Problems About Orthomcl When I Do Orthomclblastparser

Question

[User 7478]

When I do orthomclBlastParser like this:

orthomclBlastParser Hsa-Ath.txt ~/my_orthomcl_dir/compliantFasta >>similarSequences.txt

• "Hsa-Ath.txt" is the BlAST output in m8 format.
• "~/my_orthomcl_dir/compliantFasta/" is the directuory of compliant fasta files(Hsa.fasta and Ath.fasta) as produced by orthomclAdjustFasta.

But it tells me "couldn't find taxon for gene '2_Ath.fasta' at /opt/bin/orthomclBlastParser line 103, <f> line 1."???

So, what is the error? Could anyone help me? Thank you!

[Rob Syme]

The fasta headers in ~/my_orthomcl_dir/compliantFasta should look something like "org1|unique_protein_id". Everything up the the pipe character ("|") should be the taxon id. Can you post the output from head -n1 ~/my_orthomcl_dir/compliantFasta/*

[Rob Syme]

All the files in ~/myorthomcldir/compliantFasta should look something like:

org1|uniqueproteinid00 MPROTEINSEQUENCEGOESHERE* org2|uniqueproteinid01 MMOREPROTEINSEQUENCEGOESHERE*

Everything up the the pipe character ("|") should be the taxon id. If your protein ID has pipe characters in it, you might run into trouble.

Can you post the output from head -n1 ~/myorthomcldir/compliantFasta/*

[Damian Kao]

Continuing from the other question you posted, how did you do the all vs all blast? Did you removed the ID spacing from the two fasta files (Hsa and Ath) and then concatenated them together for the blast? Can you post a few lines of the blast result?

Answer 1

[User 7478]

Thanks for Rob Syme and DK! I have resolved my problems about orthomcl. When I do blastall I could not add taxon ids requiring for orthomcl, or else the results of blastall can be only shown subject_id not as the right AT1GXXXXX, but as 1_Ath.fasta, 2_Ath.fasta ⋯⋯. Then when I put the later results into orthomclLoadBlast, next do orthomclBlastParser,it will has error:"couldn't find taxon for gene '2_Ath.fasta' at /opt/bin/orthomclBlastParser line 103, line 1." I think that might be the bug of orthomcl-v2.0, because it requires sequences with taxon code, which will harm blast. I can only do blast first without taxon code, and then add taxon code on blast output-8 manually.

[wang.qiang.prc]

Today I met the same question. Would you please give me a detailed explanation?? I also found my blast results showed such things like "1_Ath.fasta, 2_Ath.fasta". How will i correct it????Thank u