comments

#8 - accessionToTaxa not matching

Issue - State: closed - Opened by ngeraldi over 6 years ago - 3 comments

#7 - Memory Required?

Issue - State: closed - Opened by chasemc over 6 years ago - 3 comments

#6 - matching old accession number

Issue - State: closed - Opened by ngeraldi over 6 years ago - 3 comments

#5 - Error: Problem creating sql file. Deleting. Error in rsqlite_import_file(conn@ptr, name, value, sep, eol, skip) : RS_sqlite_import: /tmp/RtmpFiCHWM/file7bfd7d94f1c3 line 249184308 expected 2 columns of data but found 1 In addition: There were 50 or more warnings (use warnings() to see the first 50)

Issue - State: closed - Opened by lychen83 over 6 years ago - 8 comments

#4 - read.names failing to read in names.dmp table

Issue - State: closed - Opened by afkoeppel over 6 years ago - 3 comments

#3 - read.accession2taxid error creating SQL file: malformed line

Issue - State: closed - Opened by Talitrus over 6 years ago - 8 comments

#2 - Error: with NC_ (accession numbers starting with NC)

Issue - State: closed - Opened by alizohaib7 over 7 years ago - 3 comments

#1 - Error: read.accession2taxid(list.files('.','accession2taxid.gz$'),'accessionTaxa.sql')

Issue - State: closed - Opened by alizohaib7 over 7 years ago - 3 comments

GitHub / sherrillmix/taxonomizr issues and pull requests