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grunwaldlab / effectR

An R package to call oomycete effectors
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Mafft alignment failed to save #24

Open ALongmuir01 opened 3 years ago

ALongmuir01 commented 3 years ago

I'm trying to run effectR to search for RXLR effectors. When I run the hmm.search function it runs the mafft alignment but then fails to run hmmer because there's not alignment file found. I have tried this again with the test infestans files included and it's still not working. This is my work flow:

> fasta.file <- system.file("extdata", "test_infestans.fasta", package = "effectR")
> ORF <- seqinr::read.fasta(fasta.file)
> REGEX <- regex.search(ORF, motif="RxLR")
> candidate.rxlr <- hmm.search(original.seq = fasta.file, regex.seq = REGEX , alignment.file=NULL, save.alignment=T, mafft.path = "c:/mafft/", hmm.path = "c:/Users/alongmuir/Documents/hmmer3.0_windows/")

The alignment is then printed to the console, no candidate.rxlr file is made and then I get the following message:

MAFFT alignment finished!
Starting HMM
---
Creating HMM profile

Error in hmm.search(original.seq = fasta.file, regex.seq = REGEX, alignment.file = NULL,  : 
  No MAFFT alignment found

I'm not sure if I'm doing something wrong here. Any help would be appreciated.

Tabima commented 3 years ago

Hi,

It seems to be that the path for either MAFFT or HMMER are not correctly specified. Make sure that MAFFT is at the c:/mafft/ path, also try and remove the last backslash (i.e. c:/mafft). Same with HMMER.

In addition, if you have problems after you test the new paths and make sure the programs are running correctly (as mentioned in the README file of effectR), can you send me a more comprehensive summary of the output of the run, pleas?