User: max_19

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max_1950
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Posts by max_19

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Comment: C: DBI connect failed: orthomclLoadBlast
... It's actually working now (I can access that specific DB from the cluster). apparently if you remove the space between -p and your password it works fine. $ mysql -u max -D max_orthomcl -ppassword -h host Reading table information for completion of table and column names You can tu ...
written 24 days ago by max_1950
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Comment: C: DBI connect failed: orthomclLoadBlast
... I will contact the cluster administrators then, thank you for the help! No that is not the actual host name (Just put that to show the command/arguments that were run). ...
written 24 days ago by max_1950
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Comment: C: DBI connect failed: orthomclLoadBlast
... Thanks. I tried this and I got : $ mysql -u max -D max_orthomcl -p password -h host >Enter password: ERROR 1045 (28000): Access denied for user 'max' (using password: YES) ...
written 24 days ago by max_1950
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Comment: C: DBI connect failed: orthomclLoadBlast
... Yes it is a compute cluster. I am trying to run both orthoMCL and MySQL from it. If I try to access mysql server using 'mysql' it appears to be working fine $ mysql Welcome to the MySQL monitor. Commands end with ; or \g....etc etc is there any other test I should try? ...
written 24 days ago by max_1950
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Comment: C: DBI connect failed: orthomclLoadBlast
... I made sure the credentials in the my.cnf file match those in the orthomcl.config (below) dbVendor=mysql dbConnectString=dbi:mysql:max_orthomcl dbLogin=max dbPassword=Password dbname=max_orthomcl similarSequencesTable=SimilarSequences orthologTable=Ortholog inParalo ...
written 24 days ago by max_1950
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DBI connect failed: orthomclLoadBlast
... Hi guys, I am trying to run OrthoMCL on a remote server. When I get to the orthomclLoadBlast step, I keep getting this error message: $ orthomclLoadBlast orthomcl.config similarSequences.txt > DBI connect('max_orthomcl','max',...) failed: Can't connect to > local MySQL server through so ...
mcl sequence protein orthomcl written 25 days ago by max_1950
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... That makes sense. thank you for the reply! ...
written 27 days ago by max_1950
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Thank you Philipp! may I ask two more questions? when I use makeblastdb in step 7, I don't get a resulting .fasta file as part of the output, only a .psq, .phr, and .pin file. Not sure if this is normal as I see in the above steps they got a .fasta file. Also how does one tell blastp to perform a ...
written 28 days ago by max_1950
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Comment: C: Orthomcl install schema error
... I just tried that, however I still get an error (but now it's a different error): $ orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log > can't find property dbname in config file my config file is posted above, and when i go into mysql, I can see the d ...
written 29 days ago by max_1950
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Hi Philipp, any idea why one would get such error message on step#4 (orthomclInstallSchema) orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log > Can't locate DBD/mysql.pm in @INC (you may need to install the > DBD::mysql module) > here is my o ...
written 29 days ago by max_1950

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