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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Failed to run diamond #47

Closed lavik17 closed 5 years ago

lavik17 commented 5 years ago

When running: carve genome.faa I get this error : Failed to run diamond. However, I have diamond installed :

which diamond
/opt/bin/bio//diamond

When executing

diamond --help
diamond v0.8.34.96 | by Benjamin Buchfink <buchfink@gmail.com>
Check http://github.com/bbuchfink/diamond for updates.
Syntax: diamond COMMAND [OPTIONS]
...

I've also tried a newer version of diamond (v0.9.24.125). I tested python -c 'import subprocess; subprocess.call(["diamond", "help"])' and it seems to work just fine

cdanielmachado commented 5 years ago

Can you please run: carve genome.faa -v ?

lavik17 commented 5 years ago

ok, thanks to the -v flag I found that CarveMe was looking in the wrong place. I've uninstalled carveme and reinstalled and now it finds the correct location of diamond.