Problem with merge.files


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.


I can confirm that this bug exists in Mothur 1.7.2 for PC but NOT for 1.7.2 linux.
In the interim, Cygwin’s cat command has no such bug. Nor does:

copy source1 + source2 + source3 destination

under either DOS or as a system call within Mothur if you don’t have Cygwin installed.

Thanks for bringing this problem to our attention. It will be fixed in version 1.8.