Ah! You have "out1m" rather than "outm1". Hmmm, maybe I should make that also acceptable.
Incidentally, in most case you can just write this: "outm=matched#.fq" which will be translated to "outm=matched1.fq outm2=matched2.fq", to shorten the command lines. You can do that for input also.
Incidentally, in most case you can just write this: "outm=matched#.fq" which will be translated to "outm=matched1.fq outm2=matched2.fq", to shorten the command lines. You can do that for input also.
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