I am attempting OrthoMCL to compare 10 different strains of a certain bacterial species, and went through the pipeline after installing MySql, OrthoMcl and Mcl locally.
The problem is that all the entries are in the inParalogs.txt, while the orthologs.txt is empty.
The input for the pipeline was the aminoacid fasta files (got from RAST output from assembled contigs).
I process each file through the pipeline individually.
I called on orthomcladjustfasta, orthomclfilterfasta, makeblastdb, blastall, orthomclblastparser, orthomclloadblast, orthomclpairs etc. They all ran to completion without any glitches.
My adjusted fasta header looks like this
makeblastdb and blastall commands i used for each of my sample are
makeblastdb -in mySample.goodProteins.fasta -dbtype prot -out mySample_blastDB blastall -p blastp -i mySample.goodProteins.fasta -d mySample_blastDB -o mySample_blast.csv -e 1 -m 8 -a 2 -v 1000 -b 1000
Then I call on orthomclblastparser to produce similarSequences.txt for each file.
I appreciate any help in understanding why my orthologs.txt is empty and the inparalogs.txt has about 21000 rows of data.