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<p class="MsoNormal">Hi Jon,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It looks like the script is attempting to parse a bad Genbank record, one that was truncated by an external error from NCBI, and failing (which is probably a good thing if the record is faulty).
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I noticed the record for that protein no longer is valid (it’s discontinued); the genome was replaced with this one:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">https://www.ncbi.nlm.nih.gov/genome/?term=txid1343740[Organism:noexp]<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Was this an older cached record?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Bioperl-l <bioperl-l-bounces+cjfields=illinois.edu@mailman.open-bio.org> on behalf of "Moller, Abraham" <mollera2@miamioh.edu><br>
<b>Date: </b>Tuesday, June 20, 2017 at 7:24 PM<br>
<b>To: </b>"bioperl-l@mailman.open-bio.org" <bioperl-l@mailman.open-bio.org><br>
<b>Subject: </b>[Bioperl-l] Problems downloading and parsing GenBank records<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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Hi all,<o:p></o:p></p>
<p style="margin-left:.5in">I have been using a script to parse GenBank files to find taxonomic information corresponding to bacterial genomes. After several tries, my script has failed with the following error:<o:p></o:p></p>
<p style="margin-left:.5in">...<br>
<code><span style="font-size:10.0pt">Bacteria_Actinobacteria_Streptomycetales_Streptomycetaceae_Streptomyces_Streptomyces_sp._4F</span></code><br>
<code><span style="font-size:10.0pt">Bacteria_Actinobacteria_Streptomycetales_Streptomycetaceae_Streptomyces_Streptomyces_glaucescens</span></code><br>
<code><span style="font-size:10.0pt">--------------------- WARNING ---------------------</span></code><br>
<code><span style="font-size:10.0pt">MSG: Unbalanced quote in:</span></code><br>
<code><span style="font-size:10.0pt">/locus_tag="M271_25565"</span></code><br>
<code><span style="font-size:10.0pt">/inference="COORDINATES: ab initio prediction:GeneMarkS+"</span></code><br>
<code><span style="font-size:10.0pt">/note="Derived by automated computational analysis using</span></code><br>
<code><span style="font-size:10.0pt">gene prediction method: GeneMarkS+."</span></code><br>
<code><span style="font-size:10.0pt">/codon_start=1</span></code><br>
<code><span style="font-size:10.0pt">/transl_table=11</span></code><br>
<code><span style="font-size:10.0pt">/product="membrane protein"</span></code><br>
<code><span style="font-size:10.0pt">/protein_id="YP_008791527.1"</span></code><br>
<code><span style="font-size:10.0pt">/db_xref="GeneID:17596261"</span></code><br>
<code><span style="font-size:10.0pt">/translation="MPSPTSLAPAGPTATPTRTTATARRLMAICGTLLAALLCALSVG</span></code><br>
<code><span style="font-size:10.0pt">ANSASAHAALTSTDPADGSVVKTAPREVTLNFSEGVLLSGDSVRVLDPKGKRVDTGKT</span></code><br>
<code><span style="font-size:10.0pt">AHVDGKSSTAAAGLHSGLPDG Error: External viewer error: Empty Response. Bytes read: 0 Status:</span></code>
<code><span style="font-size:10.0pt">TimeoutNo further qualifiers will be added for this feature</span></code><br>
---------------------------------------------------`<o:p></o:p></p>
<p style="margin-left:.5in">After this, the script seems to halt for hours at least, if not indefinitely...<br>
Is this a BioPerl or GenBank issue? Any help would be appreciated.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Jon Moller<br clear="all">
<o:p></o:p></p>
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-- <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Abraham (Jon) Moller <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Microbiology and Chemistry | 2016<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Cell, Molecular, and Structural Biology (CMSB) BS/MS | Liang Bioinfo Lab<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in">Microbiology Club President <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
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