make.contigs scrap output

Hello,
I’ve assembled my v4 reads (MiSeq - 2x300bp) using make.contigs with the following oligos file

primer GTGBCAGCMGCCGCGGTAA GGACTACHVGGGTWTCTAAT v4

My reads have had the index and barcodes removed - but still include primer sequence
I run the command including pdiffs=2, trimoverlap=T

Everything runs fine but I have a question regarding the scrap output (here are a few suspicious ones):

M04603_48_000000000-ATNCR_1_1101_10759_1985 | f fbdiffs=0(match), rbdiffs=0(match) fpdiffs=1(match), rpdiffs=2(match)
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGTCGTAAANCGCGNNCAGNCNGATCNGTCAGTCTGTCTTAAAAGTTCGGTGCTTAACCCCGTGATNGGATGGAAANTNCCAATCTAGAGTATCGNAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATNNGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGNGCGAAAGNCAGGGGAGCGAACGGG

M04603_48_000000000-ATNCR_1_1101_23439_1994 | f fbdiffs=0(match), rbdiffs=0(match) fpdiffs=2(match), rpdiffs=1(match)
CGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACACCCCTCCCNAATAAANCTAAAACTCANCTNAGTTGTAAAAAACTCCAGTTNACACAAAATAGACTACGAAAGTGNCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGG

M04603_48_000000000-ATNCR_1_1101_10238_2844 | f fbdiffs=0(match), rbdiffs=0(match) fpdiffs=2(match), rpdiffs=2(match)
GAGAACAATCTGCTCCAAAATAGAAATAGTGCCCAGAGTGAGAAACCCTGCTCTACAAACCCTACAGTGTACAGGCCAGCCGCCACATCAGAGAATAATCTGCNCCAAACTAGAAATAGTGCCCAGAGTGAGAAACCCTG

fpdiffs and rpdiffs all appear to pass the pdiffs cut off - yet they still don’t make it into the “trim.contigs” file. Also, why do I get an “f” code when my forward primer is a perfect match? Is there another default filter parameter I’m missing?

Thanks

I think it’s because pdiffs = fpdiffs + rpdiffs and your’s are all above 2, which is what you set. Incidentally, those sequences would get chucked because they have N’s in them.

Also, you may be interested in this post, if you are trying to use V3 chemsitry:

http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix/