Hi everyone,
I am using bio3d package for some sequence analysis because of its nice
integrated MUSCLE execution. However, I have been encountering some errors
while I was running seqaln function, which calls for installed MUSCLE program.
In my case, I stored the MUSCLE program on the desktop with pathway of
"./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from
terminal. However, when I'm calling the exepath in R, it keeps giving me error
messages. Below are some errors I have encountered. Your help will be much
appreciated.
> aa<-read.fasta("./R/test.fa", rm.dup=F)
> aln<-seqaln(aa, exepath="/Users/Fan/Desktop/muscle/src/muscle",
> file="aa_muscle.fa", protein=T)
/Users/Fan/Desktop/muscle/src/musclemuscle -in
/var/folders/v9/v95dzKP2E9SAkmd7m4T8dE+++TQ/-Tmp-//RtmpKUJVlZ/file618fb492 -out
aa_muscle.fa -stable -seqtype protein/bin/sh:
/Users/Fan/Desktop/muscle/src/musclemuscle: No such file or directory
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
cannot open file 'aa_muscle.fa': No such file or directory
I have also noticed that the example file from bio3d/seqaln does not have
quotation marks for the exepath. But it returned a different error message.
> aln<-seqaln(aa, exepath=/Users/Fan/Desktop/muscle/src/muscle,
> file="aa_muscle.fa", protein=T)
Error: unexpected '/' in "aln<-seqaln(aa, exepath=/"
or > aln<-seqaln(aa, exepath=Users/Fan/Desktop/muscle/src/muscle,
file="aa_muscle.fa", protein=T)
Error in paste(exepath, "muscle -in ", toaln, " -out ", file, " ", extra.args,
:
object 'Users' not found
Thank you for your help ahead of time!
Best wishes.
Fan
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