[maker-devel] Error from Pseudo gene identification scripts

Mon Dec 11 07:55:42 MST 2017

Hello Shinhan and Michael:

Thanks for your help. The sequence is shown below, which is reported
protein sequence by Maker2. The error occur when I run "pseudo_wrap.py".
With the blast results and predicted protein sequences by Maker2, I am
trying to predict the pseudo genes in the whole assembly (both for those in
the intergenic regions and those among the predicted proteins).

>maker-Contig2656-snap-gene-1.9-mRNA-1 protein AED:0.04 eAED:0.04
QI:43|1|1|1|0.85|0.87|8|1768|297
MGTSLDIKIKRANKVYHAGEMLSGVVVISSKDSVQHQGMSLTMEGTVNLQLSAKSVGVFE
AFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHVKGNKVLYETYHGVFVNIQYVL
RCDMRRSLLAKDLTKTCEFIVHSVPQKGKLTPSPVDFTITPETLQNVKERALLPKFLIRG
HLNSTNCAITQPLTGELVVEHSDAAIRSIELQLVRVETCGCAEGYARDATEIQNIQIADG
DVCRSLSVPIYMVFPRLFTCPTLETTNFKVEFEINVVVLLHADHLITENFPLKLCRT

#below is the blast results
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    100.000    51
0    0    220    270    424151    424303    3.23e-25    111
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    93.103    58    4
0    170    227    423367    423540    4.19e-24    108
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    85.000    60    7
1    66    123    404001    404180    5.67e-24    107
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    100.000    48
0    0    20    67    402613    402756    3.47e-20    96.7
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    50.725    69
25    1    238    297    426022    426228    6.48e-09    63.2
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    67.308    52
15    2    118    168    417125    417277    2.07e-08    61.6
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    100.000    25
0    0    145    169    419825    419899    5.54e-06    53.9
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2656    76.667    30    5
1    1    30    382922    383005    0.012    43.5
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig3808    22.545    275
175    9    15    283    112218    111490    1.13e-07    59.3
maker-Contig2656-snap-gene-1.9-mRNA-1    Contig2791    26.667    60
43    1    236    295    20108374    20108550    9.6    34.3

Many thanks

Best
Quanwei

2017-12-11 8:13 GMT-05:00 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> wrote:
>
> Thank you Carson and Michael.
>
> Best
> Quanwei
>
> 2017-12-07 23:42 GMT-05:00 Carson Holt <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> wrote:
>>
>> 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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>>
>>
>
> --
> --------------------------------------
> Shin-Han Shiu
> Michigan State University
> Department of Plant Biology
> 2265 Mol Plant Sci Bldg
> (TEL) +1-517-353-7196 <(517)%20353-7196>http://goo.gl/keiHZX <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_keiHZX&d=DwMDaQ&c=nE__W8dFE-shTxStwXtp0A&r=amxxAQj1r58HtnljR_ldsiP-fOO39FxiO68ZT1UBHoE&m=2co1_3xFiHR-sHwprAR0Wh1nMeSutUJ7n-TAibVN28c&s=Mt70of3YH2ihTytQ-XPiKJS0rOpA_YAxJEuEyLFK1BQ&e=>
> --------------------------------------
>
>
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