Question: OrthoMCL step 12: [mclxReadDimensions] could not parse header
0
gravatar for jmah
2.7 years ago by
jmah10
jmah10 wrote:

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

error orthomcl • 1.2k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by jmah10

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

ADD REPLYlink written 2.7 years ago by jmah10

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!

ADD REPLYlink written 2.7 years ago by jmah10

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ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by a.zielezinski9.0k
2
gravatar for lu.ne
2.7 years ago by
lu.ne70
lu.ne70 wrote:

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.

ADD COMMENTlink written 2.7 years ago by lu.ne70
1
gravatar for Philipp Bayer
2.7 years ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

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.'

ADD COMMENTlink written 2.7 years ago by Philipp Bayer6.6k
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