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<DIV><FONT face=Arial>Hi All,</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>I have checked error message and found that it may be
due to the script running out of outgoing port of
MYSQL.</FONT></DIV>
<DIV><FONT face=Arial>See this page: </FONT><A
href="http://lists.mysql.com/mysql/204830"><FONT
title="http://lists.mysql.com/mysql/204830
CTRL + 单击以下链接"
face=Arial>http://lists.mysql.com/mysql/204830</FONT></A><FONT
face=Arial>.</FONT></DIV>
<DIV><FONT face=Arial>How do you deal with this problem? Can't connect to MySQL
server on 'XXX' (99)</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Sincerely,</FONT></DIV>
<DIV><FONT face=Calibri><FONT face=Arial>Jinfeng Chen</FONT></DIV>
<DIV><BR></DIV></FONT>
<DIV style="FONT: 10pt Tahoma">
<DIV><FONT size=3 face=Calibri></FONT><FONT size=3
face=Calibri></FONT><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=jfchen@genetics.ac.cn
href="mailto:jfchen@genetics.ac.cn">Chen Jinfeng</A> </DIV>
<DIV><B>Sent:</B> Tuesday, December 07, 2010 8:01 PM</DIV>
<DIV><B>To:</B> <A title=dev@ensembl.org
href="mailto:dev@ensembl.org">dev@ensembl.org</A> </DIV>
<DIV><B>Subject:</B> [ensembl-dev] EST genebuilder problem: could not connet to
database?</DIV></DIV></DIV>
<DIV><BR></DIV>
<DIV><FONT face=Arial>Hi All,</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>I have troubles when using genebuilder. I think it was
about MYSQL since the genebuilder works when building protein and mRNA
alignment. </FONT><FONT face=Arial>However, these scaffolds as large as 5
Mb were failed when building EST alignment. Does any one have experience of
this kind of problem? I tried but I can not find the parameters to fix this
problem. I am looking forward to your suggestions. </FONT></DIV>
<DIV><FONT face=Arial>Thanks!</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Sincerely,</FONT></DIV>
<DIV><FONT face=Arial>Jinfeng Chen</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Error Messages:</FONT></DIV>
<DIV><FONT face=Arial>.......</FONT></DIV>
<DIV><FONT face=Arial>.......</FONT></DIV>
<DIV><FONT face=Arial>0 transcripts totally after filtering<BR>==prefiltering:
30, 90, 98, 20<BR> --1 transcripts<BR>0 transcripts totally after
filtering<BR>==prefiltering: 30, 90, 98, 20<BR> --337 transcripts<BR>20
transcripts totally after filtering<BR>==prefiltering: 30, 90, 98, 20<BR>
--47 transcripts<BR>17 transcripts totally after filtering<BR>==prefiltering:
30, 90, 98, 20<BR> --1 transcripts<BR>0 transcripts totally after
filtering<BR>==prefiltering: 30, 90, 98, 20<BR> --11 transcripts<BR>11
transcripts totally after filtering<BR>==prefiltering: 30, 90, 98, 20<BR>
--5854 transcripts<BR>49069 wrong orientation! 0:0.5<BR>51278 wrong orientation!
0:0.5<BR>51276 wrong orientation! 0:0.5</FONT></DIV>
<DIV><FONT face=Arial>Could not connect to database XXX as user ensembl
using [DBI:mysql:database=XXX;host=XXX;port=3306] as a locator:<BR>Can't connect
to MySQL server on 'XXX' (99) at
/home/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line
274.<BR></FONT> </DIV>
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