search

SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
https://wgdi.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
121 stars 22 forks source link

No "-bi" result file generation #38

Closed Wenwen012345 closed 1 year ago

Wenwen012345 commented 1 year ago

Hello. @SunPengChuan

Just for this one comparison, I ran the comparison for both species but the result file generated with the "-bi" parameter is empty. I carefully checked the .conf file but no problem was found. The comparison of the two species by themselves and the comparison of the two species with any other species produces the results normally. So I don't really understand what is causing this. Can you take a look for me?

Ro_cac.conf_et_al.zip Ro_cac.cds.zip Ro_cac.pep.zip

SunPengChuan commented 1 year ago

It would be great if the order of species comparison was the same in all the files. Note that it is not the file names, but the content that needs to be consistent. [blockinfo] blast = Ro_cac.blast blast_reverse = true gff2 = Ro.gff gff1 = Cac.gff lens2 = Ro.len lens1 = Cac.len collinearity = Ro_cac.collinearity score = 100 evalue = 1e-5 repeat_number = 20 position = order ks = Ro_cac.ks ks_col = ks_NG86 savefile = Ro_cac.block.information.csv

Wenwen012345 commented 1 year ago

It would be great if the order of species comparison was the same in all the files. Note that it is not the file names

I tried, it doesn't work. The problem should be something else.

SunPengChuan commented 1 year ago

Ro_cac.zip

Wenwen012345 commented 1 year ago

Ro_cac.zip

Okay. Thank you! Parameter adjustment is an eye test. I seem to have missed an adjustment in the right place earlier; and I was a bit dizzy from some wine yesterday. The following error occurred yesterday: ValueError: need at least one array to concatenate

Anyway, thank you very much!