make.contigs was successful, generating 2 large files stability.trim.contigs.fasta (1,900,000 kb) and stability.trim.contigs.qual (5,113,816 kb), although the other 3 files stability.contigs.report, stability.scrap.contigs.qual, and stability.scap.contigs.fasta are all 0 kb.
I moved on anyway, and was halted after the count.seqs step, because stability.trim.contigs.good.fasta has 0 kb.
I had thought it was my file names (stability.file). Tried changing that a couple times, but the same problem keeps coming up.
Really confused and stuck. Please help. Thank you!