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sherrillmix / taxonomizr

Parse NCBI taxonomy and accessions to find taxonomic assignments
GNU General Public License v2.0
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sql table failed to generate and I can't delete it to try again #68

Closed maxfarrell closed 1 month ago

maxfarrell commented 1 month ago

I got the error: Error: no such table: accessionTaxa so am trying to re-download the database. However, R seems to think it already exists. I deleted the source files in my tmpDir, but I can't seem to locate the .sql file (it's not in my set tmpDir), so I'm stuck.

Any advice on removing the .sql file so I can start again?

sherrillmix commented 1 month ago

You might need to provide a bit more detail, e.g. the exact commands and output you are running, but if I'm understanding things correctly the .sql file should be whatever you set as the first sqlFile argument to prepareDatabase() so XXX.sql in prepapreDatase('XXX.sql') or nameNode.sqlite by default. That'll be in your working directory (getwd()) by default.

maxfarrell commented 1 month ago

Hi - apologies for the lack of detail before.

I had trouble with the default call prepareDatabase('accessionTaxa.sql') so ammended it to use a local temp directory, and use the http protocol: prepareDatabase('accessionTaxa.sql', tmpDir = "../intermediate/", resume=TRUE, protocol='http')

Unfortunately the 'accessionTaxa.sql' object wasn't in my working directory after I made the first attepmt, hence my issue.

I'm now attempting to re-download the database by calling it 'accessionTaxa2.sql' and it is currently re-downloading, but if you have any other insights as to why the earlier error came up, I'd be glad to hear it.

sherrillmix commented 1 month ago

That does seem weird. Perhaps some sort of directory mismatch? Hopefully it's working for you now. I'm going to close issue but feel free to reopen if still a problem.