Comments (1)
Tabima
commented on July 20, 2024
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?
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Related Issues (19)
- Create tests
- add biblio on vignette
- Adapt shiny app
- Replace perl one-liners with R equivalent? HOT 2
- Testing package in windows HOT 3
- Tests fail when mafft is not installed. HOT 2
- System which calls HOT 1
- CRAN issues HOT 13
- Consider adding a few more examples of pathogen effectors HOT 2
- Add a column with the length of the effectR candidate in effector.summary
- Separation of MAFFT and HMM search HOT 3
- Issue related to HMM threshold HOT 1
- HMM failed, please supply a valid absolute path to ORFs HOT 18
- Regarding regex pattern
- Regarding regex pattern HOT 1
- Fatal exception (source file esl_buffer.c, line 1599): zero malloc disallowed HOT 1
- custom pattern not giving domain positions HOT 2
- Close this "Does not find CRN domains in P. infestans proteome"
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