[maker-devel] Custom Repeat Library: ProtExcluder.pl help

[Jason Stajich]

Did you install hmmer3 ? need that to get esl-sfetch not sure how you
configured the paths when you run this.


Jason
On Sun, Mar 6, 2016 at 8:48 AM Matt Simenc <mcsimenc at gmail.com> wrote:

> I am working on creating a custom repeat library. I want to use the
> ProtExcluder.pl script, found on the maker wiki at
>
>
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Basic
>
>  to trim out possible gene sequences from the default RepeatModeler output
> when run on my genome. I'm getting some errors and output in which no
> sequences are removed from my RepeatModeler library and am wondering if you
> anyone has experience with this script and can help me understand the
> errors.
>
> I am feeding ProtExcluder.pl a FASTA file from RepeatModeler and blastx
> output (default output,blast 2.2.31+) like:
>
> ProtExcluder.pl blast_output repeat_fasta 1>stdout 2>stderr
>
> - I get an output file repeat_fastanoProtFinal that contains exactly the
> same sequences as the input repeat_fasta.
>
> - stderr has these errors:
>
> Can't exec "binaries/esl-sfetch": No such file or directory at
> /share/apps/genomics/ProtExcluder1.1/mspesl-sfetch.pl line 17.
>
> Can not open the seqfile
> /home/joshd/data/azolla/blasts/repeats/RepeatModeler.celera_blastx_PT-1.1-orthofinder/AzlRptMdlrLib.celera_blastx_PT-1.1-orthofinder_1e-5.fnolowm50seq
>
> mergeunmatchedregion.pl seqfile
>
> Illegal division by zero at
> /share/apps/genomics/ProtExcluder1.1/GCcontent.pl line 122.
>
> ProtExcluder.pl created a bunch of files in the directory where it is
> trying to unsuccessfully access the fnolow50seq file, which does not exist,
> though there are files whose names have the suffix fnolow50seqm,
> fnolow50seqmGC, and fnolow50seqmns.
>
> Any help would be appreciated! I could write a script to do this but would
> rather use an already debugged one to save time. Thanks!
>
> Matt Simenc
> Der Evolutionary Genomics Lab
> California State University, Fullerton
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