Originally posted by SylvainL
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Code:
$ bbmap/bbduk.sh in=nn.fq out=stdout.fq mm=f hdist=0 edist=0 ktrim=l rcomp=f k=29 literal=CAACAGCAATATACCTTCTCGAGAGGTCT java -Djava.library.path=/path_to/bbmap/jni/ -ea -Xmx19498m -Xms19498m -cp /path_to/bbmap/current/ jgi.BBDukF in=nn.fq out=stdout.fq mm=f hdist=0 edist=0 ktrim=l rcomp=f k=29 literal=CAACAGCAATATACCTTCTCGAGAGGTCT Executing jgi.BBDukF [in=nn.fq, out=stdout.fq, mm=f, hdist=0, edist=0, ktrim=l, rcomp=f, k=29, literal=CAACAGCAATATACCTTCTCGAGAGGTCT] BBDuk version 36.84 Initial: Memory: max=19594m, free=19185m, used=409m Added 1 kmers; time: 0.043 seconds. Memory: max=19594m, free=18469m, used=1125m Input is being processed as unpaired Started output streams: 0.018 seconds. @test CTGTCCACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTC + FGGGCEGGGGIIIIIIIIIIIIIIIIGIIIIIIIIIIIIIGIIGFIIFIIIIIII Processing time: 0.006 seconds. Input: 1 reads 100 bases. KTrimmed: 1 reads (100.00%) 45 bases (45.00%) Total Removed: 0 reads (0.00%) 45 bases (45.00%) Result: 1 reads (100.00%) 55 bases (55.00%) Time: 0.076 seconds. Reads Processed: 1 0.01k reads/sec Bases Processed: 100 0.00m bases/sec
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