Benjamin Buchfink
Benjamin Buchfink
You can use the output fields `salltitles` for the full length subject title and `sscinames` for the taxon names. The database needs to be built with taxon info included, see...
You probably need to create such a database yourself.
You need to use the --taxonmap and --taxonnames options.
UniRefXX_ prefixes are removed from accessions, that is the current behaviour. Not 100% sure if that is ideal. It should be documented in any case, sorry.
It also removes `gi|` prefixes that were included in older ncbi databases. This is the complete code for the parsing: ```c++ string get_accession(const string &title) { size_t i; string t(title);...
No problem, this should do the trick: c7b19e96b7b49075cf667bd6a88d5306ae6961a7 You also need to run makedb again when using this for taxonomy mapping.
prepdb is only available when the tool was compiled with blast database support. For this you can download the github release binary or compile yourself from source.
Have you tried to repeat the computation, does the error happen frequently? Can you show me your command line and diamond version?
An example file that produces the error would be helpful. My email is [email protected].
I've been aligning your file against the nr database, it's still running but no error so far. It may not be reproducible on my system. One thing you could try...