Question: How Many Sequences That Can Run On Stand Alone Orthomcl V.1.4 ?
0
gravatar for Winmicro40
8.6 years ago by
Winmicro400
Thailand
Winmicro400 wrote:

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

orthomcl • 2.3k views
ADD COMMENTlink modified 5.8 years ago by yuchengzhang0 • written 8.6 years ago by Winmicro400
1

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?

ADD REPLYlink written 8.6 years ago by Damian Kao15k

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.

ADD REPLYlink written 8.6 years ago by Winmicro400

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?

ADD REPLYlink written 8.6 years ago by Damian Kao15k

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

ADD REPLYlink written 8.6 years ago by Winmicro400

I just run MCL program to generate all_ortho.mcl file.And I got it. How can I get file all_orthomcl.out?

ADD REPLYlink written 8.6 years ago by Winmicro400
0
gravatar for yuchengzhang
5.8 years ago by
United States
yuchengzhang0 wrote:

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/allortho.mcl failed to be generated! ".

Have you solved your problem? I hope you can tell me how you did it? Thanks a lot.

 

ADD COMMENTlink written 5.8 years ago by yuchengzhang0
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