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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?
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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 -
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 disappearsComment
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I guess there was never a reply to this problemComment
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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.--------------
EthanComment
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I found it was because I hadn't given the -species option, works fine nowComment
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