Comments (3)
sherrillmix
commented on August 31, 2024
1
That's good it ended up working for you. The package has had a few hard to replicate reports of download problems lately e.g. #27. Not sure what's causing them but I think when I get a chance I'll add an automatic md5 check after the download to at least catch when they happen. Thanks for the bug report.
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sherrillmix
commented on August 31, 2024
A bit more output might be useful for debugging but that sounds like it may be a download problem. Could you redownload NCBI_DATABASE/nucl_gb.accession2taxid.gz and/or check to see that its filesize is close to the expected 8263483 KB or that its md5 matches:
ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz.md5
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lcamVz
commented on August 31, 2024
Thank you for the quick reply.
I manually download them from the ftp and it worked I used wget -i list.txt to get all of the nucleic and protein.
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Related Issues (20)
- Disk is full (and moving tmp location doesn't solve it) HOT 10
- sql 4 protein accession: "Error in connection_import_file" HOT 4
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- `accessionToTaxa` function not converting accession numbers to taxIDs? HOT 7
- Preparing SQL for only specific taxa HOT 7
- FR: set a variable with default path for the databases HOT 5
- read.names.sql for common names HOT 2
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- Questions for the issue of taxonomizr package being terminated during operation HOT 1
- Error: disk I/O error In addition: Warning message: Couldn't set synchronous mode: disk I/O error HOT 5
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- Error in downloading database using prepareDatabase HOT 9
- prepareDatabase('accessionTaxa.sql') downloading names and nodes with getnamesandnodes() error: HOT 9
- Error:database is locked with prepareDatabase HOT 3
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