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!