OrthoMCL step 12: [mclxReadDimensions] could not parse header

Question

[jmah]

Hi all,

I'm having trouble with OrthoMCL step 12 (mlc command). I'm using a test set of two fastas with 10 proteins, five of which are identical to sequences in the other fasta. Thus, there should be five orthologs. All steps until step 12 appears to work. The orthologs.txt file in the pairs directory does have the correct 5 sequences that should match. However, when I try to run the mcl command for step 12 I get:

user@b403:~/data/my_orthomcl_dir> mcl mclInput -o orthomcl_test_output/

___ [mclxReadDimensions] could not parse header

___ [mcl] no jive

___ [mcl] failed

Is my command or input wrong? Can anyone guess what may be the problem?

Thanks for your help!

Cheers, Jasmine

[jmah]

And just for reference, here is the OrthoMCL manual which lists the steps I keep alluding to: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt

Cheers, Jasmine

[jmah]

Hi Philipp and lu.ne,

Thanks both of you for your advice! It looks like it works now with the -abc flag. Thank you very much for your help!

[Andrzej Zielezinski]

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Answer 1

[lu.ne]

Assuming your file is in abc format (A B weight, a line for each pair) then you might want to add --abc at the end of your command, I had a similar error when using mcl in the past and it was because of this omission.

Answer 2

[Philipp Bayer]

Is it possible that you have too few proteins? You have 10 proteins, but the manual says that OrthoMCL assumes entire proteomes as input: 'The input to OrthoMCL is a set of proteomes.'