RepeatMasker -> file *.fa.log

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8.7 years ago

Sarah ▴ 10

Hello,

After running RepeatMasker I obtain in the file.fa.log file: No. words: 1200; after pruning: 908

This is my command line:

perl RepeatMasker -engine crossmatch -nolow -norna -species human -no_is file.fa -species human -gff

Anyone got any suggestions?

Thanks in advance

repeatmasker • 2.1k views

ADD COMMENT • link updated 17 months ago by Ram 43k • written 8.7 years ago by Sarah ▴ 10

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did you get other output besides the file.fa.log file?

ADD REPLY • link 8.7 years ago by nterhoeven ▴ 120

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I obtain these other files: file.fa.cat, file.fa.masked, file.fa.out, file.fa.out.gff, file.fa.tbl

The contained of these files seems correct

ADD REPLY • link updated 17 months ago by Ram 43k • written 8.7 years ago by Sarah ▴ 10

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Maybe "No. words: 1200; after pruning: 908" is a status message from the crossmatch engine. I never got some output like that when using RepeatMasker, but I also did not use the crossmatch engine...

ADD REPLY • link 8.7 years ago by nterhoeven ▴ 120

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Indeed, when I use ncbi engine, I don't obtain the message.

Thanks

ADD REPLY • link 8.7 years ago by Sarah ▴ 10

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