mothur v8.0 merge.file bug


Version 8.0 for windows still has a bug with the merge.files command. Before (version7.0), it gave an error saying it couldn’t read multiple input files. Now it reads the files and combines them, but it looks like it’s leaving a strange character between the first data line of the second (and third, fourth, etc.) input file and after the last data entry in the second input file. The character is ÿ . This isn’t a major problem since I can use my text editor to do a find and replace to remove them. Unfortunately, it doesn’t leave a return at the end of the input files to note where the first input ends and the second begins (I’m assuming this character is supposed to be a new line symbol).

Again, you can get around this by making sure to leave a blank line at the end of each input file. I’m using it to merge multiple fasta files for individual samples (after running unique.seqs) and I’m not sure if it would cause a glitch if each sequence didn’t start on a new line (despite the “>” denoting a new sequence name).

Anyway, I just wanted to point this out since I posted about the previous bug. Please let me know if you have any advice or need additional information. Thanks.


I also get a special character inserted at the point where two files are joined by merge.files (running on Mac OS X), and this does cause problems later on. For example, the accession number immediately following that special character will be missed by some later processes, leading to a mismatch in the number of records between a group file and fasta file.

Thanks for reporting this. The strange character is the end-of-file character, and shouldn’t be copied into the new merged file.