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<div>Ok. I took a look and I'm relatively sure the issue you are seeing is caused by GFF3 passthrough combined with correct_est_fusion=1. This is something that only happens when both are used simultaneously and should be corrected in the current version
of MAKER.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Marc Höppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, August 6, 2014 at 12:14 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span><<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Maker GFF output with features of 0 length<br>
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Hi,
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<div>I suspect that Augustus plays a role, since the affected features are seeded by augustus (based on the name anyway).</div>
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<div>What I found was that this seems to only happen when using pre-aligned (i.e. GFF3-formatted) cdna2genome and protein2genome evidence (created by Maker in a previous run). And this seems to be quit reproducible - and doesn’t only affect CDS features. </div>
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<div>I have put the Maker output for a test scaffold here:</div>
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<div><a href="https://dl.dropboxusercontent.com/u/1918141/maker_output.tar.bz2">https://dl.dropboxusercontent.com/u/1918141/maker_output.tar.bz2</a></div>
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<div>The problematic lines: </div>
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<div style="margin: 0px; font-family: Menlo;">scaffold_563 maker five_prime_UTR 38501 38501 . - . ID=augustus_masked-scaffold_563-processed-gene-0.14-mRNA-1:five_prime_utr;Parent=augustus_masked-scaffold_563-processed-gene-0.14-mRNA-1</div>
<div style="margin: 0px; font-family: Menlo;">scaffold_563 maker exon 69967 69967 . - . ID=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1:exon:148;Parent=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1</div>
<div style="margin: 0px; font-family: Menlo;">scaffold_563 maker CDS 69967 69967 . - 1 ID=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1:cds;Parent=augustus_masked-scaffold_563-processed-gene-0.18-mRNA-1</div>
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<div style="margin: 0px; font-family: Menlo;">Strange stuff…</div>
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<div style="margin: 0px; font-family: Menlo;">Regards,</div>
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<div style="margin: 0px; font-family: Menlo;">Marc</div>
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<div>On 05 Aug 2014, at 22:49, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:</div>
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<div>One more thing. From the example you gave, is is important to note that the terminal CDS (first or last) can be a single base pair in length (start and end will be the same value). Augustus sometimes does this for example. Do you have non-CDS feature
types where this happens, or any internal CDS's where this happens?</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, August 5, 2014 at 2:21 PM<br>
<span style="font-weight:bold">To: </span>Marc Höppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>>, <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Maker GFF output with features of 0 length<br>
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<div>Were you using GFF3 pass-through or correct_est_fusion options? When you rerun do the same features still have lengths of zero (I.e. is it random or is it reproducable)?</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Marc Höppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, July 30, 2014 at 4:44 AM<br>
<span style="font-weight:bold">To: </span><<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] Maker GFF output with features of 0 length<br>
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Hi,
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<div>I’ve - more by accident - found that many of the gene builds I have generated with Maker (2.31.3) contain features with identical start and stop positions. </div>
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<div>For example:</div>
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<div style="margin: 0px; font-family: Menlo;">scaffold_2927 maker CDS 13013 13013 . + 1 ID=maker-scaffold_2927-augustus-gene-0.8-mRNA-1:cds;Parent=maker-scaffold_2927-augustus-gene-0.8-mRNA-1</div>
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<div>This occurs seemingly randomly for all sorts of feature types and I have only seen this when running Maker on full assemblies. Before I start turning every stone, any ideas about possible explanations for this phenomenon? Is this likely some MPI-related
communication issue, or NFS problems with synching data? Maker runs fine on our system, but that doesn’t mean that there aren’t any cryptic issues that only on these occasions read their head… Regarding the frequency, out of 450.000 GFF lines, 270 were affected
in the case that I looked into the most. So it is pretty rare, but still...</div>
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<div>I am currently using Maker with openmpi-1.7.4 and the file system is mounter of NFS4 and IPoIB. I now switched to Maker 2.31.6, but have no strong reason to suspect that this will make a difference.</div>
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<div>Regards,</div>
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<div>Marc</div>
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