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

[Matt Simenc]

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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