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<p>Hi Carson,</p>
<p><br>
</p>
<p>The fasta headers were the problem, when I shortened them the run completed sucessfully. Although for other scaffolds too there were similar such long fasta headers but it worked fine.</p>
<p><br>
</p>
<p>Thanks!</p>
<p>Ranjani<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Monday, October 27, 2014 12:18 PM<br>
<b>To:</b> Sivaranjani Namasivayam<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] MAKER error Failed while polishing proteins</font>
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<div class="">There is one warning message and one error message.</div>
<div class=""><br class="">
</div>
<div class="">First this one —></div>
<div class="">WARNING: The fasta file contains sequences with names longer<br class="">
than 78 characters. Long names get trimmed by BLAST, making<br class="">
it harder to identify the source of an alignmnet. You might<br class="">
want to reformat the fasta file with shorter IDs.<br class="">
File_name:/escratch3/ranjani/ranjani_Oct_16/sn1_comparisons/uniprot_top_hits_sn1prot.fa</div>
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</div>
<div class="">Also this one —> sh: File name too long</div>
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<div class="">The cause of your failures are the long sequence identifiers in your fasta. There are actually several potential downstream issues as a result, but the most immediate is that some temporary file names are going to be based off the sequence ID,
and because your seq IDs are really long, they result in file names that are bigger than the largest allowed filename for the system.</div>
<div class=""><br class="">
</div>
<div class="">Here is one example of a long ID I see in your STDERR —></div>
<div class="">SRCN_4312|tg_ortholog:TGME49_201150|EC:EC:3.6.3.12;EC:3.6.3.4;EC:3.6.3.8|scaff:scaffold00018|start:414787|end:435051|blastp_output:gi:401406237:ref:XP_003882568.1:</div>
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<div class="">You need to reformat the header of each FASTA entry to make it shorter, not just for MAKER but for programs MAKER uses. Sequence Identifiers should be separated from other comment information in the FASTA header by spaces or else the comments
become part of the identifier in accordance with FASTA format.</div>
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<div class="">Thanks,</div>
<div class="">Carson</div>
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<blockquote type="cite" class="">
<div class="">On Oct 26, 2014, at 2:35 PM, Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu" class="">ranjani@uga.edu</a>> wrote:</div>
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<div class="" style="margin-top:0px; margin-bottom:0px"><font class="" face="Calibri,Arial,Helvetica,sans-serif">Hi Carson,<br class="">
<br class="">
Attaching the error file. (The file is too big to be posted to the mailing list). There are a number of errors reported about the fasta file, but I see these errors for the other scaffolds too and I get predictions and they run finished successfully , so I
thought these errors might not be the reason..</font></div>
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</font></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><font class="" face="Calibri,Arial,Helvetica,sans-serif">Thanks,</font></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><font class="" face="Calibri,Arial,Helvetica,sans-serif">Ranjani</font></div>
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<div id="divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, October 23, 2014 3:20 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Sivaranjani Namasivayam<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] MAKER error Failed while polishing proteins</font>
<div class=""> </div>
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<div class="">The causal error will be further up the error log. You may just want to send your capture STDERR file.
<div class=""><br class="">
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<div class="">—Carson</div>
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<blockquote type="cite" class="">
<div class="">On Oct 23, 2014, at 1:05 PM, Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu" class="">ranjani@uga.edu</a>> wrote:</div>
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Hi,</div>
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I get this error when I run MAKER</div>
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ERROR: Failed while polishing proteins<br class="">
ERROR: Chunk failed at level:10, tier_type:3<br class="">
FAILED CONTIG:scaffold00006<br class="">
<br class="">
ERROR: Chunk failed at level:4, tier_type:0<br class="">
FAILED CONTIG:scaffold00006</div>
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Other scaffolds run fine, but this scaffold keeps failing. Would it mean something is wrong with the proteins in this scaffold?</div>
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Thanks,</div>
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Ranjani<br class="">
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">
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<span id="cid:53770EC7-F3FA-47FF-A190-AA10B2107483@genetics.utah.edu"><submpi2.sh.e5771113.zip></span></div>
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