> Fatal Error: "cotton_in.solexa.fasta" Well, there indeed is no such file in the directory listing you gave, so mira correctly could not find it: your listing shows a "cotton.fasta" and a "cotton.fastq". Why didn't you name one of the files as shown in the walkthrough? Regards, Bastien PS: I also notice that there is no FASTA quality file belonging to the FASTA. You should always have a quality file. PPS: Or use the fastq as input (that is, if it contains the same data as the fasta)