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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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when using MCScanX_h 0 homologous pairs imported (316812 discarded) #14

Closed tnaake closed 6 years ago

tnaake commented 6 years ago

Dear Yupeng,

when I run MCScanX_h data/at_gm_pt_vv, where at_gm_pt_vv.homology only contains two columns (I deleted column 3 manually), I get the following output:

Reading homologs and pre-processing Generating homolog list 0 homologous pairs imported (316812 discarded) 0 pairwise comparisons 0 alignments generated Pairwise collinear blocks written to ./at_gm_pt_vv.collinearity [1.861 seconds elapsed] Writing multiple syntenic blocks to HTML files at1.html at2.html ...

Actually, I am expecting that I get similar results compared to the run where I have the third column with numerical values since in the manual (http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf) it is described that you can pass a .homology file with two or three columns to MCScanX_h.

charlesfeigin commented 3 years ago

Hi @tnaake, did you ever get an answer? I am running the program in the way described but it finishes almost instantaneously with nothing found. I have extremely reliable homology relationships in my .homology file and all files are formatted correctly as far as I can tell....

ViriatoII commented 2 years ago

I had a similar problem that was solved by having a .gff file instead of .bed file in the directory:

Sp1_Sp2.blast Sp1_Sp2.gff