[maker-devel] Error from Pseudo gene identification scripts

[Carson Holt]

I’m going to CC Michael Campbell on this. I wasn’t really involved with any of the pseudogene accessory scripts and protocols that went with the MAKER-P publication nor have I really been involved with pseudogene annotation in general. So Michael might have more insight here.

—Carson

> On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> I am trying to identify pseudo genes following http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene <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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