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<p>
Quanwei, in addition to checking the sequence file, can you also send<br />
me the standard output of the run (this the text that normally prints<br />
to the terminal unless you pipe it somewhere else)? This would help<br />
in diagnosing the problem, but Shin-Han is likely correct that it is an<br />
issue in the name formatting.<br />
<br />
Nick<br />
<br />
Quoting Shin-Han Shiu <shius@msu.edu>:<br />
<br />
> Hi Mike and Carson, we will take over from here. Thanks for referring<br />
> the message to us.<br />
><br />
> Quanwei, it looks like for some reason your input sequence file is<br />
> missing "maker-Contig2656-snap-gene-1.9-mRNA-1". This can be an issue<br />
> with the sequence name since the code use space as delimiter in<br />
> places. Can you check your sequence file for this sequence and let us<br />
> know how the name after ">" look like?<br />
><br />
> Nick, sorry for bugging you. Do you have any input on this?<br />
><br />
> Shinhan<br />
><br />
><br />
> On 12/10/2017 8:37 PM, Michael Campbell wrote:<br />
>> Hi Quanwei,<br />
>><br />
>> My guess would be a file format issue, but the code has evolved<br />
>> since I worked with it. The last time that ran it the fasta header<br />
>> had to contain only the sequence ID without a space after it. That<br />
>> was the big gotcha that I remember.<br />
>><br />
>> I?ve ccd Shin-Han Shiu on this one. The pipeline was developed in his lab.<br />
>><br />
>> Thanks,<br />
>> Mike<br />
>><br />
>> On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <qwzhang0601@gmail.com<br />
>> <mailto:qwzhang0601@gmail.com>> wrote:<br />
>><br />
>>> Thank you Carson and Michael.<br />
>>><br />
>>> Best<br />
>>> Quanwei<br />
>>><br />
>>> 2017-12-07 23:42 GMT-05:00 Carson Holt <carsonhh@gmail.com<br />
>>> <mailto:carsonhh@gmail.com>>:<br />
>>><br />
>>> I?m going to CC Michael Campbell on this. I wasn?t really<br />
>>> involved with any of the pseudogene accessory scripts and<br />
>>> protocols that went with the MAKER-P publication nor have I<br />
>>> really been involved with pseudogene annotation in general. So<br />
>>> Michael might have more insight here.<br />
>>><br />
>>> ?Carson<br />
>>><br />
>>>> On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <qwzhang0601@gmail.com<br />
>>>> <mailto:qwzhang0601@gmail.com>> wrote:<br />
>>>><br />
>>>> Hello:<br />
>>>><br />
>>>> I am trying to identify pseudo genes following<br />
>>>> <a href="http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" target="_blank">http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene</a><br />
>>>> <<a href="http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" target="_blank">http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene</a>><br />
>>>><br />
>>>> After I get the blast result, I am trying to scan pseudogenes by<br />
>>>> the command "python pseudo_wrap.py parameter". But I got the<br />
>>>> following errors. Do you have any ideas and suggestions about<br />
>>>> the errors? Thanks.<br />
>>>><br />
>>>> ##below shows reported errors<br />
>>>> Traceback (most recent call last):<br />
>>>> File<br />
>>>> <br />
>>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",<br />
>>>> line 4330, in <module><br />
>>>> parse.get_qualified4(blast,fasta,E,I,L,P,Q)<br />
>>>> File<br />
>>>> <br />
>>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py",<br />
>>>> line 3050, in get_qualified4<br />
>>>> N = sizes[L[0]]<br />
>>>> KeyError: 'maker-Contig2656-snap-gene-1.9-mRNA-1'<br />
>>>> Traceback (most recent call last):<br />
>>>> File<br />
>>>> <br />
>>>> "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py",<br />
>>>> line 98, in <module><br />
>>>> oup.write("%s\t%s\t%s\t%s\n" % (all_contigs[i][0][0],<br />
>>>> IndexError: list index out of range<br />
>>>> Done!<br />
>>>><br />
>>>> Best<br />
>>>> Quanwei<br />
>>>> _______________________________________________<br />
>>>> maker-devel mailing list<br />
>>>> maker-devel@box290.bluehost.com<br />
>>>> <mailto:maker-devel@box290.bluehost.com><br />
>>>> <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMCAw&c=nE__W8dFE-shTxStwXtp0A&r=sUBp8FRSXcr7GsPWEwuzZejm3cQdsovXfs8sNKwEUz0&m=O8wVZED5PZBb8ShEI3XsYeVWU8owwPT37_nVEoRY6ak&s=mH6XtbLd3JEy6xKyCX_76sXdhbyq_e0CczfOpQvrqEk&e=" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br />
>>>> <br />
>>>> <<a href="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=" target="_blank">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=</a>><br />
>>><br />
>>><br />
><br />
> --<br />
> --------------------------------------<br />
> Shin-Han Shiu<br />
> Michigan State University<br />
> Department of Plant Biology<br />
> 2265 Mol Plant Sci Bldg<br />
> (TEL) +1-517-353-7196<br />
> <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_keiHZX&d=DwMCAw&c=nE__W8dFE-shTxStwXtp0A&r=sUBp8FRSXcr7GsPWEwuzZejm3cQdsovXfs8sNKwEUz0&m=O8wVZED5PZBb8ShEI3XsYeVWU8owwPT37_nVEoRY6ak&s=_zXpOrewnF9jjZxW98cCBUElJjHBanS6XxkTcOCwvdI&e=" target="_blank">http://goo.gl/keiHZX</a><br />
> --------------------------------------<br />
><br />
><br />
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