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Hi Folks<br>
<br>
I am running into some problems parsing iprscan results.<br>
<br>
I run iprscan as follows:<br>
<br>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size:11pt">> iprscan -cli -i
bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw
-format raw -goterms -iprlookup</span></font><br>
<br>
and obtain the iprscan output (the iprscan output file is at
<a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw">http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw</a> if anyone
is interested in the detailed output, and the initial maker gff3
file is at <a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za/~fourie/bot.all.gff">http://www.bi.up.ac.za/~fourie/bot.all.gff</a>).<br>
<br>
I then try to run the conversion to gff3, but I get very long list
of errors:<br>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size:11pt"><br>
> iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff >
domains.gff</span></font><br>
<br>
ERROR: In
maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113<br>
Use of uninitialized value $seqid in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $start in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $end in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $strand in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 255.<br>
Use of uninitialized value $off in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $pB in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $off in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $pE in subtraction (-) at
/usr/local/maker/bin/iprscan2gff3 line 267.<br>
Use of uninitialized value $seqid in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $start in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $end in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
Use of uninitialized value $strand in concatenation (.) or string at
/usr/local/maker/bin/iprscan2gff3 line 269.<br>
.......<br>
.......<br>
.......<br>
<br>
for most of the entries.<br>
<br>
Any advice or help would be sincerely appreciated!<br>
<br>
Best regards!<br>
<br>
Fourie<br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
--------------
Prof Fourie Joubert
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
<a class="moz-txt-link-abbreviated" href="mailto:fourie.joubert@up.ac.za">fourie.joubert@up.ac.za</a>
<a class="moz-txt-link-freetext" href="http://www.bi.up.ac.za">http://www.bi.up.ac.za</a>
Tel. +27-12-420-5825
Fax. +27-12-420-5800
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