cannot run :(

[pavlo888]

Hi,

First off, this looks like a great package! I am excited to use it. However, I cannot make it work :(

After a successful install, I run the following command

`
library(devtools)
library(cognac)
library(reticulate)

use_condaenv("cognac") #activate cognac env that includes MAFFT and CD_HIT

algnEnv = cognac(
fastaDir = "/Users/pablo/Downloads/cognac_fasta/",
featureDir = "/Users/pablo/Downloads/cognac_gff/",
threadVal = 4
)
`

But then I get the following error:

sh: cd-hit: command not found Error in ParseCdHit(cdHitClstrFileName, FALSE, minGeneNum, geneEnv) : Cannot open the cd-hit results... In addition: Warning messages: 1: In CreateCognacRunData(geneEnv, featureFiles, fastaFiles, faaPath) : Warning: No coding genes were able to be translated for 2_Ar_NCPPB2659_lane2_K85 2: In system(cdHitCmd) : error in running command

I am not sure what is going on since I made a specific environment with the dependencies for cognac using conda and then activated the environment in RStudio.

Any suggestion on how to deal with this issue?

Cheers,
Pablo

[rdcrawford]

Hi Pablo,

Sorry to hear you're having trouble. Looks like there was an error running cd-hit. In the "temp_cognac_files" created in your working directory for this project, there will be a file called "cdHit.log." Could you upload that here so I can see what went wrong?

Thanks,
Ryan

[pavlo888]

Hi @rdcrawford

Thanks for coming back to me. I have checked the file you requested and it is blank. There is nothing on the file. I cannot upload it here because the file is empty. On the other hand, there is a file called removed_genomes.tsv and there I can see my first genie of the list and a comment that reads "failed parsing data".

It might have something to do with the cd-hit and mafft in the environment? I mean, as far as I understand, both packages are installed in the Conda environment but to be honest I have never tried this Conda/R combination. Or maybe you know a way to install those packages directly on R or something?

Cheers,
Pablo