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<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></BODY></HTML>