I seem to be missing something obvious, but I have a read (actually lots of reads, it's just an example) that shouldn't be filtered by bbduk.sh based on average quality, but it is.
@NZ_AP014881.1_0_0/2 TGCAGCATTCTCCTGATGGCGGTCTTGATGAAGAGCTTTGTTACGGGGGTCATCCTCATCCATCAGGTCTGGTGCAGAAATAAAGCGCAAAGGCTTGGGGTTACCGCCTGCGCGCATGTCTGCCAGCATATCCTCTAGCGCGGCAGGCTCTGGGCAATTAATCTCAATCTGCTGACGGTCAGACTTTGGCAAATTGAGCAGGCGGTTGCGGGCCGACGTATCCAAAAGGCGATTGCACCAGCGCTGAACACGATATCCCGGACGATCTGGTAGCTGTTCTTCTTCCAGTTCCTCACGCAGA + <CCCCEGG6GGGGF,GEGGGC,FFGFFFCEGGCGGGGG@GGFCGGC<FCGGGGEFGFGGF@GCG,GGG@GGGGGG<GEGFGFGGGEGGFAEEC<GGGGFFFEECD<EFGGF8<G5GGGCDBGFFGEG<GCGFECG+FCGF,CC=,*DF5=,9<7C4E:EF,,=B@CGF>:GGECGG;;8G>C1,:,C:+E,9,FF<@,*6:,793G,4+13G*7*;3*=@6C7/85+C59C+<>***2C)*1*/**))<+<2)+**)4/)A)>)1+2)**51065.:091>1***0*)*).0+*(*2*90.
bbduk.sh in1=test.fq out1=test_out.fq maq=20
Bbduk version is Version 38.46. Average quality of the read seems to be ~27. Hope someone can help, thanks in advance.