I am trying to use SSPACE for scaffolding, but get stuck at the very first step: somehow SSPACE cannot read my file or else I am not sure what leads to this error:
ERROR: Invalid file in library Lib1: ~/Desktop/RawSequences/Fastq/3kbFor_pair2.fastq -- fatal
It can't be the file itself, I am using bwa for the alignment step and doing the aligning step separately works just fine.
Anyone have any ideas??