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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
114 stars 22 forks source link

wgdi -icl error #29

Closed cfz1998 closed 1 year ago

cfz1998 commented 1 year ago

Hi!@SunPengChuan When i use wgdi -icl *_collinearity.conf to find collinearity genes in one genome. I got an error! image

I don't know why. Thank you for your reply!

cfz1998 commented 1 year ago

sample1_collinearity.conf

gff1 =  sample1.gff
gff2 =  sample1.gff
lens1 = sample1.len
lens2 = sample1.len
blast = ../02.mcscanx/sample1.blast
blast_reverse = false
multiple  = 1
process = 8
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 25,25
pvalue = 1
repeat_number = 10
positon = order
savefile = sample1.coll
SunPengChuan commented 1 year ago

It looks like a problem with pandas. Could you please upload your data so I can test it? Alternatively, you can send it to me separately via email : sunpengchuan@gmail.com

cfz1998 commented 1 year ago

Actinidia_chinensis.tar.gz

cfz1998 commented 1 year ago

Hi！@SunPengChuan

My data was here. Thank you for your reply!

SunPengChuan commented 1 year ago

The GFF file you are processing has issues. Such as Lachesis_group13 Actinidia07289.t1 6088347 6108665 - 489 Lachesis_group13 Actinidia07290.t1 6088770 6091853 - 489

I'll send you the processed GFF file and the script to process it. Actinidia_chinensis.zip

cfz1998 commented 1 year ago

There is something wrong with from collections import defaultdict in my code. Thanks!