[ensembl-dev] EST genebuilder problem: could not connet to database? Can't connect to MySQL server on 'XXX' (99)

[jfchen at genetics.ac.cn]

Gene biotype descriptionsHi All,

I have checked error message and found that it may be due to the script running out of outgoing port of MYSQL.
See this page: http://lists.mysql.com/mysql/204830.
How do you deal with this problem? Can't connect to MySQL server on 'XXX' (99)

Sincerely,
Jinfeng Chen




From: Chen Jinfeng 
Sent: Tuesday, December 07, 2010 8:01 PM
To: dev at ensembl.org 
Subject: [ensembl-dev] EST genebuilder problem: could not connet to database?


Hi All,

I have troubles when using genebuilder. I think it was about MYSQL since the genebuilder works when building protein and mRNA alignment. 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. 
Thanks!

Sincerely,
Jinfeng Chen

Error Messages:
.......
.......
0 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --1 transcripts
0 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --337 transcripts
20 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --47 transcripts
17 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --1 transcripts
0 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --11 transcripts
11 transcripts totally after filtering
==prefiltering: 30, 90, 98, 20
  --5854 transcripts
49069 wrong orientation! 0:0.5
51278 wrong orientation! 0:0.5
51276 wrong orientation! 0:0.5
Could not connect to database XXX as user ensembl using [DBI:mysql:database=XXX;host=XXX;port=3306] as a locator:
Can't connect to MySQL server on 'XXX' (99) at /home/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 274.
 


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