I think I see the problem - you're using the wrong file name for the reads:
bbduk.sh in=interleaved.gz out=trimmed.fq.gz ktrim=r k=23 hdist=1 mink=11 tpe tbo minlen=90 ref=truseq.fa.gz,nextera.fa.gz
bbmap.sh maxindex=200 in=trimmed.fq.fq mhist=mhist.txt bhist=bhist.txt qhist=qhist.txt qahist=qahist.txt
...
Reads Used: 0 (0 bases)
Normally, BBMap should throw an exception saying it can't find the input file if it does not exist, so I assume there is an empty file named "trimmed.fq.fq".
bbduk.sh in=interleaved.gz out=trimmed.fq.gz ktrim=r k=23 hdist=1 mink=11 tpe tbo minlen=90 ref=truseq.fa.gz,nextera.fa.gz
bbmap.sh maxindex=200 in=trimmed.fq.fq mhist=mhist.txt bhist=bhist.txt qhist=qhist.txt qahist=qahist.txt
...
Reads Used: 0 (0 bases)
Normally, BBMap should throw an exception saying it can't find the input file if it does not exist, so I assume there is an empty file named "trimmed.fq.fq".
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