I’m getting unknown file format errors when I run make.contigs on .gz fastq. I’ve gotten this error in 1.40.1 (centos server) and 1.40.3 (both mac and linux desktop)
Thanks for reporting this issue. We are working on a fix. In the meantime, you can workaround the problem by decompressing your files and running them as fastq files. You can follow the progress on the fix on github here, https://github.com/mothur/mothur/issues/462.