[maker-devel] Error from Pseudo gene identification scripts

[Quanwei Zhang]

Hello:

I am trying to identify pseudo genes following
http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene

After I get the blast result, I am trying to scan pseudogenes by the
command "python pseudo_wrap.py parameter". But I got the following errors.
Do you have any ideas and suggestions about the errors? Thanks.

##below shows reported errors
Traceback (most recent call last):
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",
line 4330, in <module>
    parse.get_qualified4(blast,fasta,E,I,L,P,Q)
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",
line 3050, in get_qualified4
    N = sizes[L[0]]
KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'
Traceback (most recent call last):
  File
"/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py",
line 98, in <module>
    oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],
IndexError: list index out of range
Done!

Best
Quanwei
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