I made the list.files file using the names of the fastq files. I then do the make.contigs command and it goes on until it stops at some Errors:
Could not open ./Schloss\P\Oyster-Oakland-17_S17_L001_R1_001.1ffastatemp
Could not open ./Schloss\P\Oyster-Oakland-17_S17_L001_R1_001.1fqualtemp
And so onâ€¦ additionally I canâ€™t seem to find these files in the folder, perhaps they werenâ€™t made correctly or at all?
This presents a problem later on when these reads are skipped because it couldnâ€™t find a pair. So it skips a lot of contigs and then crashes.