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<p>Hi Mike and Carson, we will take over from here. Thanks for
referring the message to us.</p>
<p>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?<br>
</p>
<p>Nick, sorry for bugging you. Do you have any input on this?<br>
</p>
<p>Shinhan<br>
</p>
<br>
<div class="moz-cite-prefix">On 12/10/2017 8:37 PM, Michael Campbell
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:13CDC27C-DDE2-4439-B13C-9185CD56CD2A@gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div>
<div><span style="background-color: rgba(255, 255, 255, 0);">Hi
Quanwei,</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);">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.</span><br>
</div>
</div>
<div><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);">I’ve
ccd Shin-Han Shiu on this one. The pipeline was developed in
his lab.</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);">Thanks,</span></div>
<div><span style="background-color: rgba(255, 255, 255, 0);">Mike</span></div>
<div><br>
On Dec 8, 2017, at 8:46 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" moz-do-not-send="true">qwzhang0601@gmail.com</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div>
<div>Thank you Carson and Michael.<br>
<br>
</div>
Best<br>
</div>
Quanwei<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2017-12-07 23:42 GMT-05:00 Carson
Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank" moz-do-not-send="true">carsonhh@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div
style="word-wrap:break-word;line-break:after-white-space">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.
<div><br>
</div>
<div>—Carson<br>
<div><br>
<blockquote type="cite">
<div>
<div class="h5">
<div>On Dec 7, 2017, at 2:44 PM, Quanwei
Zhang <<a href="mailto:qwzhang0601@gmail.com" target="_blank" moz-do-not-send="true">qwzhang0601@gmail.com</a>>
wrote:</div>
<br
class="m_6807041835693246805Apple-interchange-newline">
</div>
</div>
<div>
<div>
<div class="h5">
<div dir="ltr">
<div>
<div>Hello:<br>
<br>
I am trying to identify pseudo genes
following <a href="http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" target="_blank" moz-do-not-send="true">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 the
command "python pseudo_wrap.py
parameter". But I got the following
errors. Do you have any ideas and
suggestions about the errors?
Thanks.<br>
<br>
</div>
<div>##below shows reported errors<br>
</div>
<div>Traceback (most recent call
last):<br>
File
"/gs/gsfs0/users/qzhang/tools/<wbr>maker2_pseudogene/pseudo_pkg//<wbr>ParseBlast.py",
line 4330, in <module><br>
parse.get_qualified4(blast,<wbr>fasta,E,I,L,P,Q)<br>
File
"/gs/gsfs0/users/qzhang/tools/<wbr>maker2_pseudogene/pseudo_pkg//<wbr>ParseBlast.py",
line 3050, in get_qualified4<br>
N = sizes[L[0]]<br>
<span style="color:rgb(255,0,0)">KeyError:
'maker-Contig2656-snap-gene-1.<wbr>9-mRNA-1'</span><br>
Traceback (most recent call last):<br>
File
"/gs/gsfs0/users/qzhang/tools/<wbr>maker2_pseudogene/pseudo_pkg/<wbr>script_step3b.py",
line 98, in <module><br>
oup.write("%s\t%s\t%s\t%s\n" %
(all_contigs[i][0][0],<br>
<span style="color:rgb(255,0,0)">IndexError:
list index out of range</span><br>
Done!<br>
<br>
</div>
Best<br>
</div>
Quanwei<br>
</div>
</div>
</div>
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<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
--------------------------------------
Shin-Han Shiu
Michigan State University
Department of Plant Biology
2265 Mol Plant Sci Bldg
(TEL) +1-517-353-7196
<a class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_keiHZX&d=DwMDaQ&c=nE__W8dFE-shTxStwXtp0A&r=sUBp8FRSXcr7GsPWEwuzZejm3cQdsovXfs8sNKwEUz0&m=INRHprJZS3nvj3I7v7qRvlfE1rmWrIY_tWRnylEUFO0&s=vgKsVpK-Ie-YtMflGCeMoYOPLBVpWJP62soYw76Aqmo&e=">http://goo.gl/keiHZX</a>
--------------------------------------</pre>
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