MCScanX not read input files

Question

[a.e.wright]

Dear all,

I want to run MCScanX but get the following output

Reading BLAST file and pre-processing

Generating BLAST list

0 matches imported (0 discarded)

0 pairwise comparisons

0 alignments generated

I prepared the blastp file eg

ENSAPLP00000004179.1 ENSGALP00000049077.1 58.333 408 129 6 225 627 83 454 6.77e-143

ENSAPLP00000004179.1 ENSGALP00000006137.5 74.085 355 13 3 41 395 55 330 1.44e-137

ENSAPLP00000004179.1 ENSGALP00000054156.1 100.000 105 0 0 523 627 1 105 1.16e-63

and gff file eg

APKB744031.1 ENSAPLP00000005679.1 75392 88641

APKB742734.1 ENSAPLP00000011909.1 1428474 1438892

GG2 ENSGALP00000053618.1 117714320 117748433

GG1 ENSGALP00000027958.4 195007141 195013426

Any suggestions as to what I've done wrong?

Thanks!

[h.mon]

Did you try running the example files available at MCScanX site? If the examples work correctly and your files don't, compare them to find out what you did wrong.

[a.e.wright]

Thanks! I tried some example files and they didn't work so it must be a problem with my installation.

I tried to install MCScanX. Xcode is installed. I got the following error

dissect_multiple_alignment.cc:252:17: error: use of undeclared identifier 'getopt' while ((c = getopt(argc, argv, "g:c:o:")) != -1) ^ dissect_multiple_alignment.cc:257:32: error: use of undeclared identifier 'optarg' sprintf(gpath,"%s",optarg); ^ dissect_multiple_alignment.cc:261:32: error: use of undeclared identifier 'optarg' sprintf(spath,"%s",optarg); ^ dissect_multiple_alignment.cc:265:32: error: use of undeclared identifier 'optarg' sprintf(opath,"%s",optarg); ^ dissect_multiple_alignment.cc:269:17: error: use of undeclared identifier 'optopt' if (optopt!='g' || optopt!='c' || optopt!='o') ^ dissect_multiple_alignment.cc:269:32: error: use of undeclared identifier 'optopt' if (optopt!='g' || optopt!='c' || optopt!='o') ^ dissect_multiple_alignment.cc:269:47: error: use of undeclared identifier 'optopt' if (optopt!='g' || optopt!='c' || optopt!='o') ^ 7 errors generated. make: * [mcscanx] Error 1

[a.e.wright]

I think I have now installed it properly (using https://ubuntuforums.org/showthread.php?t=2205151) and get

make g++ struct.cc mcscan.cc read_data.cc out_utils.cc dagchainer.cc msa.cc permutation.cc -o MCScanX g++ struct.cc mcscan_h.cc read_homology.cc out_homology.cc dagchainer.cc msa.cc permutation.cc -o MCScanX_h g++ struct.cc dup_classifier.cc read_data.cc out_utils.cc dagchainer.cc cls.cc permutation.cc -o duplicate_gene_classifier g++ dissect_multiple_alignment.cc -o downstream_analyses/dissect_multiple_alignment g++ detect_collinear_tandem_arrays.cc -o downstream_analyses/detect_collinear_tandem_arrays cd downstream_analyses/ && /Applications/Xcode.app/Contents/Developer/usr/bin/make javac -g Cubic.java javac -g bar_plotter.java javac -g branch.java javac -g circle_plotter.java javac -g dot_plotter.java javac -g dual_synteny_plotter.java javac -g family_circle_plotter.java javac -g family_tree_plotter.java javac -g family_tree_plotter_chr.java javac -g family_tree_plotter_show_length.java

However, with the test files I still get

./MCScanX ~/Desktop/test/ Reading BLAST file and pre-processing Generating BLAST list 0 matches imported (0 discarded) 0 pairwise comparisons 0 alignments generated

[h.mon]

It could be a MacOs-specific problem. I just downloaded and compiled MCScanX, and run it on one example:

./MCScanX_h examples/at_gm_pt_vv

Output:

Reading homologs and pre-processing Generating homolog list 308348

homologous pairs imported (8464 discarded) 4090 pairwise comparisons

[...]

Print statistics: Species # of collinear homolog pairs # of

homolog pairs Percentage at&gm 17559 58038 30.2543

at&pt 14323 46944 30.5108 at&vv 7390 24086 30.6817

gm&pt 34564 92901 37.2052 gm&vv 18311 47652 38.4265

pt&vv 15754 38727 40.6796 Done! [2.549 seconds elapsed]

I use Debian. You could try to find a linux machine, or open an issue on github.

Answer 1

[pmcarlton]

I know it's old, but in case anyone has the same problem (I just did) -- I solved it by making sure that both the .blast and the .gff files were TAB-delimited. I had the "0 matches imported" problem when the .gff file was space-delimited.

The tr command can be used to change it easily:

< file.gff tr ' ' '\t' > file_tab.gff