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Dee-chen / Tree2gd

GNU General Public License v3.0
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some error about step 5 #17

Open lfp-a opened 1 year ago

lfp-a commented 1 year ago

After running the whole program, I found a lot of data missing. After checking, I found that there was a problem in the step5.

When I run step5, he has the following error, is there any way to solve this problem? image

I tried to contact the server administrator to see if this upper limit could be raised, but he said that this setting is related to the underlying data of the server, so it is not convenient to change. Can I change the parameters in the package to solve this problem? thank you

lfp-a commented 1 year ago

I have checked again, it should not be this problem, but there are a lot of data missing in the calculation of ka/ks in step5. If we check the file of step5, it is all_gene_pairs.list, which contains only 129967 pairs of genes, has abnormally few data. But I looked at all_pep.fa and found 5,147,373 sequences. I also don't know how to obtain the file all_gene_pairs.list, and I don't know how to solve this problem.