<div dir="ltr"><div>Hello Shinhan and Michael:<br><br></div>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).<br><div><div><br>>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<br>MGTSLDIKIKRANKVYHAGEMLSGVVVISSKDSVQHQGMSLTMEGTVNLQLSAKSVGVFE<br>AFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHVKGNKVLYETYHGVFVNIQYVL<br>RCDMRRSLLAKDLTKTCEFIVHSVPQKGKLTPSPVDFTITPETLQNVKERALLPKFLIRG<br>HLNSTNCAITQPLTGELVVEHSDAAIRSIELQLVRVETCGCAEGYARDATEIQNIQIADG<br>DVCRSLSVPIYMVFPRLFTCPTLETTNFKVEFEINVVVLLHADHLITENFPLKLCRT<br><br><br></div><div>#below is the blast results <br></div><div>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 100.000 51 0 0 220 270 424151 424303 3.23e-25 111<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 93.103 58 4 0 170 227 423367 423540 4.19e-24 108<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 85.000 60 7 1 66 123 404001 404180 5.67e-24 107<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 100.000 48 0 0 20 67 402613 402756 3.47e-20 96.7<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 50.725 69 25 1 238 297 426022 426228 6.48e-09 63.2<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 67.308 52 15 2 118 168 417125 417277 2.07e-08 61.6<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 100.000 25 0 0 145 169 419825 419899 5.54e-06 53.9<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2656 76.667 30 5 1 1 30 382922 383005 0.012 43.5<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig3808 22.545 275 175 9 15 283 112218 111490 1.13e-07 59.3<br>maker-Contig2656-snap-gene-1.9-mRNA-1 Contig2791 26.667 60 43 1 236 295 20108374 20108550 9.6 34.3</div><div><br></div><div><br></div><div>Many thanks</div><div><br></div><div>Best</div><div>Quanwei<br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-12-11 8:13 GMT-05:00 Shin-Han Shiu <span dir="ltr"><<a href="mailto:shius@msu.edu" target="_blank">shius@msu.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<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.<wbr>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><div><div class="h5">
<br>
<div class="m_-9039773173711307090moz-cite-prefix">On 12/10/2017 8:37 PM, Michael Campbell
wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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">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="m_-9039773173711307090h5">
<div>On Dec 7, 2017, at 2:44 PM, Quanwei
Zhang <<a href="mailto:qwzhang0601@gmail.com" target="_blank">qwzhang0601@gmail.com</a>>
wrote:</div>
<br class="m_-9039773173711307090m_6807041835693246805Apple-interchange-newline">
</div>
</div>
<div>
<div>
<div class="m_-9039773173711307090h5">
<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">http://shiulab.plantbiology.ms<wbr>u.edu/index.php/Protocol:Pseud<wbr>ogene</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,fas<wbr>ta,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/s<wbr>cript_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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</blockquote>
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<br>
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</div>
</blockquote>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre class="m_-9039773173711307090moz-signature" cols="72">--
------------------------------<wbr>--------
Shin-Han Shiu
Michigan State University
Department of Plant Biology
2265 Mol Plant Sci Bldg
(TEL) <a href="tel:(517)%20353-7196" value="+15173537196" target="_blank">+1-517-353-7196</a>
<a class="m_-9039773173711307090moz-txt-link-freetext" href="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=" target="_blank">http://goo.gl/keiHZX</a>
------------------------------<wbr>--------</pre>
</font></span></div>
</blockquote></div><br></div>