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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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recommended parameter causes error #114

Closed mmp3 closed 3 years ago

mmp3 commented 3 years ago

The command:

$ carve --dna genome.fa

produces the following warning message amongst its output to the console:

The host system is detected to have 133 GB of RAM. It is recommended to use this parameter for better performance:
 -c1

However, adding the proposed parameter -c1 to the command results in an error:

$ carve --dna genome.fa   -c1
carve: error: unrecognized arguments: -c1
cdanielmachado commented 3 years ago

That warning is coming from diamond, not from CarveMe.

To pass along additional parameters to diamond you can do the following:

$ carve --dna genome.fa --diamond-args "-c1"