I tried to use merge.files to combine/concatenate multiple fasta files into one new file. Unfortunately, it won’t read past my first file. For example, when I give it the command “merge.files(input=fileX-fileY-fileZ, output=fileXYZ)” it gives me the message “could not opent fileY” and “could not open fileZ”. It only outputs the data in fileX into the output. It doesn’t matter the order I enter the files either. If I typed “fileZ-fileY-fileX” it’s only able to access the first file (fileZ in this cases).
This has been consistent across several tests with different files, so I think it’s a bug. My files are simple tab-delimited formatted fasta files, so I don’t understand why mothur can’t open them. I can open them fine in a text editor and there aren’t any strange characters. I also don’t have my filename extensions hidden, so I’m entering the correct filename.
I’m running mothur off a windows based pc. Can someone look into this glitch? Thanks.