merge.sfffiles error


I have downloaded some .sff files from a test dataset off the ENA and am trying to merge them using the merge.sfffiles command but mothur doesn’t seem to recognise them. For example, the error message “[WARNING]: can’t find …/mothur/454Reads.N26~40.sff, ignoring.
Unable to open 454Reads.N26~42.sff. Trying default …/mothur/454Reads.N26~42.sff” comes up.

Please can you advise?


I suspect one of two things is happening. First, we commonly see this type of error when the file isn’t really in the folder you think it is. Can you run system(ls) from your mothur prompt? Second, the ~ character might be causing problems. Can you change the file name by removing that character and try again with the new file name?

Thank you Pat.

You were right- changing the file name to remove the ~ character allowed the command to work.