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Genome size is about 1.5Gbp and transcripts are around 22Gbp 😳. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Fields, Christopher J <cjfields@illinois.edu><br>
<b>Sent:</b> Thursday, January 16, 2020 9:03:46 AM<br>
<b>To:</b> Boyher, Adam <ABoyher@danforthcenter.org>; maker-devel@yandell-lab.org <maker-devel@yandell-lab.org><br>
<b>Subject:</b> Re: [maker-devel] Maker failing</font>
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<p class="MsoNormal">It’s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size. I recall it being worse when using a network file system at that time.</p>
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<p class="MsoNormal">chris</p>
<p class="MsoNormal"> </p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt; color:black">From: </span>
</b><span style="font-size:12.0pt; color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher@danforthcenter.org><br>
<b>Date: </b>Wednesday, January 15, 2020 at 7:57 PM<br>
<b>To: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>[maker-devel] Maker failing</span></p>
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<p class="MsoNormal">Hi</p>
<p class="MsoNormal">I’ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I’ve recently started annotating a larger genome with more evidence. But I’m not sure that’s the issue anymore. The most recent run yielded this
error:</p>
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<p class="MsoNormal">ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete</p>
<p class="MsoNormal">MAKER will need to delete the file, before trying again</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">--> rank=12, hostname=pacifica.datasci.danforthcenter.org</p>
<p class="MsoNormal">ERROR: Failed while polishig ESTs</p>
<p class="MsoNormal">ERROR: Chunk failed at level:2, tier_type:3</p>
<p class="MsoNormal">FAILED CONTIG:Chromosome10_0</p>
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<p class="MsoNormal">Any idea what could cause that?</p>
<p class="MsoNormal"><br>
Adam</p>
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<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows 10</p>
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