[maker-devel] Error from Pseudo gene identification scripts

[panchyni at msu.edu]

Quanwei, in addition to checking the sequence file, can you also send
me the standard output of the run (this the text that normally prints
to the terminal unless you pipe it somewhere else)? This would help
in diagnosing the problem, but Shin-Han is likely correct that it is an
issue in the name formatting.

Nick

Quoting Shin-Han Shiu <shius at msu.edu>:

> Hi Mike and Carson, we will take over from here. Thanks for referring 
> the message to us.
>
> Quanwei, it looks like for some reason your input sequence file is 
> missing "maker-Contig2656-snap-gene-1.9-mRNA-1". This can be an issue 
> with the sequence name since the code use space as delimiter in 
> places. Can you check your sequence file for this sequence and let us 
> know how the name after ">" look like?
>
> Nick, sorry for bugging you. Do you have any input on this?
>
> Shinhan
>
>
> On 12/10/2017 8:37 PM, Michael Campbell wrote:
>> Hi Quanwei,
>>
>> My guess would be a file format issue, but the code has evolved 
>> since I worked with it. The last time that ran it the fasta header 
>> had to contain only the sequence ID without a space after it. That 
>> was the big gotcha that I remember.
>>
>> I?ve ccd Shin-Han Shiu on this one. The pipeline was developed in his lab.
>>
>> Thanks,
>> Mike
>>
>> On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <qwzhang0601 at gmail.com 
>> <mailto:qwzhang0601 at gmail.com>> wrote:
>>
>>> Thank you Carson and Michael.
>>>
>>> Best
>>> Quanwei
>>>
>>> 2017-12-07 23:42 GMT-05:00 Carson Holt <carsonhh at gmail.com 
>>> <mailto:carsonhh at gmail.com>>:
>>>
>>>    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
>>>>    <mailto: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
>>>>    _______________________________________________
>>>>    maker-devel mailing list
>>>>    maker-devel at box290.bluehost.com
>>>>    <mailto:maker-devel at box290.bluehost.com>
>>>>    https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwIFAw&c=nE__W8dFE-shTxStwXtp0A&r=sUBp8FRSXcr7GsPWEwuzZejm3cQdsovXfs8sNKwEUz0&m=O8wVZED5PZBb8ShEI3XsYeVWU8owwPT37_nVEoRY6ak&s=mH6XtbLd3JEy6xKyCX_76sXdhbyq_e0CczfOpQvrqEk&e=
>>>>    
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=nE__W8dFE-shTxStwXtp0A&r=rf2UnAHeUSb4ulp2JbXt_w&m=4eCUx-nUmZ43poIB8geM9XkIKXoND4Yzi4aw4bXAfUU&s=2GYyuVGmT8vENvvk0LPCHjSUEmEzXdcyOnhXDjoTEcQ&e=>
>>>
>>>
>
> -- 
> --------------------------------------
> Shin-Han Shiu
> Michigan State University
> Department of Plant Biology
> 2265 Mol Plant Sci Bldg
> (TEL) +1-517-353-7196
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> --------------------------------------
>
>
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