Re: Some error messages in the output log of Maker

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Re: Some error messages in the output log of Maker

Carson Holt-2
Augustus can sometimes produce alternate models. It normally only happens with hints and not with the raw prediction though. MAKER by default will only keeps the best scoring one (scored by AED). But EVM technically gets to see all of the raw models. Its the kind of thing where I would have to have the exact data and contig you used to run to see if this is something easily pulled apart for EVM.

—Carson


On Apr 5, 2017, at 6:57 AM, Ray Cui <[hidden email]> wrote:

Dear Carson,

        I think I found the reason for this here https://sourceforge.net/p/evidencemodeler/mailman/message/27284428/
        These messages are from EVM. The second type of message is due to incomplete gene models, so it's not a big deal. The first type is because of the overlapping gene models predicted by Augustus. This is a bit strange. Does maker allow Augustus to produce alternative spliced variants?

Best Regards,
Ray

Dr. Rongfeng (Ray) Cui
Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:+49 (0)221 496 
Mobile:           +49 0221 37970 496



On Wed, Apr 5, 2017 at 1:33 PM, Ray Cui <[hidden email]> wrote:
Hi Carson,

      I saw these messages in the log, is this a concern? I'm using Maker beta 3.
       Message 1:

Error with prediction: augustus_masked lend_intergenic: 730288, rend_intergenic: 664875  at /beegfs/group_dv/software/source/EVidenceModeler-1.1.1/evidence_modeler.pl line 3218.

        Message 2:
Sorry, prediction pred_gff:gth_m.PLPscf119:hit:7108:43932 fails validation.
(GTT)    TA     683590-683765   GC      ATG
(GCA)    AG     701228-701409   GT      AGG
(GGA)    AG     704938-705037   GT      AGG
(GGC)    AG     721672-721792   GT      AGG
(TTG)    AG     730110-730288   AC      GAA
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, terminal, 730110, 730288
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, internal, 701228, 701409
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, internal, 704938, 705037
-recovered pred_gff:gth_m.PLPspolishing proteins


     PS: I am still keep being kicked out of the maker mailing list due to some reason, if you can forward the msg. there it would be great.
         
Best Regards,
Ray

Dr. Rongfeng (Ray) Cui
Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496 
Mobile:           +49 0221 37970 496





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Re: Some error messages in the output log of Maker

Carson Holt-2
Most of the parameters affect the command line used to run blast/exonerate. In that case it will rerun. Some like the percent coverage parameter are post run filters. For those, it just re-parses. I don’t remember off the top of my head which ones fall into which category, but most fall into the first one.

—Carson

On Apr 6, 2017, at 1:18 AM, Ray Cui <[hidden email]> wrote:

Hi Carson,

    Yet another question: if I change the blast and exonerate parameters in the bopts file, will maker automatically rerun blast and exonerate (or, parse the existing output with the new cutoffs)?

Thanks
Ray 

On Apr 5, 2017 6:01 PM, "Carson Holt" <[hidden email]> wrote:
Augustus can sometimes produce alternate models. It normally only happens with hints and not with the raw prediction though. MAKER by default will only keeps the best scoring one (scored by AED). But EVM technically gets to see all of the raw models. Its the kind of thing where I would have to have the exact data and contig you used to run to see if this is something easily pulled apart for EVM.

—Carson


On Apr 5, 2017, at 6:57 AM, Ray Cui <[hidden email]> wrote:

Dear Carson,

        I think I found the reason for this here https://sourceforge.net/p/evidencemodeler/mailman/message/27284428/
        These messages are from EVM. The second type of message is due to incomplete gene models, so it's not a big deal. The first type is because of the overlapping gene models predicted by Augustus. This is a bit strange. Does maker allow Augustus to produce alternative spliced variants?

Best Regards,
Ray

Dr. Rongfeng (Ray) Cui
Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496 
Mobile:           +49 0221 37970 496



On Wed, Apr 5, 2017 at 1:33 PM, Ray Cui <[hidden email]> wrote:
Hi Carson,

      I saw these messages in the log, is this a concern? I'm using Maker beta 3.
       Message 1:

Error with prediction: augustus_masked lend_intergenic: 730288, rend_intergenic: 664875  at /beegfs/group_dv/software/source/EVidenceModeler-1.1.1/evidence_modeler.pl line 3218.

        Message 2:
Sorry, prediction pred_gff:gth_m.PLPscf119:hit:7108:43932 fails validation.
(GTT)    TA     683590-683765   GC      ATG
(GCA)    AG     701228-701409   GT      AGG
(GGA)    AG     704938-705037   GT      AGG
(GGC)    AG     721672-721792   GT      AGG
(TTG)    AG     730110-730288   AC      GAA
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, terminal, 730110, 730288
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, internal, 701228, 701409
-recovered pred_gff:gth_m.PLPscf119:hit:7108:43932, internal, 704938, 705037
-recovered pred_gff:gth_m.PLPspolishing proteins


     PS: I am still keep being kicked out of the maker mailing list due to some reason, if you can forward the msg. there it would be great.
         
Best Regards,
Ray

Dr. Rongfeng (Ray) Cui
Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496 
Mobile:           +49 0221 37970 496






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