make.contigs and demultiplexing

Hello,
I have a problem with make.contigs and demultiplexing. I have 2 .fastq files (one forward and one reverse) containing seqs from 40 samples.
After [mothur > make.contigs(file=stability.files, processors=8)] the assembly is fine but some of them are reverse complements.
I tried different versions of make contigs such as [mothur > make.contigs(ffastq=./SAMP1-40_S2_L001_R1_001.fastq, rfastq=./SAMP1-40_S2_L001_R2_001.fastq,oligos=./test.oligos, checkorient=t)] but again it does not seem to work since all sequences go to ‘./SAMP1-40_S2_L001_R1_001.scrap.contigs.fasta’.
Do you know how i could set the orientation of my contigs to always start from my barcodes and my forward primer?

Could you post your oligos file and a few sequence from your forward and reverse files?

here you can see two seqs
@M02542:38:000000000-ABF47:1:1101:19393:1063 1:N:0:2
ACATAAAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAANAAGCNNNNAGTNNGACTTTGGGTTGGGTCGCCCGGTCCGCCTTTGGTGTGNACCGNGCNGCTCNTCNCTAANGCCGGCGATGCGCTCCTGTCCTNAACTGGCNGGGTCGTGCCTCCGGTGCTGTNACTTTGAAGNAATTAGAGNGNTCAAAGCAAGNCNACGCTCNGNATACATTAGCNTNGGATAACATCATAGGATTTCGGNCCTATTACGTTGNCNTNCGGGATCGGAGTAATGNTT
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG#:DFG####::D##:CFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD#:BFG#:B#:BFF#:B#:B@F#:BFGGGGGGGGGGGGGGGGGGG#6@FGGGG#5@FGGGGGGGFGGGGGGGGGG#4=CFGGGGC#3=FEFGGF#3#3=CFDGGGG8#2#/2>EC8#*#*2:FFGGGGF#2#2:CFGFGGGGFFGFGFFGGFG>#.1>DFFFF>FF5#,#.#(.8?FE@GFBFFFFA)#-4
@M02542:38:000000000-ABF47:1:1101:12170:1063 1:N:0:2
GAACCCAAACACTTTGGTTTCCCGTAAGGCGCCGAATGAGTCATTAAAAATTAACATCATNCGATNNNNAGTNNGCATAGTTTATGGTTAAGACTACGACGGTATCTGATCNTCTTNGANCCCCNAANTTTCNTTCTTGATTAATGAAAACATCCNTGGCAAANTCTTTCGCAGTAGTTAGTCTTNAATAAATCCNAGAATTTCACNTCTGACAATTNANTACTAATGNCCCCAACTATNCNTATTAATCATTACGTCGATCTTAGAAACCAACAAANTNANATCAAACGTCCTATTTNAT
+
CCCCCGGGCFGGGFGGGFGGGGGGGGEFGGGGGGGGGGGDEFFGGGFFGGGGFGGGGCFG#:CF@####96:##:::CCCFGGGGGGFFGGEFGGGGDGGGGGGGFEFGGG#+:DF#::#:BFG#:B#:BDD#:BFFG9FGGGDFFFGGGGFGGG#8<DFCEF#+:@FDFGGGCFGGFEFGAFGG#64D@GGGGD#5>D@FECFGG#16DFFGGGGC#6#*49=<CG,#4=7FGGGGC;#2#/2>FFFCDFG#(#0#–83<4?E>F??BFFB#(-

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And here is the .oligos
primer CAGCCGCGGTAATTCCAGCT CAGCCGCGGTAATTCCAGCT
BARCODE ACACTGTC ACACTGTC D2.1.ns31
BARCODE ACACTTGC ACACTTGC D2.2.ns31
BARCODE ACAGAAAA ACAGAAAA D2.3.ns31
BARCODE ACAGAGAG ACAGAGAG D2.4.ns31
BARCODE ACAGATTG ACAGATTG D2.5.ns31
BARCODE ACAGCAAA ACAGCAAA D2.6.ns31
BARCODE ACAGCGAG ACAGCGAG D2.7.ns31
BARCODE ACAGCGGC ACAGCGGC D2.8.ns31
BARCODE ACAGCTTG ACAGCTTG D2.9.ns31
BARCODE ACAGGCCA ACAGGCCA D2.10.ns31
BARCODE ACAGTCTT ACAGTCTT D2.11.ns31
BARCODE ACAGTGCG ACAGTGCG D2.12.ns31
BARCODE ACATAAAG ACATAAAG D2.13.ns31
BARCODE ACATCACC ACATCACC D2.14.ns31
BARCODE ACATCCCG ACATCCCG D2.15.ns31

In total we have 40 samples but only 2 fastq files

As you will see the first sequence corresponds to sample D2.13.ns31 but the second sequence starts from the reverse primer.

As a result half of my contigs start with the reverse primer(no barcode) and I cannot demultiplex

Thanks a lot!