- all sequences in scrap

Good morning!
I’m trying to split my forward and reverse fastq files by sample for submission to SRA using an oligos file but all the sequences end up in the scrap files. I analyzed this data in v1.42.0 and have tried the command there as well as v1.43.0 and still no luck. When I ran make.contigs in the old version with the same exact files, the sequences worked just fine, so I’m kind of at a loss here.
Sam1-30_S13_L001_R1_001.fastq Sam1-30_S13_L001_R2_001.fastq, oligos=2016Snook_Map.txt, checkorient=t, qfile=F, fasta=F)

I’ve included a link to my file, oligos, and original logfile (from the make.contigs I ran in the previous version).

Any help would be greatly appreciated!

AndreaMothur files

Could you post the fastq files so I can track down the issue for you?

They should be in the drive link above now.
In the meantime, I was able to split them using the split.groups command and the groups file from the original make.contigs command. But any assistance would still be greatly appreciated!