Originally posted by sst
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Originally posted by hugh_hang View Postthank you, but what does the '--' means? just make the bash know the GFF file as stdin?
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Originally posted by sst View PostYou need to terminate your list of HMMs with two minus signs ('--') to separate them from the GFF input:
$ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm -- test.gff test > gff3result.txt
Adding an additional option afterthe HMM list should be fine as well -- just make sure the GFF file and HMMs do not immediately follow each other.
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Originally posted by hugh_hang View PostHi, I'm a genometools user, I'm here to report a problem (or maybe bug) when I was using ltrdigest on Ubuntu 10.04
I invoked command as follow:
$ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm test.gff test > gff3result.txt
and it returned error as follow:
gt ltrdigest: error: missing argument
Usage: gt ltrdigest [option ...] gff3_file indexname
I checked every directory and find nothing unusual. Would someone please help me find out what was wrong.
Thank you
$ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm -- test.gff test > gff3result.txt
Adding an additional option afterthe HMM list should be fine as well -- just make sure the GFF file and HMMs do not immediately follow each other.
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Originally posted by htetre View PostHello,
I am using genometools and yesterday when using suffixerator I was provided an error message of illegal characters. When I opened my fasta file in Textwrangler and checked for the invisibles to be shown this is what I saw:
>ˇ˛C?o?n?t?i?g?2?_?c?1?6?6?6?
?T?T?G?T?G?T?T?T?T?T?A?G?T?T?T?A?T?T?G?C?A?T?T?T?T?A?G?A?A?A
?A?A?G?T?C?A?T?T?T?T?T?G?T?G?T?T?T?T?T?G?T?C?C?A?T?T?A?C?G?T
?T?T?T?A?C?G?T?A?T?T?T?G?A?G?T?T?T?T?C?G?A?T?
looks like the file is corrupt? And it continues this way everytime I download.
Is there a program or something I can do to fix the file?
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Hello,
I am using genometools and yesterday when using suffixerator I was provided an error message of illegal characters. When I opened my fasta file in Textwrangler and checked for the invisibles to be shown this is what I saw:
>ˇ˛C?o?n?t?i?g?2?_?c?1?6?6?6?
?T?T?G?T?G?T?T?T?T?T?A?G?T?T?T?A?T?T?G?C?A?T?T?T?T?A?G?A?A?A
?A?A?G?T?C?A?T?T?T?T?T?G?T?G?T?T?T?T?T?G?T?C?C?A?T?T?A?C?G?T
?T?T?T?A?C?G?T?A?T?T?T?G?A?G?T?T?T?T?C?G?A?T?
looks like the file is corrupt? And it continues this way everytime I download.
Is there a program or something I can do to fix the file?
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You need to specify a prefix for the output filenames with the "-outfileprefix" option. I also see that you are not specifying a file of tRNAs for PBS prediction, though I think that may be optional.
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problem of LTRdigest in GenomeTools
Hi, I'm a genometools user, I'm here to report a problem (or maybe bug) when I was using ltrdigest on Ubuntu 10.04
I invoked command as follow:
$ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm test.gff test > gff3result.txt
and it returned error as follow:
gt ltrdigest: error: missing argument
Usage: gt ltrdigest [option ...] gff3_file indexname
I checked every directory and find nothing unusual. Would someone please help me find out what was wrong.
Thank youTags: None
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