problem of LTRdigest in GenomeTools

[hugh_hang]

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 you

[SES]

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.

[htetre]

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?

[SES]

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?

Are you sure the file was finished downloading? If so, it could be a corrupted file but I've never seen that from likes of NCBI or EMBL, though I suppose it's possible. I would check the file size on the server with that of the download and see if anything looks off.

[sst]

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 you

You 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.

[hugh_hang]

You 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.

thank you, but what does the '--' means? just make the bash know the GFF file as stdin?

[sst]

thank you, but what does the '--' means? just make the bash know the GFF file as stdin?

It is just an empty placeholder option to make the option parser aware that what follows is no longer an argument to the '-hmms' option, but rather the two arguments of the tool itself -- a terminator of sorts.

[hugh_hang]

It is just an empty placeholder option to make the option parser aware that what follows is no longer an argument to the '-hmms' option, but rather the two arguments of the tool itself -- a terminator of sorts.

I see, thank you!