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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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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