<div dir="ltr"><div><div>Thank you Nick. The output is shown below. <br><br>Traceback (most recent call last):<br> File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", line 4330, in <module><br> parse.get_qualified4(blast,fasta,E,I,L,P,Q)<br> File "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg//ParseBlast.py", 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 "/gs/gsfs0/users/qzhang/tools/maker2_pseudogene/pseudo_pkg/script_step3b.py", 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>NOTE: DatabaseOp not imported<br>Program : tfasty34<br>Pair list: ../maker2.blastn.m_parsed_G500.PE_I500.PS1.pairs<br>Fasta1 : ../../prediction2_final.proteins.fasta<br>Fasta2 : ../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord.fa<br>Fasta dir: /gs/gsfs0/users/qzhang/tools/maker2_pseudogene/fasta36.3.8e/bin/<br>Working d: <br>Flags : -A -m 3 -q<br>E thres : 1.0<br>Read gene pairs...<br> 0 pairs<br>Read fasta files...<br>Do sw...<br>Done!<br>Read BLOSUM50 matrix...<br>Read the sw.out file...<br>Compare sequences:<br> total: 0 alignments<br>Done!<br>Check parameter file...<br> default: ml_t=30<br> default: ev_t=5<br> default: ml_p=0.05<br> default: id_t=40<br>Filter ../maker2.blastn.m...<br> E:5 I:40 L:30 P:0.05<br>Get pseudoexons...<br> pseudoexon file: ../<a href="http://maker2.blastn.m_parsed_G500.PE">maker2.blastn.m_parsed_G500.PE</a><br>Get phase 1 pseudogene...<br> phase1 ps file: ../maker2.blastn.m_parsed_G500.PE_I500.PS1<br>Get pair file and subject coordinates...<br> pair file : ../maker2.blastn.m_parsed_G500.PE_I500.PS1.pairs<br> coordinates: ../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord<br>Get phase 1 pseudogene sequences...<br> phase 1 ps sequence: ../maker2.blastn.m_parsed_G500.PE_I500.PS1.subj_coord.fa<br>Find stop and framshifts...<br> Smith-Waterman outputs: ../maker2.blastn.m_parsed_G500.PE_I500.PS1_pairs.sw.*<br> Final output: ../maker2.blastn.m_parsed_G500.PE_I500.PS1_pairs.sw.out.disable_count<br><br>The pseudogene pipeline has finished!<br><br><br></div>Best<br></div>Quanwei<br></div><div class="gmail_extra"><br><div class="gmail_quote">2017-12-11 10:01 GMT-05:00 <span dir="ltr"><<a href="mailto:panchyni@msu.edu" target="_blank">panchyni@msu.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div>
<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<span class=""><br>
<br>
Quoting Shin-Han Shiu <<a href="mailto:shius@msu.edu" target="_blank">shius@msu.edu</a>>:<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.<wbr>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></span>
>> I?ve ccd Shin-Han Shiu on this one. The pipeline was developed in his lab.<span class=""><br>
>><br>
>> Thanks,<br>
>> Mike<br>
>><br>
>> On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" target="_blank">qwzhang0601@gmail.com</a><br></span><span class="">
>> <mailto:<a href="mailto:qwzhang0601@gmail.com" target="_blank">qwzhang0601@gmail.com</a>><wbr>> 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 <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a><br></span>
>>> <mailto:<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>>:<br>
>>><br>
>>> I?m going to CC Michael Campbell on this. I wasn?t really<span class=""><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></span>
>>> ?Carson<span class=""><br>
>>><br>
>>>> On Dec 7, 2017, at 2:44 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" target="_blank">qwzhang0601@gmail.com</a><br></span></p><div><div class="h5">
>>>> <mailto:<a href="mailto:qwzhang0601@gmail.com" target="_blank">qwzhang0601@gmail.com</a>><wbr>> 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.<wbr>msu.edu/index.php/Protocol:<wbr>Pseudogene</a><br>
>>>> <<a href="http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" target="_blank">http://shiulab.plantbiology.<wbr>msu.edu/index.php/Protocol:<wbr>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/<wbr>maker2_pseudogene/pseudo_pkg//<wbr>ParseBlast.py",<br>
>>>> line 4330, in <module><br>
>>>> parse.get_qualified4(blast,<wbr>fasta,E,I,L,P,Q)<br>
>>>> File<br>
>>>> <br>
>>>> "/gs/gsfs0/users/qzhang/tools/<wbr>maker2_pseudogene/pseudo_pkg//<wbr>ParseBlast.py",<br>
>>>> line 3050, in get_qualified4<br>
>>>> N = sizes[L[0]]<br>
>>>> KeyError: 'maker-Contig2656-snap-gene-1.<wbr>9-mRNA-1'<br>
>>>> Traceback (most recent call last):<br>
>>>> File<br>
>>>> <br>
>>>> "/gs/gsfs0/users/qzhang/tools/<wbr>maker2_pseudogene/pseudo_pkg/<wbr>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>
>>>> ______________________________<wbr>_________________<br>
>>>> maker-devel mailing list<br>
>>>> <a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.<wbr>com</a><br></div></div>
>>>> <mailto:<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.<wbr>bluehost.com</a>><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=amxxAQj1r58HtnljR_ldsiP-fOO39FxiO68ZT1UBHoE&m=p2cRRr06c6fbtMo9iCwpKi0X1QnRoogK33tX5Bfd5ek&s=SeSN1OfBVQVhi5forovCTfSJGCO1bR7Q7LuCcWlhctI&e=" target="_blank">http://box290.bluehost.com/<wbr>mailman/listinfo/maker-devel_<wbr>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.<wbr>proofpoint.com/v2/url?u=http-<wbr>3A__box290.bluehost.com_<wbr>mailman_listinfo_maker-<wbr>2Ddevel-5Fyandell-2Dlab.org&d=<wbr>DwMFaQ&c=nE__W8dFE-<wbr>shTxStwXtp0A&r=<wbr>rf2UnAHeUSb4ulp2JbXt_w&m=<wbr>4eCUx-<wbr>nUmZ43poIB8geM9XkIKXoND4Yzi4aw<wbr>4bXAfUU&s=<wbr>2GYyuVGmT8vENvvk0LPCHjSUEmEzXd<wbr>cyOnhXDjoTEcQ&e=</a>><span class=""><br>
>>><br>
>>><br>
><br>
> --<br>
> ------------------------------<wbr>--------<br>
> Shin-Han Shiu<br>
> Michigan State University<br>
> Department of Plant Biology<br>
> 2265 Mol Plant Sci Bldg<br>
> (TEL) <a href="tel:(517)%20353-7196" value="+15173537196" target="_blank">+1-517-353-7196</a><br>
> <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_keiHZX&d=DwMCAw&c=nE__W8dFE-shTxStwXtp0A&r=amxxAQj1r58HtnljR_ldsiP-fOO39FxiO68ZT1UBHoE&m=p2cRRr06c6fbtMo9iCwpKi0X1QnRoogK33tX5Bfd5ek&s=pk3W0L_Z0dlNJDAdwrb7dA0_NSdr21LVNthDV6V43qg&e=" target="_blank">http://goo.gl/keiHZX</a><br>
> ------------------------------<wbr>--------<br>
><br>
><br>
</span><p></p>
</div>
</blockquote></div><br></div>