<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)"><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">Hi all,</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">I am parsing a BLASTX report and got the following error for some sequences.</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">It always happen with sub-sequences of 1 base. I found some posts on this issue, but they are old.</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">I am use the latest version installed through cpan.</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px"><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;font-size:13.3333330154419px"><b>$ perl -MBio::Perl -le &#39;print Bio::Perl-&gt;VERSION;&#39;</b></div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;font-size:13.3333330154419px"><b>1.006924</b></div><div><br></div></div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">Any help is appreciated.</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">Thiago</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px"><br></div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">------------- EXCEPTION: Bio::Root::Exception -------------</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">MSG: Undefined sub-sequence (241,242). Valid range = 96 - 242</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Error::throw</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Bio::Search::HSP::HSPI::matches /usr/share/perl5/Bio/Search/HSP/HSPI.pm:716</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Bio::Search::SearchUtils::_adjust_contigs /usr/share/perl5/Bio/Search/SearchUtils.pm:431</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Bio::Search::SearchUtils::tile_hsps /usr/share/perl5/Bio/Search/SearchUtils.pm:201</div><div style="margin:0px;padding:0px;border:0px;vertical-align:baseline;color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.3333330154419px">STACK: Bio::Search::Hit::GenericHit::frac_aligned_hit /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1319</div></div><div><br></div>-- <br><div class="gmail_signature">=================================<br>Thiago Motta Venancio, M.Sc., PhD<br><a href="http://venancio.openwetware.org/" target="_blank">http://venancio.openwetware.org/</a><br>=================================</div>
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