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12.4 years ago
Winmicro40
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Hello,I'm a student in Bioinformatics program.
In my project,I have run 293,799 sequences on OrthoMCL V.1.4.
It 's done in all against all part and generate "all_ortho.mtx" file.
But it stopped in Run MCL program step.
I tried in mode 1,3,4,5 of OrthoMCL but it 's not work.
I 'm not sure that Is it the limitation of the program or limitation of server that I used.
What should I do with this problem?
Thank you in advances for every answers.
Thongpan
You need to be more specific with what happened. What do you mean it stopped at the mcl step? Was there an error? Did it not run at all? Did it hang?
Hi,I go to orthomcl.log in the last line just show Run MCL program /home/thongpan/bin/ORTHOMCLV1.4/test/bin/mcl /home/thongpan/bin/ORTHOMCLV1.4/Dec_2_2/tmp/all_ortho.mtx -I 1.5 -o /home/thongpan/bin/ORTHOMCLV1.4/Dec_2_2/tmp/all_ortho.mcl In tmp directory,It shows every files (include all_ortho.mtx) except all_ortho.mcl output file.What should I do next? Thank you for your answers.
So you did your all vs all blast, you loaded the results into the mysql database, you've generated the pairs. Now you want to run mcl on the pairs file. What happens exactly when you run the mcl command? Does it stop immediately? Does it show an error on your screen?
In my previous data,it just about 150,000 sequences and I can get allorthomcl.out.I think that the problem may not come from MCL program.(Actually,I never run only MCL command) But in some runs it shows -->Unexpected error (should not have happened): /home/thongpan/bin/ORTHOMCLV1.4/Dec22/tmp/allortho.mcl failed to be generated! No such file or directory
I just run MCL program to generate all_ortho.mcl file.And I got it. How can I get file all_orthomcl.out?
Hello, I met the same problem using orthomcl v1.4. The last step it stopped and gave the information like
Unexpected error (should not have happened): /home/usr/bin/ORTHOMCLV1.4/Aug_22/tmp/all*ortho.mcl failed to be generated!.Have you solved your problem? I hope you can tell me how you did it? Thanks a lot.