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  • RepeatMasker output

    Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a separate option to save the output?

  • #2
    Can you find a file named *.log2?
    I advise you to check it and make sure that there is no error message in it. Or can you provide the command line you use?

    feixue1039

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    • #3
      Thanks for your reply - I can't find a *.log2 file either

      I ran it as follows: RepeatMasker ../../H99index/H99+mito.fa -lib output_repeats.fa
      Then I added the -dir . and some extra output options, -a and -small, to see if that helped, but still nothing. It appears to run fine without throwing any errors, and I can see the files it makes as it runs but when it finishes this all disappears

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      • #4
        I guess there was never a reply to this problem

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        • #5
          When I run it, it saves the output files to the same directory as the input files are in. So I would guess you have an error along the way.
          --------------
          Ethan

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          • #6
            I found it was because I hadn't given the -species option, works fine now

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