You were correct. The assembly seems to be running as normal after deleting the specification for the "qual" file in the manifest file. Thanks J From: Bastien Chevreux <bach@xxxxxxxxxxxx> Reply-To: <mira_talk@xxxxxxxxxxxxx> Date: Monday, 29 October, 2012 5:41 PM To: <mira_talk@xxxxxxxxxxxxx> Subject: [mira_talk] Re: Manifest file input error On Oct 29, 2012, at 15:21 , Jackie Lighten <jackie.lighten@xxxxxx> wrote: > ³Fatal error (may be due to problems of the input data or parameters): > "Some errors occured during loading phase, please check the log." > [?] > data=winterANDacadian_in.454.fasta winterANDacadian_in.454.fasta.qual > [?] > Any ideas what I am doing wrong? Hmmm ? you should have checked (or send along) the output log as normally MIRA will have given a detailed diagnostic of what it did not like. That being said: I *think* it's the ".qual" file ? it may be that I told MIRA to automatically load .qual files for every .fasta file it finds, but I think the manifest loader did not expect to be given .qual files per se. Maybe I should change that. Please tell whether my guess was correct. B.