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
114 stars 22 forks source link

ERROR: inconsistency between the following pep and nuc seqs #12

Closed xuzhougeng closed 3 years ago

xuzhougeng commented 3 years ago

when I run the wgdi ks , i met the following error

#---  ERROR: inconsistency between the following pep and nuc seqs  ---#
>gene_name
cds seq
>gene_name
pep seq

which: no bl2seq in (xxx)
Run bl2seq (-p tblastn) or GeneWise to see the inconsistency.

When search the bl2seq, I found the bl2seq was only in legacy blast (see https://www.biostars.org/p/17580/

Could I ignore this error, or how could I solve the problem.

SunPengChuan commented 3 years ago

In most cases, it is a sequence alignment problem. I think it is necessary to check it. Once you know the reason, you can ignore it.

SunPengChuan commented 2 years ago

This error occurs when there is a stop-codon （such as *） in the sequence.

YZW0118 commented 1 year ago

Excause me, have you solved your problem? I met the same problem recently.

fatelitier commented 1 year ago

Excause me, have you solved your problem? I met the same problem recently.

I had the same problem. Did you solve it? Could you share some ideas?

SunPengChuan commented 1 year ago

The ks value is blank for the gene pair triggering the warning. If not widespread, no need to pay much attention.