From dandence at gmail.com  Mon Oct  2 08:17:57 2017
From: dandence at gmail.com (Daniel Ence)
Date: Mon, 2 Oct 2017 09:17:57 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
Message-ID: <F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>

Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink
The fasta headers in this file are different from the fasta header that the file you used has: 
>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1

Let us know if that helps, 
Daniel

> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> I intend to rename genes for Genebank submission
> 
> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
> 
> the output of BLAST RESULT looks like this
> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
> 
> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
> 
> I got the following result
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
> 
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
> 
> What can I do?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
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From michael.s.campbell1 at gmail.com  Mon Oct  2 08:30:43 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 09:30:43 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
Message-ID: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 

Thanks,
Mike


> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hello-
> 
> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
> 
> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
> 
> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
> 
> Thanks for your help,
> 
> Best,
> 
> Chris Willett
> 
>   
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: 2252 Genome Science Building
> phone:
> 919-843-8663
> fax:
> 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From michael.s.campbell1 at gmail.com  Mon Oct  2 14:19:51 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:19:51 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
Message-ID: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
> On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi Mike-
> 
> I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?
> 
> Thanks for your help,
> 
> Best,
> 
> Chris
> 
> 
> 
>> On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com <mailto:michael.s.campbell1 at gmail.com>> wrote:
>> 
>> Hi Chris,
>> 
>> This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 
>> 
>> Thanks,
>> Mike
>> 
>> 
>>> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu <mailto:willett4 at email.unc.edu>> wrote:
>>> 
>>> Hello-
>>> 
>>> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
>>> 
>>> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
>>> 
>>> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
>>> 
>>> Thanks for your help,
>>> 
>>> Best,
>>> 
>>> Chris Willett
>>> 
>>>   
>>> 
>>> 
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Research Associate Professor
>>> Department of Biology
>>> CB#3280 Coker Hall
>>> University of North Carolina, Chapel Hill
>>> Chapel Hill, NC, 27599-3280 
>>> 
>>> Office: 2252 Genome Science Building
>>> phone:
>>> 919-843-8663
>>> fax:
>>> 919-962-1625
>>> 
>>> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
> 

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From michael.s.campbell1 at gmail.com  Mon Oct  2 14:35:55 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:35:55 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
	<FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
Message-ID: <4C4E3DE7-CE28-4DF7-B234-E88701CAD172@gmail.com>

Hi Chris,

It?s this line here:
model_gff=/proj/willetlb/users/cwillett/MAKER_analyses/dovetail_ann/SDv1.0_est-forward-SDv2.1.gff

Anything passed to model_gff is treated as sacred by MAKER and will be kept regardless of AED. If you pass it in as pred_gff= then it will be subject to the AED filters.

I hope this helps,
Mike
> On Oct 2, 2017, at 3:28 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> <maker_opts.ctl_full8>




From daren.card at gmail.com  Wed Oct  4 10:53:42 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 4 Oct 2017 10:53:42 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
Message-ID: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>

Hi all,

I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?

I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).

Any help would be greatly appreciated.
Daren Card

University of Texas Arlington

###################################################
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=3, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

deleted:0 hits
deleted:0 hits
###################################################




From carsonhh at gmail.com  Wed Oct  4 11:03:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 10:03:52 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
Message-ID: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>

The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.

?Carson


> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi all,
> 
> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
> 
> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
> 
> Any help would be greatly appreciated.
> Daren Card
> 
> University of Texas Arlington
> 
> ###################################################
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
> #-------------------------------#
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=3, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
> #-------------------------------#
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> deleted:0 hits
> deleted:0 hits
> ###################################################
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From qwzhang0601 at gmail.com  Wed Oct  4 17:31:09 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 18:31:09 -0400
Subject: [maker-devel] About eAED
Message-ID: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>

Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I
found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be
the reason of the great difference between AED and eAED. For this gene it
has a very low AED score, is it still a reliable gene model if its eAED
equals 1?

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei
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From xvazquezc at gmail.com  Wed Oct  4 17:35:41 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 5 Oct 2017 09:35:41 +1100
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>

Carson commented on this here
https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:

> Hello:
>
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
> I found there are several hundred genes with eAED 1.
>
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
> be the reason of the great difference between AED and eAED. For this gene
> it has a very low AED score, is it still a reliable gene model if its eAED
> equals 1?
>
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
> QI:75|0|0|1|0|0|2|111|35
>
> Thanks
>
> Best
> Quanwei
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From carsonhh at gmail.com  Wed Oct  4 17:38:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:38:00 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <77155DA5-6454-4B25-BCF6-DE6B077BA548@gmail.com>

eAED is an extended AED calculation that does some inference about the evidence (i.e. checks reading frame and not just overlap, and may infer support for an exon if by splice sites are confirmed etc.). If eAED is 1 that means that while there is evidence supporting the model, the evidence is more likely to be spurious, so it may be a false model.

?Carson

 
> On Oct 4, 2017, at 4:31 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct  4 17:39:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:39:52 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
Message-ID: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>

This one is an even better explanation than the answer I just gave. Thank you.

?Carson

> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> 
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From eennadi at gmail.com  Mon Oct  2 00:03:01 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Oct 2017 06:03:01 +0100
Subject: [maker-devel] Error with Maker_functional_gff
Message-ID: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>

Hello,
I intend to rename genes for Genebank submission

I downloaded swissprot.fa from NCBI and used blast MAKER generated file to
swissprot.

the output of BLAST RESULT looks like this

snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1
49.315  73      37      0       43      115     874     946     2.61e-14
    71.6


I attempted to run maker_funtional_gff using the swissprot.fa downloaded
and the blastp result


I got the following result

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 2897906.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 2897906.

Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin;
AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP;
AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName:
Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1;
Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor



Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 1608599.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 1608599.

Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X
methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase


What can I do?



Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From willett4 at email.unc.edu  Mon Oct  2 10:04:38 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 15:04:38 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
Message-ID: <DBEB554A-5809-4EB8-AC78-8B410E73B0C4@ad.unc.edu>

Hi Mike-

Thanks for getting back to me. I was using the grep -cP '\tgene\t? syntax to count the numbers and it seems to be giving me the same numbers I got before when I was counting either the transcripts or the genes in the fasta output files from our original run. I will have to look at the files a bit more to see if I can find some examples of genes that fit what you are suggesting.

Best,

Chris


On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From willett4 at email.unc.edu  Mon Oct  2 14:28:19 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 19:28:19 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
Message-ID: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>

Hi Mike-

Here is the control file for the last run of MAKER with keep_preds=0 and here is an example of one mRNA retained from the gff file:

Chromosome_6    maker   mRNA    556000  557215  .       +       .       ID=maker-Chromosome_6-exonerate_est2genome-gene-5.3-mRNA-1;Parent=maker-Chromosome_6-exonerate_est2genome-gene-5.3;Name=TCALIF_02833-PA;_AED=1.00;_eAED=1.00;_QI=15|0|0|0|1|1|2|75|338;score=100;Alias=TCALIF_02833-PA

Thanks,

Chris






On Oct 2, 2017, at 3:19 PM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hi Mike-

I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?

Thanks for your help,

Best,

Chris



On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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From qwzhang0601 at gmail.com  Wed Oct  4 21:35:55 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 22:35:55 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
Message-ID: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>

Thank you all.  Most time, the AED is equal to or lower than eAED, but
there are some genes whose eAED is smaller than AED. I feel the eAED is
more stringent than AED. Would you give me an example, under what condition
eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do
you think eAED is a better choice to filter gene models than AED?

Best
Quanwei



2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> This one is an even better explanation than the answer I just gave. Thank
> you.
>
> ?Carson
>
> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
>> Hello:
>>
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
>> I found there are several hundred genes with eAED 1.
>>
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>> be the reason of the great difference between AED and eAED. For this gene
>> it has a very low AED score, is it still a reliable gene model if its eAED
>> equals 1?
>>
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>> QI:75|0|0|1|0|0|2|111|35
>>
>> Thanks
>>
>> Best
>> Quanwei
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From carsonhh at gmail.com  Wed Oct  4 21:38:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:38:25 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
Message-ID: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>

The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

?Carson


> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
> 
> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
> 
> Best
> Quanwei
> 
>  
> 
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> This one is an even better explanation than the answer I just gave. Thank you.
> 
> ?Carson
> 
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>> 
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>> 
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> Hello:
>> 
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>> 
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>> 
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>> 
>> Thanks
>> 
>> Best
>> Quanwei
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
>> 
>> 
>> -- 
>> Xabier V?zquez-Campos, PhD
>> Research Associate
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From carsonhh at gmail.com  Wed Oct  4 21:43:28 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:43:28 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
Message-ID: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>

eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn?t exist, it just means you should spend a little more time deciding if you really believe it or not.

?Carson


> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> 
>> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
>> 
>> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
>> 
>> Best
>> Quanwei
>> 
>>  
>> 
>> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
>> This one is an even better explanation than the answer I just gave. Thank you.
>> 
>> ?Carson
>> 
>>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>>> 
>>> Carson commented on this here
>>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>>> 
>>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>>> Hello:
>>> 
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>>> 
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>>> 
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>>> 
>>> Thanks
>>> 
>>> Best
>>> Quanwei
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Xabier V?zquez-Campos, PhD
>>> Research Associate
>>> NSW Systems Biology Initiative
>>> School of Biotechnology and Biomolecular Sciences
>>> The University of New South Wales
>>> Sydney NSW 2052 AUSTRALIA
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
> 

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From qwzhang0601 at gmail.com  Wed Oct  4 22:25:24 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 23:25:24 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
	<C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
Message-ID: <CAOW6FSKZzHUVFm=b+3V82whb+gWNdAgERfO=e5f1k1HSRGz=kw@mail.gmail.com>

Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> eAED can be better for edge cases, but neither is perfect. Low AED
> generally correlates with better models. But a high AED does not mean the
> model doesn?t exist, it just means you should spend a little more time
> deciding if you really believe it or not.
>
> ?Carson
>
>
>
> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> The previous linked comment explains in detail ?>
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> Basically the middle support of exon is inferred from edge support even
> though no overlap exists (so eAED infers support and AED does not).
>
> ?Carson
>
>
> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Thank you all.  Most time, the AED is equal to or lower than eAED, but
> there are some genes whose eAED is smaller than AED. I feel the eAED is
> more stringent than AED. Would you give me an example, under what condition
> eAED can be smaller than AED?
>
> The default maker2 gene set includes all genes with AED less than 1.  Do
> you think eAED is a better choice to filter gene models than AED?
>
> Best
> Quanwei
>
>
>
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:
>
>> This one is an even better explanation than the answer I just gave. Thank
>> you.
>>
>> ?Carson
>>
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
>> wrote:
>>
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-
>> ko/iC4KTuIitGEJ
>>
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>>> Hello:
>>>
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1).
>>> But I found there are several hundred genes with eAED 1.
>>>
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>>> be the reason of the great difference between AED and eAED. For this gene
>>> it has a very low AED score, is it still a reliable gene model if its eAED
>>> equals 1?
>>>
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>>> QI:75|0|0|1|0|0|2|111|35
>>>
>>> Thanks
>>>
>>> Best
>>> Quanwei
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>> --
>> Xabier V?zquez-Campos, *PhD*
>> *Research Associate*
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
>
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From dandence at gmail.com  Thu Oct  5 09:00:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Thu, 5 Oct 2017 10:00:21 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
	<F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>
	<CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
Message-ID: <ECCCAE79-FEDA-4C6E-B7E4-A8FC0C3AD1C2@gmail.com>

Hi Emmanuel, 

I can?t tell whether it?s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you?ll run after all the blasts are complete. 

Assembly isn?t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. 

How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I?d recommend starting with a  review like this one: http://www.sciencedirect.com/science/article/pii/S1672022912000095 <http://www.sciencedirect.com/science/article/pii/S1672022912000095>

~Daniel

> On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Daniel,
> 
> Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now
> 
> it looks like this
> 
> MUCPR_041061-RA	sp|P10978|POLX_TOBAC	49.315	73	37	0	43	115	874	946	2.95e-14	71.6
> MUCPR_026643-RA	sp|Q00451|PRF1_SOLLC	86.207	87	11	1	243	328	257	343	3.65e-32	126
> 
> Is it ok?
> 
> I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?
> 
> I wish to assemble my sequence into scaffold can you advice on the best software to use?
> 
> I attempted using SSPACE: a new stand-alone scaffolding tool for small and large genomes
> but am having problem with the library. Funny enough the software does not have support to solve problems
> 
> Thanks
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink <http://www.uniprot.org/downloads#uniprotkblink>
> The fasta headers in this file are different from the fasta header that the file you used has: 
> >sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1
> 
> Let us know if that helps, 
> Daniel
> 
>> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Hello,
>> I intend to rename genes for Genebank submission
>> 
>> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
>> 
>> the output of BLAST RESULT looks like this
>> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
>> 
>> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
>> 
>> I got the following result
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
>> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
>> 
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
>> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
>> 
>> What can I do?
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
> 

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From daren.card at gmail.com  Fri Oct  6 07:23:36 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Fri, 6 Oct 2017 07:23:36 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
Message-ID: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>

Dear Carson,

Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.

Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.

Thank you,
Daren Card


################################################
doing repeat masking
re reading repeat masker report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
doing blastx repeats
re reading blast report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
deleted:2 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=NA, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

examining contents of the fasta file and run log
################################################



> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>> 
>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>> 
>> Any help would be greatly appreciated.
>> Daren Card
>> 
>> University of Texas Arlington
>> 
>> ###################################################
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=3, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>> #-------------------------------#
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> deleted:0 hits
>> deleted:0 hits
>> ###################################################
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Sat Oct  7 16:34:46 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sat, 7 Oct 2017 22:34:46 +0100
Subject: [maker-devel] jbrowse not working
Message-ID: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse.

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Sun Oct  8 19:37:12 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 8 Oct 2017 18:37:12 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
Message-ID: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>

MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).

The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/ <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/>

?Carson





> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Dear Carson,
> 
> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
> 
> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
> 
> Thank you,
> Daren Card
> 
> 
> ################################################
> doing repeat masking
> re reading repeat masker report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
> doing blastx repeats
> re reading blast report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
> deleted:2 hits
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=NA, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> examining contents of the fasta file and run log
> ################################################
> 
> 
> 
>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>> 
>> ?Carson
>> 
>> 
>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Hi all,
>>> 
>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>> 
>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>> 
>>> Any help would be greatly appreciated.
>>> Daren Card
>>> 
>>> University of Texas Arlington
>>> 
>>> ###################################################
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>> #-------------------------------#
>>> deleted:0 hits
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=3, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>> #-------------------------------#
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> deleted:0 hits
>>> deleted:0 hits
>>> ###################################################
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 

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From carsonhh at gmail.com  Mon Oct  9 19:35:49 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 9 Oct 2017 18:35:49 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
Message-ID: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>

Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Please,
> I ran the command line
> 
> maker2jbrowse muc1_genome_snap2.all.gff
> 
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
> 
> Please what does it mean? How can I view it in jbrowse. 
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From eennadi at gmail.com  Mon Oct  9 23:42:35 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 10 Oct 2017 05:42:35 +0100
Subject: [maker-devel] jbrowse not working
In-Reply-To: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
Message-ID: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge ?d
dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse
/Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse
-d
/Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log
\-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the
jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31
contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of
> the file? That can happen if you use the -n option with gff3_merge.
> Alternatively it?s possible one of the individual contig gff3 used to build
> the merged gff3 is truncated. If that is the case then gff3_merge should
> have thrown some sort of error or warning when you run it.
>
> Thanks,
> Carson
>
>
>
>
> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Please,
> I ran the command line
>
> maker2jbrowse muc1_genome_snap2.all.gff
>
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
>
> Please what does it mean? How can I view it in jbrowse.
>
> Thanks
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
>
>
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From jacques.dainat at nbis.se  Tue Oct 10 04:24:34 2017
From: jacques.dainat at nbis.se (Jacques Dainat)
Date: Tue, 10 Oct 2017 11:24:34 +0200
Subject: [maker-devel] MAKER annotation submission (EMBLmyGFF3)
Message-ID: <967873FE-D61F-4233-A004-C877A60A2AC1@nbis.se>

Hi MAKER users,

I take advantage to this mailing list to share a tool that I hope will be useful for MAKER's users. One of the steps once we are happy of our wonderful annotation is to submit it to the public archives through one of the three INSDC databases (EMBL-EBI / NCBI / DDBJ).
We developed EMBLmyGFF3, allowing to easily convert any kind of GFF3 annotation to the EMBL flat file format in order to submit to the European Nucleotide Archive (ENA) Database that is part of EMBL-EBI.
It works well, amongst others, with the MAKER annotation output. We hope the tool will ease the submission process of your annotations.

You will find it here:
https://github.com/NBISweden/EMBLmyGFF3

A typical usage case will look like that (where ERSXXXXXX and PRJXXXXXX are the accession number and the project ID provided by EMBL-EBI prior to any submission):
./EMBLmyGFF3.py maker.gff3 maker.fa --data_class STD --topology linear --molecule_type 'genomic DNA' --table 1 --species 'Drosophila melanogaster (fly)' --taxonomy INV --accession ERSXXXXXXX --project_id PRJXXXXXXX --rg MYGROUP -o result.embl

Best regards,

Jacques Dainat, PhD
---------------------------------------
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
---------------------------------------
Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics


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From mcsimenc at gmail.com  Wed Oct 11 09:53:36 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 07:53:36 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons with
 EST only?
Message-ID: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence
supporting gene models in my MAKER annotation where the left side shows
number of genes with EST support only, the right side shows number of genes
with protein support only, and the intersection shows number of genes with
EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be
fraction of exons that overlap an EST alignment and possibly also a protein
alignment. If that is the case then we can't calculate the number of genes
that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to
get this?

Thanks!!!
Matt Simenc
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From michael.s.campbell1 at gmail.com  Wed Oct 11 10:18:54 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Wed, 11 Oct 2017 11:18:54 -0400
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
Message-ID: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> Hey MAKER people,
> 
> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
> 
> QI summary has:
> 
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
> 
> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
> 
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
> 
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 11 10:22:54 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Oct 2017 09:22:54 -0600
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
Message-ID: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>

Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL <https://github.com/The-Sequence-Ontology/GAL>

?Carson


 
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Matt,
> 
> I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.
> 
> To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.
> 
> Hope this helps,
> Mike
> 
>> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>> 
>> Hey MAKER people,
>> 
>> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
>> 
>> QI summary has:
>> 
>> Fraction of exons that overlap an EST alignment
>> Fraction of exons that overlap EST or Protein alignments
>> 
>> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
>> 
>> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
>> 
>> Thanks!!!
>> Matt Simenc
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From mcsimenc at gmail.com  Wed Oct 11 23:19:04 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 21:19:04 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
Message-ID: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Also look at GAL for building GFF3 feature queries ?>
> https://github.com/The-Sequence-Ontology/GAL
>
> ?Carson
>
>
>
>
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <
> michael.s.campbell1 at gmail.com> wrote:
>
> Hi Matt,
>
> I have a hacky way that I?ve done it. It requires running MAKER two more
> times but they are quicker runs.
>
> To identify the genes that have protein support I pass all of the
> annotation back to MAKER using the model_gff option in the maker_opts.ctl
> file. Then I pull out all of the protein2genome features from the big MAKER
> GFF3 file and pass them in using the protein_gff option. I turn off all
> repeat masking and run MAKER. It runs fast because it doesn?t have to run
> any gene finders, align evidence, or repeatmask. In the output any gene
> with an AED less than 1 has protein support. Then I do the same thing with
> est2genome lines from the big GFF3 file and put them in as est_gff. The
> output of that one gives you genes with EST support. Then the genes with an
> AED of less than one in both sets have support from protein and EST.
>
> Hope this helps,
> Mike
>
> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>
> Hey MAKER people,
>
> I would like to make a Venn diagram showing the kinds of evidence
> supporting gene models in my MAKER annotation where the left side shows
> number of genes with EST support only, the right side shows number of genes
> with protein support only, and the intersection shows number of genes with
> EST and protein support.
>
> QI summary has:
>
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
>
> Please correct me if I'm wrong, because I am interpreting the first to be
> fraction of exons that overlap an EST alignment and possibly also a protein
> alignment. If that is the case then we can't calculate the number of genes
> that overlap only EST or (EST and protein) from the QI information.
>
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to
> get this?
>
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From scott at scottcain.net  Thu Oct 12 18:33:05 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:33:05 -0400
Subject: [maker-devel] GMOD hackathon before PAG San Diego in January
Message-ID: <CA+JTaoytocv6efRcY6LqKXRjPZXeqa9JFFStCPxE0VunjmB-Nw@mail.gmail.com>

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From daren.card at gmail.com  Thu Oct 12 21:22:54 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Thu, 12 Oct 2017 21:22:54 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
Message-ID: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>

Hi Carson,

Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.

Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.

I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.

What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.

Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.

Thanks,
Daren


> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
> 
> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
> 
> ?Carson
> 
> 
> 
> 
> 
>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Dear Carson,
>> 
>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>> 
>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>> 
>> Thank you,
>> Daren Card
>> 
>> 
>> ################################################
>> doing repeat masking
>> re reading repeat masker report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>> doing blastx repeats
>> re reading blast report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>> deleted:2 hits
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=NA, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> examining contents of the fasta file and run log
>> ################################################
>> 
>> 
>> 
>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>> 
>>> ?Carson
>>> 
>>> 
>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>> 
>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>> 
>>>> Any help would be greatly appreciated.
>>>> Daren Card
>>>> 
>>>> University of Texas Arlington
>>>> 
>>>> ###################################################
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>> #-------------------------------#
>>>> deleted:0 hits
>>>> collecting blastx repeatmasking
>>>> processing all repeats
>>>> in cluster::shadow_cluster...
>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>> --> rank=3, hostname=moonunit0
>>>> ERROR: Failed while processing all repeats
>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>> #-------------------------------#
>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> deleted:0 hits
>>>> deleted:0 hits
>>>> ###################################################
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
> 




From robert.zimmermann at univie.ac.at  Wed Oct 11 14:42:14 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Wed, 11 Oct 2017 21:42:14 +0200
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
Message-ID: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>

Hello,

I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 

My gene prediction section of the maker_opts.ctl file looks like this:
...
augustus_species=all_combined #Augustus gene prediction species model
...
pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
?

It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.

Thanks for your help!

Bob


From xvazquezc at gmail.com  Thu Oct 12 01:09:32 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 12 Oct 2017 17:09:32 +1100
Subject: [maker-devel] choosing the right gene model
Message-ID: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>

Hi there,

I was visualising the annotations and I realised that in some cases, what
it seems to be a gene is splitted according to one of the gene models,
despite that the other 2, est2genome and prot2genome suggest that it isn't
the case.



Although the opposite also happens.


?
For some reason, the "out of place" model is always (or almost) the one
from Genemark.

How much weight does carry the RNAseq and protein data on this decision (if
any)?
How exactly is the final gene selected?

Cheers,
Xabi

-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From jan.nagel at fabi.up.ac.za  Thu Oct 12 02:37:07 2017
From: jan.nagel at fabi.up.ac.za (Jan FABI)
Date: Thu, 12 Oct 2017 09:37:07 +0200
Subject: [maker-devel] Maker problem
Message-ID: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution
to it online.

I am running maker on a new genome, using BRAKER trained models for
Augustus and GeneMark. This was successful and performed as expected,
except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with
intron models. I have made sure that the input fasta does not contain
characters other than ATCGN or contains "windows"/non-UNIX carriage
returns.

I include the relevant portion of the log below. Could you help me
determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus
--species=Np_2017_braker --UTR=off
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 >
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

-- 
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : jan.nagel at fabi.up.ac.za

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

-- 
This message and attachments are subject to a disclaimer.
Please refer to 
http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf for full 
details.
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From scott at scottcain.net  Thu Oct 12 18:40:33 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:40:33 -0400
Subject: [maker-devel] Call for presentations at GMOD workshop at PAG
Message-ID: <CA+JTaoyZEYHX0RyKMW7+3d+wic+PyshCUUfhzCzeroXnmyVECw@mail.gmail.com>

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From carsonhh at gmail.com  Fri Oct 13 10:37:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:37:25 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
Message-ID: <C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>

So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.

Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi <http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi>

?Carson



> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi Carson,
> 
> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
> 
> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
> 
> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
> 
> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
> 
> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
> 
> Thanks,
> Daren
> 
> 
>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>> 
>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>> 
>> ?Carson
>> 
>> 
>> 
>> 
>> 
>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Dear Carson,
>>> 
>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>> 
>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>> 
>>> Thank you,
>>> Daren Card
>>> 
>>> 
>>> ################################################
>>> doing repeat masking
>>> re reading repeat masker report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>> doing blastx repeats
>>> re reading blast report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>> deleted:2 hits
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=NA, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> examining contents of the fasta file and run log
>>> ################################################
>>> 
>>> 
>>> 
>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> 
>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>> 
>>>> ?Carson
>>>> 
>>>> 
>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>> 
>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>> 
>>>>> Any help would be greatly appreciated.
>>>>> Daren Card
>>>>> 
>>>>> University of Texas Arlington
>>>>> 
>>>>> ###################################################
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>> #-------------------------------#
>>>>> deleted:0 hits
>>>>> collecting blastx repeatmasking
>>>>> processing all repeats
>>>>> in cluster::shadow_cluster...
>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>> --> rank=3, hostname=moonunit0
>>>>> ERROR: Failed while processing all repeats
>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>> #-------------------------------#
>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> deleted:0 hits
>>>>> deleted:0 hits
>>>>> ###################################################
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>> 
>> 
> 

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From carsonhh at gmail.com  Fri Oct 13 10:42:41 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:42:41 -0600
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
In-Reply-To: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
References: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
Message-ID: <947BFB2F-A893-417B-A043-07CE71F6F97E@gmail.com>

Hi Bob,

pred_gff is a way to get models MAKER cannot run into the analysis. Input to pred_gff will not get hints since MAKER is not running the program. Setting augustus_species allows MAKER to run Augustus with and without hints and then those models compete against each other. You cannot just run with hints as the raw model is also used as a filter to help reduce false positive gene models that result from bad hints. If the gff3 you are providing is the same as the MAKER run of Augustus, I would recommend not providing it. If it is different in some way, then you can leave it in.  If you run under MPI (it?s ok to run MPI on a single machine), then MAKER will parallelize the Augustus run by running multiple configs and contig chunks at the same time.

Thanks,
Carson





> On Oct 11, 2017, at 1:42 PM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hello,
> 
> I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 
> 
> My gene prediction section of the maker_opts.ctl file looks like this:
> ...
> augustus_species=all_combined #Augustus gene prediction species model
> ...
> pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
> model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
> est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
> protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
> ?
> 
> It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.
> 
> Thanks for your help!
> 
> Bob
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Fri Oct 13 10:50:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:50:26 -0600
Subject: [maker-devel] Maker problem
In-Reply-To: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
References: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
Message-ID: <FE4BF464-D049-415D-9AC2-D013B0FB727B@gmail.com>

If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example ?> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke (mario.stanke at uni-greifswald.de <mailto:mario.stanke at uni-greifswald.de>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

?Carson


> On Oct 12, 2017, at 1:37 AM, Jan FABI <jan.nagel at fabi.up.ac.za> wrote:
> 
> Dear Maker team
> 
> I am experiencing a problem while running maker and cannot find a solution to it online. 
> 
> I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. 
> 
> This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. 
> 
> I include the relevant portion of the log below. Could you help me determine the cause of this error.
> 
> 
> 
> setting up GFF3 output and fasta chunks
> preparing ab-inits
> running  augustus.
> #--------- command -------------#
> Widget::augustus:
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx-VirtualBox
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 
> 
> -- 
> Regards 
> Jan Nagel
> ----------------------------------------------------------------------
> PhD Genetics student
> Department of Genetics
> Forestry and Agricultural Biotechnology Institute (FABI) 
> FABI 1, Room 1-55
> University of Pretoria
> 74 Lunnon Rd. Hillcrest
> 0002
> Gauteng Province
> South Africa
> 
> Email : jan.nagel at fabi.up.ac.za <mailto:jan.nagel at fabi.up.ac.za>
> 
> Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961 <http://www.fabinet.up.ac.za/index.php/people-profile?profile=961>
> This message and attachments are subject to a disclaimer.
> Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf <http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf> for full details.
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 10:56:43 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:56:43 -0600
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
Message-ID: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>

Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it?s evidence, so it?s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it?s a fungi, I often find GeneMark can have that affect).

?Carson


> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi there,
> 
> I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.
> 
> <split-gene.png>
> 
> Although the opposite also happens.
> 
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one from Genemark.
> 
> How much weight does carry the RNAseq and protein data on this decision (if any)?
> How exactly is the final gene selected?
> 
> Cheers,
> Xabi
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 11:56:30 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 10:56:30 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
	<CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
Message-ID: <2D6E11BC-6853-458D-AEB1-12EF74D041A3@gmail.com>

The master_datastore_index.log file has a list of failed and finished contigs.  You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.

Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it?s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).

You will need to see if you can identify which contig file is truncated and rerun it.

?Carson






> On Oct 9, 2017, at 10:42 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> Thanks for the reply
> 
> I generated the off with this command gff3_merge ?d dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
> I had to rerun browse with the following command
> 
> maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb
> 
> Although its showing
> 
> WARNING: No matching features found for mRNA I don't know what it means
> 
> I don't understand what it means
> 
> 
> Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host
> 
> 
> The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?
> 
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.
> 
> Thanks,
> Carson
> 
> 
> 
> 
>> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Please,
>> I ran the command line
>> 
>> maker2jbrowse muc1_genome_snap2.all.gff
>> 
>> The command created some folders. However, at the end it read
>> No reference sequences defined in configuration, nothing to do.
>> 
>> Please what does it mean? How can I view it in jbrowse. 
>> 
>> Thanks
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> 

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From xvazquezc at gmail.com  Fri Oct 13 15:26:40 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Sat, 14 Oct 2017 07:26:40 +1100
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
	<821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
Message-ID: <CAL0hg4Hxgrfhbah+7euuQV0YSCjYkV+WqxVu4_QYyf38pYts3Q@mail.gmail.com>

Actually, it's a fungal genome. Although not very typical, almost half of
it are repeats. Worth mention that Genemark generates a lot of predictions
that overlap LTRs and other complex repeats, something that neither SNAP or
Augustus do. Have you seen this before?

On 14 Oct. 2017 02:56, "Carson Holt" <carsonhh at gmail.com> wrote:

> Both transcript and protein evidence will go into the AED calculation for
> overlap support. So in both cases the chosen model had better overlap
> (protein evidence will not count toward the eAED overlap calculation if it
> is out of frame with the model it is supposed to be supporting). The larger
> merged model generates a clutering affect on it?s evidence, so it?s
> evidence set for AED calculation is slightly different than the SNAP and
> Augustus model would generate. In both cases, I think GeneMark is hurting
> more than it is helping. You may want to just drop it from the analysis
> (unless it?s a fungi, I often find GeneMark can have that affect).
>
> ?Carson
>
>
> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Hi there,
>
> I was visualising the annotations and I realised that in some cases, what
> it seems to be a gene is splitted according to one of the gene models,
> despite that the other 2, est2genome and prot2genome suggest that it isn't
> the case.
>
> <split-gene.png>
>
> Although the opposite also happens.
>
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one
> from Genemark.
>
> How much weight does carry the RNAseq and protein data on this decision
> (if any)?
> How exactly is the final gene selected?
>
> Cheers,
> Xabi
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From z2.stewart at qut.edu.au  Sun Oct 15 00:02:08 2017
From: z2.stewart at qut.edu.au (ZACHARY STEWART)
Date: Sun, 15 Oct 2017 05:02:08 +0000
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
Message-ID: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>

Hello MAKER team,


I am hoping I could have a bit of your time if that isn't a problem. I am currently performing the advanced repeat library construction as described on the MAKER wiki, and everything appears to work as expected until I reach "2.1.5 Building examplars". At this point I encounter a problem previously documented in the Google group (title: advanced repeat masking library constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta" and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify what you meant by simplifying the sequence names. The genomic contig names are in a format such as ">001676F" and I modified the MITE library to have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]" which I have not tried changing since I suspect the name is important for later reassociation. If you could point me in the right direction that would be very appreciated.


Regards,

Zac.
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From eennadi at gmail.com  Sun Oct 15 16:32:10 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sun, 15 Oct 2017 22:32:10 +0100
Subject: [maker-devel] Backlash running through my sequence
Message-ID: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>

Hi all,
I am trying to running annotation on some of my sequences but noticed that
i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From xvazquezc at gmail.com  Mon Oct 16 02:26:56 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Mon, 16 Oct 2017 18:26:56 +1100
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
In-Reply-To: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
References: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
Message-ID: <CAL0hg4Gz=vfaDkQEb3J-JPDw0TiRsmH2Fae2YsKX5AtZe0YYjA@mail.gmail.com>

Hi Zac,
The contig names you indicate shouldn't give any problems. And if you
changed the names of MITE.lib right after creation and before using it
downstream, it shouldn't be an issue.

Have you confirmed if the prior blastx output has any results?

Also, be sure you use the same version of makeblastdb and blastx/blastn. I
remember reading before running the protocol for first time that in some
cases, switching versions could give problems.
And be careful if you copy/paste from the wiki page, there are a few typos
and dashes instead of minus characters in the command line option flags,
all of which will result in errors

Xabi

On 15 October 2017 at 16:02, ZACHARY STEWART <z2.stewart at qut.edu.au> wrote:

> Hello MAKER team,
>
>
> I am hoping I could have a bit of your time if that isn't a problem. I am
> currently performing the advanced repeat library construction as described
> on the MAKER wiki, and everything appears to work as expected until I reach
> "2.1.5 Building examplars". At this point I encounter a problem previously
> documented in the Google group (title: advanced repeat masking library
> constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta"
> and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify
> what you meant by simplifying the sequence names. The genomic contig names
> are in a format such as ">001676F" and I modified the MITE library to
> have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta
> has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]"
> which I have not tried changing since I suspect the name is important for
> later reassociation. If you could point me in the right direction that
> would be very appreciated.
>
>
> Regards,
>
> Zac.
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From yuejiaxing at gmail.com  Mon Oct 16 03:54:42 2017
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Mon, 16 Oct 2017 10:54:42 +0200
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>

Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning
message about uninitialized value (see the warning message below) although
still finished the installation.

[jxyue at paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/bu
ild/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm
line 3082.
Use of uninitialized value $line in substitution (s///) at
/home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/
cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors
about cannot find my specified snaphmm model for the annotation, despite
that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the
"maker_opts.ctl" file and this configuration information has been
successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap
/home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm
/tmp/maker_m8TVEQ/chrI.abinit_masked.0 >
/tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap
S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta >
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening
file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot
about the path to  my specified hmm file and instead looks for this file in
its default installation location)

It is worth noting that the parallel installation and run with
maker-3.00.0-beta finish smoothly without any problem. So I suspect both
the installation warning and the executing error are caused by the changes
during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check
about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker
(e.g. 3.00.0-beta in this particular case) when the user finish the
registration in the maker download page? This will help users to roll back
to older version when needed.  Also this helps for the version control when
other developers develop annotation pipelines that use maker as a
dependency package. Thanks for the consideration!


Best,
Jia-Xing

-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Facult? de M?decine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/
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From carsonhh at gmail.com  Mon Oct 16 11:20:32 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 16 Oct 2017 10:20:32 -0600
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
Message-ID: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



> On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi all,
> I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
>  I attached the sequence
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications><sample_1.fasta>

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From cjfields at illinois.edu  Tue Oct 17 14:11:39 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 17 Oct 2017 19:11:39 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
Message-ID: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson Holt <carsonhh at gmail.com>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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From carsonhh at gmail.com  Tue Oct 17 14:33:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Oct 2017 13:33:26 -0600
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
	<CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
Message-ID: <30F2FDFE-3B4E-4951-89D8-63C2FC772B63@gmail.com>

Thanks. The map_fasta_ids script was empty in the bin directory for some reason, so the installer through an error because it could not find the #!/usr/bin/perl line. I have put it back in the bin directory where it was supposed to be and the issue goes away for the install.

For the second issue, I think I found it and have updated a new tar ball to the website.

Also here is a link to download the old 3.00-beta, although I would not recommend making it part of a pipeline because version 3 is still beta and still has bugs (you should use 2.31.9 instead for piplines).  ?> http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz <http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz>

?Carson


 
> On Oct 16, 2017, at 2:54 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
> 
> Dear maker developers,
> 
> I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation. 
> 
> [jxyue at paralog src]$ ./Build install
> Building MAKER
> Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
> Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
> Installing MAKER...
> Building MAKER
> ...
> 
> Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
> #-------------------------------#
> 
> # (my comment: up to now everything looks fine)
> ....
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
> /maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
> #-------------------------------#
> ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
> ZOE library version 2017-03-01
> ERROR: Snap failed
> --> rank=NA, hostname=paralog.itc.unipi.it <http://paralog.itc.unipi.it/>
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chrI
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chrI
> 
> examining contents of the fasta file and run log
> 
> # (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)
> 
> It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!
> 
> Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!
> 
> 
> Best,
> Jia-Xing
> 
> -- 
> Jia-Xing Yue 
> 
> Population Genomics and Complex Traits Group
> Tour Pasteur 8eme etage
> Facult? de M?decine
> Institute for Research on Cancer and Aging, Nice (IRCAN)
> CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
> 28 Avenue de Valombrose
> 06107 NICE Cedex 2
> France
> 
> Personal website: http://www.iamphioxus.org/ <http://www.iamphioxus.org/>
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From patrick.tranvan at unil.ch  Wed Oct 18 06:47:35 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Wed, 18 Oct 2017 11:47:35 +0000
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>,
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <1508327278733.19140@unil.ch>

Hi Carson,


1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?


2) I am trying to annotate a 1GB specie but it's superslow.

I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ?

Cheers,

Patrick Tran Van


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From carsonhh at gmail.com  Wed Oct 18 10:09:10 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 18 Oct 2017 09:09:10 -0600
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <1508327278733.19140@unil.ch>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
	<1508327278733.19140@unil.ch>
Message-ID: <486FE3D5-0902-4B05-A3E1-96642C68E422@gmail.com>

MAKER can coordinate parallelization under MPI in a way it can?t even with multiple simultaneous runs. Because processes can comunicate among themselves under MPI, MAKER can break larger contigs into chunks or even pull off individual steps and pass them onto another processor, then receive the results back from that processor. So multiple BLAST, RepeatMasker, Exonerate, and prediction processes can all run at the same time for the same contig. Then they all pass their result back to the parent process so it can produce output for that contig. MPI was chosen as the parallelization framework rather than threads because it works both within a single machine as well as across multiple machines, so you can scale up to hundreds of processes if needed.

?Carson


> On Oct 18, 2017, at 5:47 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi Carson, 
> 
> 1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?
> 
> 2) I am trying to annotate a 1GB specie but it's superslow.
> I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ? 
> 
> Cheers,
> 
> Patrick Tran Van
> 
> 

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From jhumann at wsu.edu  Wed Oct 18 15:38:41 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Wed, 18 Oct 2017 20:38:41 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
Message-ID: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>

Hello,

I was wondering if there was any way to enable the '-fix_nucleotides' option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu


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From robert.zimmermann at univie.ac.at  Thu Oct 19 10:25:08 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:25:08 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
Message-ID: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>

Hi Maker Developers,

I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.

Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?

Thanks for your help!

Best,
Bob

?

Department of Molecular Evolution and Development
Universit?t Wien
Althanstra?e 14 (UZA I), Zimmer 2.019 
1090 Vienna
Austria

+43 1 427757002




From robert.zimmermann at univie.ac.at  Thu Oct 19 10:28:17 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:28:17 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
Message-ID: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>

Correction to the above numbers, the median lengths are 1414 and 1256.

> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hi Maker Developers,
> 
> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
> 
> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
> 
> Thanks for your help!
> 
> Best,
> Bob
> 
> ?
> 
> Department of Molecular Evolution and Development
> Universit?t Wien
> Althanstra?e 14 (UZA I), Zimmer 2.019 
> 1090 Vienna
> Austria
> 
> +43 1 427757002
> 




From carsonhh at gmail.com  Thu Oct 19 10:44:07 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 09:44:07 -0600
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
	<CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
Message-ID: <62F04A76-F3F1-4044-B4AD-129B15A9EEB2@gmail.com>

You should look at both in a browser to get a better idea of what?s going on. What MAKER does is take the evidence given, clusters it (strand specific clustering) then uses the transcript evidence as intron hints to the predictors and protein alignments as exon hints (will also use polished protein hints to generate intron hints in the absence of transcript intron hints). Finally it uses overlapping transcript evidence to generate UTR. So look at it in a browser. See if the apparent overlap clusters are different in extent, also look for mRNA-seq evidence being merged. If the cluster is falsely merging between two loci because the mRNA-seq is merged, one of two things will happen you will get multiple models since the predictor can?t make a single model work within the cluster using the hints, or you will get a model with a really long UTR that is blocking other models from existing in the region. Also as depending on the mRNA-seq evidence coming in, you may be generating false models because of noise in the data. Essentially everything is transcribed at a basal level, so as you get more and more mRNA-seq, you generate more and more spurious alignments. So more evidence might gernate fewer long alignments for true loci or by falsely merging genes while simultaneously adding a number of very short spurious results.

?Carson



> On Oct 19, 2017, at 9:28 AM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Correction to the above numbers, the median lengths are 1414 and 1256.
> 
>> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
>> 
>> Hi Maker Developers,
>> 
>> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
>> 
>> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
>> 
>> Thanks for your help!
>> 
>> Best,
>> Bob
>> 
>> ?
>> 
>> Department of Molecular Evolution and Development
>> Universit?t Wien
>> Althanstra?e 14 (UZA I), Zimmer 2.019 
>> 1090 Vienna
>> Austria
>> 
>> +43 1 427757002
>> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Thu Oct 19 12:32:44 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 11:32:44 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Oct 19 13:46:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 12:46:17 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
	<SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <052F801C-3B37-4B0F-B40A-A905F5F2B1CE@gmail.com>

Yes. That is the current version.

?Carson

> On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?
>  
> Jodi
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Thursday, October 19, 2017 10:33 AM
> To: Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] fix nucleotides option on MWAS
>  
> Hi Jodi,
>  
> I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).
>  
> Somewhere inside the script there will be a line like this ?>
>  $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
>  
> You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.
>  
> Thanks,
> Carson
>  
>  
> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>> wrote:
>  
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>
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From jhumann at wsu.edu  Thu Oct 19 13:45:43 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Thu, 19 Oct 2017 18:45:43 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
Message-ID: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?

Jodi

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <jhumann at wsu.edu>
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] fix nucleotides option on MWAS

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu<mailto:jhumann at wsu.edu>> wrote:

Hello,

I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu<mailto:jhumann at wsu.edu>


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>

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From eennadi at gmail.com  Mon Oct 23 08:30:07 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 23 Oct 2017 14:30:07 +0100
Subject: [maker-devel] Contamination report from NCBI
Message-ID: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>

Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this
contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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SUBID     	BioProject	BioSample	Organism
--------------------------------------------------------
SUB3124577	PRJNA414658	SAMN07821433	Mucuna pruriens

[] We ran your sequences through our Contamination Screen. The screen found 
contigs that need to be trimmed and/or excluded. Please adjust the 
sequences appropriately and then resubmit your sequences. After you remove the 
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

Note that hits in eukaryotic genomes to mitochondrial sequences can be ignored 
when specific criteria are met. Those criteria are explained below.

Note that mismatches between the name of the adaptor/primer identified in the screen 
and the sequencing technology used to generate the sequencing data should not be used 
to discount the validity of the screen results as the adaptors/primers of many 
different sequencing platforms share sequence similarity.



[] Some of the sequences hit primers or adaptors used in Illumina or 
454 or other sequencing strategies or platforms.  Primers at the 
end of a sequence should be removed. However, if primers are 
present within sequences then you should strongly consider 
splitting the sequences at the primers because the primer sequence 
could have been the region of overlap, causing a misassembly.


Screened 26,016 sequences, 396,641,426 bp.
Note: 5,610 sequences with runs of Ns 10 bp or longer (or those longer that 20 MB) were split before screening.
428 sequences with locations to mask/trim
(31 split spans to exclude, 397 split spans with locations to mask/trim)

Trim:
Sequence name, length, span(s), apparent source
contig_10109	13138	13078..13138	adaptor:NGB00847.1
contig_10200	20270	1..76	adaptor:NGB00847.1
contig_10202	22517	1..44	adaptor:NGB00360.1
contig_10218	55661	55592..55661	adaptor:NGB00847.1
contig_10283	11575	1..79	adaptor:NGB00847.1
contig_1038	91134	91073..91134	adaptor:NGB00360.1
contig_104	10061	10005..10061	adaptor:NGB00360.1
contig_10405	24076	1..43	adaptor:NGB00847.1
contig_10425	16694	16639..16694	adaptor:NGB00360.1
contig_10447	37445	37233..37445	adaptor:NGB00360.1
contig_10466	19368	1..52	adaptor:NGB00847.1
contig_10576	12053	12003..12053	adaptor:NGB00360.1
contig_1059	34516	34457..34516	adaptor:NGB00847.1
contig_106	49997	1..45	adaptor:NGB00360.1
contig_10695	27664	1..38	adaptor:NGB01029.1
contig_10753	12481	12413..12481	adaptor:NGB00847.1
contig_10822	33522	33441..33522	adaptor:NGB00847.1
contig_1083	10637	1..23	adaptor:NGB01096.1
contig_10851	36752	36682..36752	adaptor:NGB00360.1
contig_10878	27925	27848..27925	adaptor:NGB00360.1
contig_10965	23597	1..57	adaptor:NGB00360.1
contig_10968	7413	1..40	adaptor:NGB00847.1
contig_1099	35847	1..70	adaptor:NGB00360.1
contig_11034	10224	10166..10224	adaptor:NGB00360.1
contig_11058	32994	1..23	adaptor:NGB01088.1
contig_11138	17426	1..73	adaptor:NGB00847.1
contig_11166	6306	6266..6306	adaptor:NGB00360.1
contig_11182	26558	1..30	adaptor:NGB01096.1
contig_11216	15160	1..59	adaptor:NGB00847.1
contig_11269	14732	14655..14732	adaptor:NGB00847.1
contig_11306	28246	28199..28246	adaptor:NGB00360.1
contig_1136	28186	1..73	adaptor:NGB00847.1
contig_1141	58119	58028..58119	adaptor:NGB00847.1
contig_11416	8561	8539..8561	adaptor:NGB01088.1
contig_11504	8890	8840..8890	adaptor:NGB00360.1
contig_1158	17422	17398..17422	adaptor:NGB01088.1
contig_11647	7021	1..69	adaptor:NGB00847.1
contig_11684	17442	17418..17442	adaptor:NGB01096.1
contig_11752	38337	38314..38337	adaptor:NGB01088.1
contig_11767	6366	6324..6366	adaptor:NGB00847.1
contig_11791	22415	1..43	adaptor:NGB00847.1
contig_11792	58260	1..29	adaptor:NGB01096.1
contig_1187	39501	39462..39501	adaptor:NGB01029.1
contig_12059	10094	1..72	adaptor:NGB00360.1
contig_12130	13210	13164..13210	adaptor:NGB00360.1
contig_12164	17561	17539..17561	adaptor:NGB01096.1
contig_12169	14178	139..196	adaptor:NGB00360.1
contig_12183	15822	61..112	adaptor:NGB00360.1
contig_12266	11704	11640..11704	adaptor:NGB00360.1
contig_12300	9550	9360..9550	adaptor:NGB01088.1
contig_12324	49997	49891..49997	adaptor:NGB00847.1
contig_12423	45971	45860..45918	adaptor:NGB00360.1
contig_12441	15141	1..42	adaptor:NGB00847.1
contig_12514	14655	1..69	adaptor:NGB00847.1
contig_12515	5355	5326..5355	adaptor:NGB01088.1
contig_12535	22496	22458..22496	adaptor:NGB01029.1
contig_12544	19615	19559..19615	adaptor:NGB00360.1
contig_12558	20026	20007..20026	adaptor:NGB01088.1
contig_12613	6880	6793..6880	adaptor:NGB00847.1
contig_12701	18439	18330..18382	adaptor:NGB00360.1
contig_12713	13341	13274..13341	adaptor:NGB00360.1
contig_12723	17913	1..38	adaptor:NGB01088.1
contig_12730	55277	55249..55277	adaptor:NGB01096.1
contig_12739	6792	1..48	adaptor:NGB00360.1
contig_12787	30950	1..19	adaptor:NGB01096.1
contig_1279	18699	18670..18699	adaptor:NGB01088.1
contig_12815	5168	5091..5168	adaptor:NGB00847.1
contig_12846	20753	1..70	adaptor:NGB00360.1
contig_1288	34784	1..31	adaptor:NGB01096.1
contig_12888	12204	1..23	adaptor:NGB01096.1
contig_12919	10315	1..71	adaptor:NGB00360.1
contig_13031	8972	8938..8972	adaptor:NGB01093.1
contig_13088	6275	1..22	adaptor:NGB01088.1
contig_13140	36197	1..48	adaptor:NGB00360.1
contig_13233	16414	16355..16414	adaptor:NGB00847.1
contig_1330	33261	1..44	adaptor:NGB00847.1
contig_13319	19747	1..20	adaptor:NGB01096.1
contig_13367	36004	35868..35931	adaptor:NGB00847.1
contig_13395	5338	1..79	adaptor:NGB00360.1
contig_1341	30756	30734..30756	adaptor:NGB01088.1
contig_13481	9637	9600..9637	adaptor:NGB00360.1
contig_13506	5704	5662..5704	adaptor:NGB00360.1
contig_13548	5814	79..121	adaptor:NGB00360.1
contig_13567	21576	1..47	adaptor:NGB00847.1
contig_13669	8336	1..24	adaptor:NGB01088.1
contig_13718	23500	1..25	adaptor:NGB01096.1
contig_13783	18720	1..41	adaptor:NGB00847.1
contig_13830	32395	32367..32395	adaptor:NGB01096.1
contig_13845	15572	15493..15572	adaptor:NGB00360.1
contig_13854	10932	1..48	adaptor:NGB00360.1
contig_13943	37701	37674..37701	adaptor:NGB01096.1
contig_13957	7159	1..30	adaptor:NGB01096.1
contig_14014	29735	29672..29735	adaptor:NGB00360.1
contig_14027	21418	21340..21418	adaptor:NGB00360.1
contig_14032	47642	1..53	adaptor:NGB00847.1
contig_14047	26936	1..28	adaptor:NGB01088.1
contig_14048	45832	1..22	adaptor:NGB01088.1
contig_14061	11471	1..179	adaptor:NGB01096.1
contig_14113	17661	1..67	adaptor:NGB00360.1
contig_14173	17601	1..41	adaptor:NGB00847.1
contig_1418	31840	1..248	adaptor:NGB00847.1
contig_14194	7456	7294..7456	adaptor:NGB01096.1
contig_14210	8814	1971..2025	adaptor:NGB00360.1
contig_14223	12513	12489..12513	adaptor:NGB01096.1
contig_14317	21472	21410..21472	adaptor:NGB00360.1
contig_14424	6040	5973..6040	adaptor:NGB00360.1
contig_14425	6404	6379..6404	adaptor:NGB01096.1
contig_14426	31457	31398..31457	adaptor:NGB00847.1
contig_14458	6814	6623..6814	adaptor:NGB01088.1
contig_14524	9488	9431..9488	adaptor:NGB00847.1
contig_14584	20433	1..96	adaptor:NGB00847.1
contig_1459	32979	1..32	adaptor:NGB01096.1
contig_14601	19077	1..28	adaptor:NGB01096.1
contig_14641	21747	1..45	adaptor:NGB00847.1
contig_14664	48155	48118..48155	adaptor:NGB00360.1
contig_14711	11854	11827..11854	adaptor:NGB01096.1
contig_14736	21360	1..37	adaptor:NGB01029.1
contig_14749	12830	1..33	adaptor:NGB01093.1
contig_14966	9962	9891..9962	adaptor:NGB00360.1
contig_14999	5248	1..41	adaptor:NGB00360.1
contig_15010	17976	1..43	adaptor:NGB00360.1
contig_15011	26484	26462..26484	adaptor:NGB01096.1
contig_15017	9331	9291..9331	adaptor:NGB00360.1
contig_1503	63533	1..33	adaptor:NGB01096.1
contig_15032	32240	32157..32240	adaptor:NGB00847.1
contig_15060	15050	15010..15050	adaptor:NGB00847.1
contig_15065	13062	12996..13062	adaptor:NGB00360.1
contig_15070	29943	1..29	adaptor:NGB01096.1
contig_15132	20431	1..71	adaptor:NGB00847.1
contig_15169	7086	7051..7086	adaptor:NGB00846.1
contig_15174	19921	1..23	adaptor:NGB01096.1
contig_15194	16100	16039..16100	adaptor:NGB00847.1
contig_15212	9272	1..50	adaptor:NGB00847.1
contig_15215	15591	1..58	adaptor:NGB00360.1
contig_15271	37699	37647..37699	adaptor:NGB00847.1
contig_15276	11087	11031..11087	adaptor:NGB00847.1
contig_15309	10118	1..42	adaptor:NGB00847.1
contig_15320	7963	7901..7963	adaptor:NGB00847.1
contig_15334	5683	1..36	adaptor:NGB00846.1
contig_15364	17306	76..139	adaptor:NGB00847.1
contig_15374	28301	28263..28301	adaptor:NGB00360.1
contig_15377	10470	10428..10470	adaptor:NGB00360.1
contig_15398	24069	23999..24069	adaptor:NGB00847.1
contig_15500	9289	9271..9289	adaptor:NGB01096.1
contig_15507	25565	1..22	adaptor:NGB01088.1
contig_15523	5782	5762..5782	adaptor:NGB01088.1
contig_15529	10225	10143..10225	adaptor:NGB00360.1
contig_15569	9645	9612..9645	adaptor:NGB01090.1
contig_15596	7163	1..42	adaptor:NGB00360.1
contig_15605	18521	1..31	adaptor:NGB01096.1
contig_15672	8446	1..213	adaptor:NGB01088.1
contig_15686	22141	58..90	adaptor:NGB00847.1
contig_15708	18098	17996..18098	adaptor:NGB00847.1
contig_15736	18284	18252..18284	adaptor:NGB01096.1
contig_15777	17192	1..45	adaptor:NGB00360.1
contig_15812	8602	1..77	adaptor:NGB00360.1
contig_15959	10936	10913..10936	adaptor:NGB01096.1
contig_15972	11324	1..71	adaptor:NGB00360.1
contig_15974	24312	24243..24312	adaptor:NGB00847.1
contig_16057	8838	8775..8838	adaptor:NGB00847.1
contig_16088	7608	1..71	adaptor:NGB00360.1
contig_16142	10392	1..53	adaptor:NGB00847.1
contig_1617	14870	255..310	adaptor:NGB00360.1
contig_16183	9226	9205..9226	adaptor:NGB01088.1
contig_16188	62666	62586..62666	adaptor:NGB00847.1
contig_16370	7868	1..42	adaptor:NGB00847.1
contig_16416	19512	1..21	adaptor:NGB01088.1
contig_1645	25016	24951..25016	adaptor:NGB00360.1
contig_16510	31845	31776..31845	adaptor:NGB00847.1
contig_16529	17342	1..45	adaptor:NGB00360.1
contig_16558	9338	9097..9338	adaptor:NGB00360.1
contig_16573	6590	6521..6590	adaptor:NGB00847.1
contig_16608	7397	7324..7397	adaptor:NGB00847.1
contig_16631	11055	1..50	adaptor:NGB00360.1
contig_16641	5482	1..190	adaptor:NGB01088.1
contig_1667	35244	35200..35244	adaptor:NGB01029.1
contig_16682	14500	1..71	adaptor:NGB00847.1
contig_16699	6216	6148..6216	adaptor:NGB00360.1
contig_16734	12674	12625..12674	adaptor:NGB00360.1
contig_16790	6341	1..51	adaptor:NGB00360.1
contig_16807	7512	1..36	adaptor:NGB01096.1
contig_16817	20743	1..155	adaptor:NGB01088.1
contig_16839	6969	1..69	adaptor:multiple
contig_16870	10948	1..49	adaptor:NGB00847.1
contig_16880	5622	5549..5622	adaptor:NGB00360.1
contig_16889	9182	1..40	adaptor:NGB00360.1
contig_16911	6691	1..28	adaptor:NGB01088.1
contig_16921	9432	9358..9432	adaptor:NGB00360.1
contig_16951	14285	14262..14285	adaptor:NGB01088.1
contig_17021	12242	1..75	adaptor:NGB00360.1
contig_17092	22712	1..64	adaptor:NGB00360.1
contig_17147	7706	7685..7706	adaptor:NGB01096.1
contig_17195	15668	15643..15668	adaptor:NGB01096.1
contig_17214	7881	7819..7881	adaptor:NGB00847.1
contig_17299	7861	7830..7861	adaptor:NGB01088.1
contig_17344	8915	8765..8823	adaptor:NGB00360.1
contig_17361	8425	1..26	adaptor:NGB01096.1
contig_17422	11017	10964..11017	adaptor:NGB00360.1
contig_17471	5988	5964..5988	adaptor:NGB01096.1
contig_17505	10208	1..74	adaptor:NGB00360.1
contig_17506	6091	1..61	adaptor:NGB00360.1
contig_17520	6084	6028..6084	adaptor:NGB00360.1
contig_17538	5796	5766..5796	adaptor:NGB01096.1
contig_17558	7066	6837..7066	adaptor:NGB01080.1
contig_17561	15165	1..206	adaptor:NGB01083.1
contig_17594	6976	1..26	adaptor:NGB01088.1
contig_17655	14371	14177..14371	adaptor:NGB01088.1
contig_17671	17801	1..50	adaptor:NGB00847.1
contig_17680	5752	5693..5752	adaptor:NGB00847.1
contig_17738	6456	1..44	adaptor:NGB00360.1
contig_17741	10917	10889..10917	adaptor:NGB01096.1
contig_17775	5928	1..79	adaptor:NGB00847.1
contig_17804	11597	11562..11597	adaptor:NGB00846.1
contig_17872	11319	11278..11319	adaptor:NGB00847.1
contig_17876	5647	5613..5647	adaptor:NGB01083.1
contig_17925	9923	1..22	adaptor:NGB01088.1
contig_17938	5246	1..23	adaptor:NGB01088.1
contig_18016	8044	1..29	adaptor:NGB01096.1
contig_18017	6668	6647..6668	adaptor:NGB01096.1
contig_18044	11330	11299..11330	adaptor:NGB01096.1
contig_18049	10560	1..88	adaptor:NGB00847.1
contig_18173	12243	1..159	adaptor:NGB01096.1
contig_18175	8788	8765..8788	adaptor:NGB01096.1
contig_18177	11418	11340..11418	adaptor:multiple
contig_18182	11901	11832..11901	adaptor:NGB00847.1
contig_18201	6059	6038..6059	adaptor:NGB01096.1
contig_18222	11216	11136..11216	adaptor:NGB00847.1
contig_18228	8386	8361..8386	adaptor:NGB01088.1
contig_18321	5922	5897..5922	adaptor:NGB01096.1
contig_18370	5400	5085..5116	adaptor:NGB00747.1
contig_18453	5849	1..38	adaptor:NGB00360.1
contig_1846	23210	1..64	adaptor:NGB00360.1
contig_18479	5209	1..44	adaptor:NGB00360.1
contig_18486	5749	5726..5749	adaptor:NGB01088.1
contig_18488	5217	1..19	adaptor:NGB01088.1
contig_1969	65776	1..60	adaptor:NGB00360.1
contig_197	9215	1..83	adaptor:NGB00847.1
contig_1977	13765	1..35	adaptor:NGB01093.1
contig_1999	53427	53398..53427	adaptor:NGB01096.1
contig_2125	11803	11769..11803	adaptor:NGB01083.1
contig_2151	9544	1..37	adaptor:NGB01029.1
contig_2179	38972	1..67	adaptor:NGB00360.1
contig_2186	31110	30935..31110	adaptor:NGB01096.1
contig_2203	60314	60124..60187	adaptor:NGB00847.1
contig_2278	33271	1..36	adaptor:NGB01090.1
contig_2305	17957	1..58	adaptor:NGB00360.1
contig_2361	48816	48764..48816	adaptor:NGB00847.1
contig_242	49604	49535..49604	adaptor:NGB00360.1
contig_2429	76318	76242..76318	adaptor:NGB00847.1
contig_2430	70439	70373..70439	adaptor:NGB00847.1
contig_2459	63920	1..96	adaptor:NGB00847.1
contig_2485	31300	31260..31300	adaptor:NGB00360.1
contig_2508	25152	25095..25152	adaptor:NGB00847.1
contig_2650	36583	1..58	adaptor:NGB00847.1
contig_2668	22089	22052..22089	adaptor:NGB01029.1
contig_2735	13614	1..19	adaptor:NGB01088.1
contig_2781	50403	1..70	adaptor:NGB00847.1
contig_2800	30768	22802..22846	adaptor:NGB00360.1
contig_2824	44109	1..38	adaptor:NGB00847.1
contig_2888	19121	1..89	adaptor:NGB00360.1
contig_2900	36871	1..32	adaptor:NGB01088.1
contig_2949	25959	25916..25959	adaptor:NGB00360.1
contig_2970	20833	1..46	adaptor:NGB00360.1
contig_2986	16429	1..43	adaptor:NGB00360.1
contig_3069	38956	38904..38956	adaptor:NGB00847.1
contig_3106	9135	1..87	adaptor:NGB00847.1
contig_3124	70101	70072..70101	adaptor:NGB01088.1
contig_3129	30402	30379..30402	adaptor:NGB01088.1
contig_3147	10611	10586..10611	adaptor:NGB01096.1
contig_3190	117726	117687..117726	adaptor:NGB01029.1
contig_3243	44291	44273..44291	adaptor:NGB01096.1
contig_3276	57911	1..42	adaptor:NGB00360.1
contig_341	67008	1..22	adaptor:NGB01096.1
contig_3542	16855	1..60	adaptor:NGB00847.1
contig_3595	29288	1..79	adaptor:NGB00847.1
contig_3712	73078	1..78	adaptor:NGB00847.1
contig_3840	40472	40414..40472	adaptor:NGB00360.1
contig_3868	33875	33819..33875	adaptor:NGB00360.1
contig_3903	40080	40010..40080	adaptor:NGB00847.1
contig_3996	44010	43970..44010	adaptor:NGB00360.1
contig_4001	26085	1..73	adaptor:NGB00847.1
contig_4014	30676	30590..30676	adaptor:NGB00360.1
contig_4019	49543	1..76	adaptor:NGB00360.1
contig_4036	58848	58696..58848	adaptor:NGB00846.1
contig_4084	41308	41210..41308	adaptor:NGB00360.1
contig_4095	24801	1..70	adaptor:NGB00847.1
contig_4098	27393	1..189	adaptor:NGB01096.1
contig_410	57740	57678..57740	adaptor:NGB00360.1
contig_4172	20870	9717..9749	adaptor:NGB01096.1
contig_4318	55870	55805..55870	adaptor:NGB00360.1
contig_432	58593	58569..58593	adaptor:NGB01088.1
contig_4323	87370	87304..87370	adaptor:NGB00847.1
contig_4365	27401	27350..27401	adaptor:NGB00847.1
contig_4516	14480	1..98	adaptor:NGB00847.1
contig_452	34031	1..23	adaptor:NGB01096.1
contig_4530	63069	63006..63069	adaptor:NGB00360.1
contig_4651	67570	67518..67570	adaptor:NGB00847.1
contig_4679	20970	1..38	adaptor:NGB00360.1
contig_4686	7411	1..24	adaptor:NGB01096.1
contig_4743	37926	1..79	adaptor:NGB00360.1
contig_4765	11248	11167..11248	adaptor:NGB00360.1
contig_4801	91339	1..50	adaptor:NGB00360.1
contig_4812	37300	37121..37300	adaptor:NGB01093.1
contig_4820	80899	80862..80899	adaptor:NGB00360.1
contig_4904	9220	1..52	adaptor:NGB00847.1
contig_4916	29759	29718..29759	adaptor:NGB00847.1
contig_4924	19015	1..49	adaptor:NGB00847.1
contig_4939	23620	23574..23620	adaptor:NGB01029.1
contig_4956	40890	1..24	adaptor:NGB01088.1
contig_4994	71509	71447..71509	adaptor:NGB00847.1
contig_501	34157	34116..34157	adaptor:NGB00847.1
contig_5036	13162	1..77	adaptor:NGB00360.1
contig_5052	64212	1..170	adaptor:NGB01096.1
contig_5063	35265	35243..35265	adaptor:NGB01096.1
contig_5090	27510	27441..27510	adaptor:NGB00847.1
contig_5157	5988	5805..5988	adaptor:NGB00847.1
contig_5168	6086	6051..6086	adaptor:NGB00846.1
contig_5176	9131	1..41	adaptor:NGB00360.1
contig_5243	44178	1..88	adaptor:NGB00847.1
contig_5270	39229	39177..39229	adaptor:NGB00847.1
contig_5452	30446	1..36	adaptor:NGB00846.1
contig_5576	58918	1..34	adaptor:NGB01096.1
contig_5582	108611	1..87	adaptor:NGB00847.1
contig_5590	55235	55210..55235	adaptor:NGB01088.1
contig_5700	8246	1..82	adaptor:NGB00847.1
contig_5815	99837	1..63	adaptor:NGB00847.1
contig_5820	11616	1..202	adaptor:NGB00847.1
contig_5878	55755	1..26	adaptor:NGB01096.1
contig_59	12390	1..24	adaptor:NGB01096.1
contig_5959	11737	11532..11737	adaptor:NGB01096.1
contig_6065	11492	1..32	adaptor:NGB01088.1
contig_6067	19311	1..39	adaptor:NGB01029.1
contig_6092	14700	1..37	adaptor:NGB01029.1
contig_6194	32760	1..19	adaptor:NGB01088.1
contig_620	10761	1..206	adaptor:NGB01029.1
contig_6259	83001	1..50	adaptor:NGB00360.1
contig_6321	29279	29260..29279	adaptor:NGB01096.1
contig_6408	14690	1..74	adaptor:NGB00360.1
contig_6455	68530	68497..68530	adaptor:NGB01090.1
contig_6513	12061	11986..12061	adaptor:NGB00847.1
contig_6542	45321	1..41	adaptor:NGB00360.1
contig_6569	19579	19500..19579	adaptor:NGB00847.1
contig_6628	13125	13107..13125	adaptor:NGB01096.1
contig_6673	6733	6699..6733	adaptor:NGB01088.1
contig_6676	13298	13265..13298	adaptor:NGB01088.1
contig_6692	17411	1..43	adaptor:NGB00847.1
contig_6703	57771	1..63	adaptor:NGB00360.1
contig_6785	8258	8237..8258	adaptor:NGB01088.1
contig_6908	53004	52732..52792	adaptor:NGB00847.1
contig_6940	18777	18580..18777	adaptor:NGB00360.1
contig_6941	42032	41980..42032	adaptor:NGB00847.1
contig_6945	53258	1..71	adaptor:NGB00360.1
contig_6986	49101	1..21	adaptor:NGB01088.1
contig_701	57358	1..28	adaptor:NGB01096.1
contig_7017	41786	1..88	adaptor:NGB00360.1
contig_7035	53503	53477..53503	adaptor:NGB01096.1
contig_7046	12860	12812..12860	adaptor:NGB00360.1
contig_7081	27746	1..78	adaptor:NGB00847.1
contig_7082	26783	1..73	adaptor:NGB00847.1
contig_7083	44465	1..70	adaptor:NGB00847.1
contig_7117	33739	33661..33739	adaptor:NGB00360.1
contig_7197	5439	5361..5439	adaptor:NGB00360.1
contig_720	34826	34755..34826	adaptor:NGB00360.1
contig_7210	16719	1..30	adaptor:NGB01096.1
contig_7225	51589	51483..51519	adaptor:NGB01090.1
contig_7228	37410	1..64	adaptor:NGB00360.1
contig_7296	6652	1..80	adaptor:NGB00847.1
contig_7317	11682	1..30	adaptor:NGB01088.1
contig_7323	47612	47560..47612	adaptor:NGB00847.1
contig_7353	50534	50506..50534	adaptor:NGB01096.1
contig_7478	44000	43977..44000	adaptor:NGB01088.1
contig_7510	11029	1..22	adaptor:NGB01096.1
contig_7540	12614	12566..12614	adaptor:NGB00360.1
contig_7587	74260	74065..74260	adaptor:NGB00847.1
contig_7607	14652	1..31	adaptor:NGB01088.1
contig_7612	27455	27299..27354	adaptor:NGB00360.1
contig_7705	39772	1..49	adaptor:NGB00360.1
contig_7729	22305	1..172	adaptor:NGB00360.1
contig_7747	11568	11502..11568	adaptor:NGB00847.1
contig_7750	52785	52748..52785	adaptor:NGB01029.1
contig_7800	20628	20588..20628	adaptor:NGB00360.1
contig_7851	53514	53439..53514	adaptor:NGB00360.1
contig_7989	51399	1..97	adaptor:NGB00847.1
contig_7992	9120	9035..9120	adaptor:NGB00360.1
contig_7995	103073	103034..103073	adaptor:NGB00360.1
contig_8000	16924	1..85	adaptor:NGB00847.1
contig_8071	73728	73657..73728	adaptor:NGB00360.1
contig_809	20474	20399..20474	adaptor:NGB00360.1
contig_8139	33627	1..25	adaptor:NGB01088.1
contig_8165	17003	16958..17003	adaptor:NGB00847.1
contig_8207	30300	30275..30300	adaptor:NGB01096.1
contig_821	111683	111656..111683	adaptor:NGB01096.1
contig_8236	30705	1..70	adaptor:NGB00360.1
contig_8261	49091	1..181	adaptor:NGB00847.1
contig_8265	28139	27940..28139	adaptor:NGB00360.1
contig_8307	32654	32591..32654	adaptor:NGB00360.1
contig_8340	12953	12925..12953	adaptor:NGB01096.1
contig_8389	19738	1..75	adaptor:NGB00847.1
contig_8399	35159	1..147	adaptor:NGB01096.1
contig_8569	19455	1..38	adaptor:multiple
contig_8735	42362	42335..42362	adaptor:NGB01088.1
contig_8737	22308	1..70	adaptor:NGB00360.1
contig_8790	14216	14198..14216	adaptor:NGB01096.1
contig_8797	6889	1..95	adaptor:NGB00847.1
contig_8815	39194	1..80	adaptor:NGB00360.1
contig_886	10028	1..76	adaptor:NGB00360.1
contig_8861	12192	12145..12192	adaptor:NGB00360.1
contig_8909	11109	11042..11109	adaptor:NGB00360.1
contig_8932	8331	8281..8331	adaptor:NGB00847.1
contig_8975	8730	8671..8730	adaptor:NGB00847.1
contig_8992	12682	12661..12682	adaptor:NGB01088.1
contig_8994	7982	7950..7982	adaptor:NGB01096.1
contig_9017	8069	7896..8069	adaptor:NGB00360.1
contig_9045	35343	535..598	adaptor:NGB00847.1
contig_9082	10766	1..28	adaptor:NGB01096.1
contig_9271	17773	17750..17773	adaptor:NGB01096.1
contig_9273	12180	1..180	adaptor:NGB01096.1
contig_9287	6067	1..77	adaptor:NGB00847.1
contig_9474	33382	33060..33111	adaptor:NGB00360.1
contig_9495	19348	19274..19348	adaptor:NGB00847.1
contig_9540	30855	30836..30855	adaptor:NGB01088.1
contig_9591	10604	1..41	adaptor:NGB00847.1
contig_9628	15083	1..34	adaptor:NGB01096.1
contig_9677	5510	5486..5510	adaptor:NGB01088.1
contig_9693	9823	1..84	adaptor:NGB00847.1
contig_9825	54363	54309..54363	adaptor:NGB00847.1
contig_9863	14033	14013..14033	adaptor:NGB01088.1
contig_9993	35388	1..26	adaptor:NGB01096.1


From xvazquezc at gmail.com  Mon Oct 23 17:02:47 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Tue, 24 Oct 2017 09:02:47 +1100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's
actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the
contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the
"Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a
different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com> wrote:

> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this
> contamination report.
>
> Please how do I use maker to effect the correction
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From cjfields at illinois.edu  Mon Oct 23 18:21:06 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 23 Oct 2017 23:21:06 +0000
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
Message-ID: <8B4331B5-9D10-478A-91A5-80AF702CD9CD@illinois.edu>

It looks like the adapter is primarily at the ends, which is easy to remove.  However, I agree, removing these and redoing the assembly may improve the assembly quality.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Xabier V?zquez-Campos <xvazquezc at gmail.com>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>, "Ence, daniel" <d.ence at ufl.edu>
Subject: Re: [maker-devel] Contamination report from NCBI

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations
Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
Xabier V?zquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From mmokrejs at gmail.com  Tue Oct 24 05:23:38 2017
From: mmokrejs at gmail.com (=?UTF-8?Q?Martin_MOKREJ=c5=a0?=)
Date: Tue, 24 Oct 2017 12:23:38 +0200
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>

Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
> 
> Good day.
> 
> Please I submitted my sequence to NCBI and they sent back this contamination report.
> 
> Please how do I use maker to effect the correction

-- 
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/



From eennadi at gmail.com  Tue Oct 24 05:44:20 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 24 Oct 2017 11:44:20 +0100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
Message-ID: <CAOXM=CX=AiSo-u8gQ7de1KrgZLUbBZ2GXPbdU6kG3hjrUBjE1A@mail.gmail.com>

Thanks!
Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications



On Oct 24, 2017 11:23 AM, "Martin MOKREJ?" <mmokrejs at gmail.com> wrote:

> Hi Emmanuel,
>   use trimmomatic or cutadapt to remove the adapters and check the output
> file for unremoved cases. Once they are all removed redo the assembly.
> Martin
>
> Emmanuel Nnadi wrote:
> > Hello
> >
> > Good day.
> >
> > Please I submitted my sequence to NCBI and they sent back this
> contamination report.
> >
> > Please how do I use maker to effect the correction
>
> --
> Martin Mokrejs, Ph.D.
> Adapter/artefact removal from datasets based on the following technologies:
>   454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
> http://www.bioinformatics.cz/software/supported-protocols/
>
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From qwzhang0601 at gmail.com  Tue Oct 24 11:54:13 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Tue, 24 Oct 2017 12:54:13 -0400
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
Message-ID: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>

Dear Carson:

Thank you again for your suggestions. I just get the new genome assembly of
NMR and start to do gene annotation. I understand you ideas about this. But
can I simply use the old genome transcripts as transcript evidence, and
just following the standard Maker2 pipeline? I set est2genome=1 and provide
the mRNA sequences in the fasta format for the first round training of SNAP.

For transcripts I have the following choices. I think the first choice is
more reliable and better, right?
(1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded
those sequences in fasta format.
(2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by
trinity for each sample and then get the transcripts. But I think most of
the RNA-seq should have been submitted to NCBI.

BTW, if we use the RefSeq data from NCBI, we can download the mRNA
sequences, coding sequences or protein sequences. I wonder which type of
data are the best to train the SNAP? For Augustus, we will use BUSCO to
train it.

Many thanks.

Best
Quanwei




2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> You can try using the est2genome=1 option to map the old models forward
> onto the new assembly as if they were ESTs (add a line that says
> est_forward=1 to the control file to maintain old naming and set est=1 to
> the old model transcript file). Then provide the final models as a pred_gff
> for a subsuquent run (i.e. a traditional MAKER run where you are annotating
> the new assembly with transcript and protein evidence and ab initio
> predictors). Don?t supply the old models to est= on that run.
>
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will
> change. So by doing it this way, you will at least be able to move many
> models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are
> just letting old models compete against new annotations. They will be
> rejected if they have no evidence support, or can be kept if they score
> better than alternate models from SNAP/Augustus. That way you have the
> chance to integrate old models while at the same time rejecting some old
> models that have no evidence overlap.
>
> ?Carson
>
>
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been
> assembled and annotated a few years ago. We can download the gene
> annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder
> how can I fully make use of existing annotations. On the other hand, since
> the previous genome is not very well assemblies, some genes annotation
> maybe false positives. I hope those false positive genes in previous
> annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Tue Oct 24 17:26:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 24 Oct 2017 16:26:00 -0600
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
	<CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
Message-ID: <C02680FC-A5ED-4CD9-8517-3018CA1A0D69@gmail.com>

Yes. If you use est2genome it will just align the model, and then find the longest ORF. So it is a quick way to jsut align old models to the new assembly. Alternatively you can just do de novo annotation.

?Carson



> On Oct 24, 2017, at 10:54 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Dear Carson:
> 
> Thank you again for your suggestions. I just get the new genome assembly of NMR and start to do gene annotation. I understand you ideas about this. But can I simply use the old genome transcripts as transcript evidence, and just following the standard Maker2 pipeline? I set est2genome=1 and provide the mRNA sequences in the fasta format for the first round training of SNAP.
> 
> For transcripts I have the following choices. I think the first choice is more reliable and better, right?
> (1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded those sequences in fasta format.
> (2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by trinity for each sample and then get the transcripts. But I think most of the RNA-seq should have been submitted to NCBI. 
> 
> BTW, if we use the RefSeq data from NCBI, we can download the mRNA sequences, coding sequences or protein sequences. I wonder which type of data are the best to train the SNAP? For Augustus, we will use BUSCO to train it. 
> 
> Many thanks. 
> 
> Best
> Quanwei
> 
> 
> 
> 
> 2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> You can try using the est2genome=1 option to map the old models forward onto the new assembly as if they were ESTs (add a line that says est_forward=1 to the control file to maintain old naming and set est=1 to the old model transcript file). Then provide the final models as a pred_gff for a subsuquent run (i.e. a traditional MAKER run where you are annotating the new assembly with transcript and protein evidence and ab initio predictors). Don?t supply the old models to est= on that run.
> 
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will change. So by doing it this way, you will at least be able to move many models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are just letting old models compete against new annotations. They will be rejected if they have no evidence support, or can be kept if they score better than alternate models from SNAP/Augustus. That way you have the chance to integrate old models while at the same time rejecting some old models that have no evidence overlap.
> 
> ?Carson
> 
> 
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been assembled and annotated a few years ago. We can download the gene annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder how can I fully make use of existing annotations. On the other hand, since the previous genome is not very well assemblies, some genes annotation maybe false positives. I hope those false positive genes in previous annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From daren.card at gmail.com  Wed Oct 25 07:17:13 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 25 Oct 2017 07:17:13 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
	<C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>
	<97656D7C-3613-4B0B-9D99-0441AC28ABCC@gmail.com>
	<49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
Message-ID: <0406D4C3-9C43-4198-B2EA-241C6C504425@gmail.com>

Hi Carson (and CCed MAKER list for the record),

Thanks for troubleshooting my issue further. Good to hear that the run should ultimately work, but strange it isn?t for me. I?ll keep playing with it and will hopefully get it sorted out by running through the list you suggested. 

Thanks again for the help,
Daren


> On Oct 24, 2017, at 11:27 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> I cannot seem to replicate this. I ran with MAKER 2.31.8 and 2.31.9, both with and without the GFF3 file (total of 4 runs). It succeeded without issues in every case.
> 
> The only things I can think to try are.
> 1. Reinstall BLAST+. Even though you have 2.6.0, just try it anyways. Also Install rmblast 2.6.0 for use wth RepeatMasker (requires that you install from source).
> 2. Maker sure you run ./configure inside RepeatMasker to let it know about the new rmblast installation.
> 3. Change the location of blast and related scripts in maker_exe.ctl otherwise MAKER won?t know to use your new installation.
> 4. delete the mpi_blastdb directory under MAKER?s output directory tp force it to rebuild all BLAST indexes.
> 5. delete any fle with a ?.db? extension in the maker output directory to force it to rebuld all GFF3 indexes.
> 6. Update BioPerl to the current CPAN version.
> 
> Also here is a link to the results I got for your contig (version 2.31.8 using the repeat masking GFF3 file) ?> http://weatherby.genetics.utah.edu/data/scaffold-1.tgz
> 
> ?Carson
> 
> 
> 
>> On Oct 17, 2017, at 6:46 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi Carson,
>> 
>> Thanks for offering to take a further look at this. I?ve uploaded all the files that I think you?d need to run MAKER on your systems, but let me know if you need anything else. My username is ?guest_5038?. 
>> 
>> Repeat annotations GFF is from RepeatModeler, with simple repeats filtered away. Transcript evidence was from Trinity assembly of several RNAseq libraries. Several sets of protein evidence from related species. Also have augustus HMM trained based on the genome assembly using BUSCO with retraining turned on. 
>> 
>> The command I?ve used is below, and here are the software versions I?m working with: 
>> 
>> Maker - 2.31.8
>> BLAST - 2.6.0
>> Augustus - 3.2.3
>> RepeatMasker - 4.0.6
>> 
>> mpiexec -n 12 maker -base CroVir_rnd1_chr1 round1_maker_opts.chr1.ctl maker_bopts.ctl maker_exe.ctl
>> 
>> Thanks again!
>> Daren
>> 
>> 
>>> On Oct 13, 2017, at 10:37 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.
>>> 
>>> Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>>> 
>>> ?Carson
>>> 
>>> 
>>> 
>>>> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi Carson,
>>>> 
>>>> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
>>>> 
>>>> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
>>>> 
>>>> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
>>>> 
>>>> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
>>>> 
>>>> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
>>>> 
>>>> Thanks,
>>>> Daren
>>>> 
>>>> 
>>>>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>>>>> 
>>>>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>>>>> 
>>>>> ?Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>> 
>>>>>> Dear Carson,
>>>>>> 
>>>>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>>>>> 
>>>>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>>>>> 
>>>>>> Thank you,
>>>>>> Daren Card
>>>>>> 
>>>>>> 
>>>>>> ################################################
>>>>>> doing repeat masking
>>>>>> re reading repeat masker report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>>>>> doing blastx repeats
>>>>>> re reading blast report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>>>>> deleted:2 hits
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> collecting blastx repeatmasking
>>>>>> processing all repeats
>>>>>> in cluster::shadow_cluster...
>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>> --> rank=NA, hostname=moonunit0
>>>>>> ERROR: Failed while processing all repeats
>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> examining contents of the fasta file and run log
>>>>>> ################################################
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>>>> 
>>>>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>>>>> 
>>>>>>> ?Carson
>>>>>>> 
>>>>>>> 
>>>>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>>>> 
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>>>>> 
>>>>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>>>>> 
>>>>>>>> Any help would be greatly appreciated.
>>>>>>>> Daren Card
>>>>>>>> 
>>>>>>>> University of Texas Arlington
>>>>>>>> 
>>>>>>>> ###################################################
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> deleted:0 hits
>>>>>>>> collecting blastx repeatmasking
>>>>>>>> processing all repeats
>>>>>>>> in cluster::shadow_cluster...
>>>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>>>> --> rank=3, hostname=moonunit0
>>>>>>>> ERROR: Failed while processing all repeats
>>>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> deleted:0 hits
>>>>>>>> deleted:0 hits
>>>>>>>> ###################################################
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 




From venyao at qq.com  Wed Oct 25 02:25:25 2017
From: venyao at qq.com (=?ISO-8859-1?B?V2VuIFlhbw==?=)
Date: Wed, 25 Oct 2017 15:25:25 +0800
Subject: [maker-devel] NNN in maker output transcript
Message-ID: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>

Dear guys,


Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.


Thanks!


Wen Yao
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From dandence at gmail.com  Wed Oct 25 10:42:04 2017
From: dandence at gmail.com (Daniel Ence)
Date: Wed, 25 Oct 2017 11:42:04 -0400
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <4913D7BA-CD9B-4B7F-83EF-B8072B4950A6@gmail.com>

Hi Wen Yao, 

Do you mean that some of the transcript sequences contain ?N? characters or that an entire transcript sequence is ?NNN??  



> On Oct 25, 2017, at 3:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 10:42:34 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:42:34 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>

The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.

?Carson




> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 10:43:37 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:43:37 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
	<96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
Message-ID: <F55EEB1B-9F79-474A-8AE4-5232566D7380@gmail.com>

Also you can check the source of the model by looking a the name. i.e. does it have, augustus, snap, or est2genome in the name?

?Carson

> On Oct 25, 2017, at 9:42 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.
> 
> ?Carson
> 
> 
> 
> 
>> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
>> 
>> Dear guys,
>> 
>> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
>> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
>> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
>> 
>> Thanks!
>> 
>> Wen Yao
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Thu Oct 26 16:34:33 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Thu, 26 Oct 2017 22:34:33 +0100
Subject: [maker-devel] How to remove contigs from GFF file
Message-ID: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>

Hello,

I need to remove sequences from my GFF file can someone help me with
command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in
gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>
 [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ:
gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From bmoore at genetics.utah.edu  Fri Oct 27 08:17:41 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:17:41 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <98FAE3F3-7C52-4EDA-8FBB-5F43DB7D54C9@umail.utah.edu>

Those look suspiciously like the remnants of end-of-line control characters.  Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I?d look at the upstream path of where your files come from and how they?ve been processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server).  One bizarre example we?ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted to MS format.  Good luck?

Barry

On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From bmoore at genetics.utah.edu  Fri Oct 27 08:24:44 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:24:44 +0000
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
	<CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
Message-ID: <FB1F1E37-1246-4A10-BD9A-BF0644528F15@umail.utah.edu>

Also, you could probably build these overlap sets on the command line by subsetting the MAKER GFF3 file and then using BedTools intersect for overlap queries.

Barry

On Oct 11, 2017, at 10:19 PM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL

?Carson



On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?

Thanks!!!
Matt Simenc
_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
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From dandence at gmail.com  Fri Oct 27 09:51:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Fri, 27 Oct 2017 10:51:21 -0400
Subject: [maker-devel] How to remove contigs from GFF file
In-Reply-To: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
References: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
Message-ID: <D0CA7ADF-64A3-4B15-ACA3-26FA95B1C5F9@gmail.com>

Hi Emmanuel, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this ?grep -v ?scaffold_name? gff3_file?. 

~Daniel



> On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> 
> I need to remove sequences from my GFF file can someone help me with command line for such removal
> 
> ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
> ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 27 17:00:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Oct 2017 16:00:17 -0600
Subject: [maker-devel] "ALRM" isn't numeric in exit - MAKER warning
 message
In-Reply-To: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
References: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
Message-ID: <399AB5BD-2FC5-45F4-9AC8-1665CCFEA0D1@gmail.com>

Hi Marivi,

The only time MAKER uses the ALRM signal is during exit. Sometimes MPI_Finalize can freeze (it has to do with the fact it is being called from Perl). So we set an alarm just in case. Then if it takes to long we assume it is frozen and let things exit in a less than graceful way rather than let it block forever (it is already finished after all). The complaint you get may be because your system doesn?t support the alarm signal or forks.pm (which tries to intercept signals) is having an issue. Or it may just be ugliness related to parts of the process being killed with other parts still being active (it is an ungraceful exit after all). Or it may be another source of the ALRM all together (but I assume it is the MAKER ALRM given that it happens right after MAKER says it is finished). 

Thanks,
Carson



> On Oct 27, 2017, at 1:03 PM, Marivi Colle <collemar at msu.edu> wrote:
> 
> Hi Carson,
> 
> After running MAKER, I checked my std output and here's the message at the end of the file. I was wondering what this warning message means?
> 
> 
> Start_time: 1508465182
> End_time:   1508950543
> Elapsed:    485361
> 
> 
> Maker is now finished!!!
> 
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184
> 
> 
> Thank you.
> Marivi
> 
> 
> -- 
> Marivi G. Colle
> Research Associate
> Department of Horticulture
> Michigan State University
> 1066 Bogue St., East Lansing
> Michigan 48824-1325, USA

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From patrick.tranvan at unil.ch  Sat Oct 28 09:14:59 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Sat, 28 Oct 2017 14:14:59 +0000
Subject: [maker-devel] Advice on my pipeline
In-Reply-To: <651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
References: <6b029690bace4d3fbae77c0bb1bddce8@prdexch02.ad.unil.ch>
	<A39F4213-70A8-4E07-AB13-00C427E4F244@gmail.com>
	<1498470630221.84642@unil.ch>
	<696C51C6-5606-4ECB-A8B8-9C077182FFFA@gmail.com>
	<1498908228256.16549@unil.ch>
	<58E904BF-9AB8-4AC7-B10B-C902F414E03D@gmail.com>
	<1505986013492.52354@unil.ch>,
	<651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
Message-ID: <1509200133044.96929@unil.ch>

Hi Carson,


If I want to look for alternative splicing variant, can I just add the option


alt_splice=1


only at the last round of maker or do I have to set it since the beggining ? (and perform the 4 rounds with this option).

Cheers,

Patrick


________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: Friday, September 22, 2017 10:08 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Advice on my pipeline

The gff3 passthrough options are there to help users get old data into MAKER when they have lost access to the original files. But for iterative running of the pipeline, it is more effective just to rerun in place so MAKER can access the raw alignment reports. The raw reports from the alignments have more detail than what is stored in the GFF3. Details that are lost when trying to use the GFF3 as input.

?Carson


On Sep 21, 2017, at 3:26 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hi Carson,

I have a doubt for the round 2, so in a previous reply you said:

" Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory). "



Does it means that I don't need to modify the section :

#-----Re-annotation Using MAKER Derived GFF3

?

If I let everything by default such as :


altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no


It will not look again for repeat and protein + transcriptome alignment ?

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, July 3, 2017 10:50 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

maker2zff is just for SNAP training and not for gene filtering (please do not use it for filtering, it does not do what you think).

So the final annotation set after maker with correct_est_fusion is 16,850. To decide which set is better, look at them in a browser (gene counts are not useful for guaging result). A well annotated genome will have evidence clusters that closely match the final models. A poorly annoted genome will have evidence clusters that are split or merged by the models.

The corrected_est_fusion does two things. It trims long overlapping UTR fragments, and it stops evidence clusters from being merged on BLASTP evidence alone (so gene predictors will get unmerged hint regions if clusters are split).

You may also find that using jaccard_clip with Trinity has reduced sensitivity for the transcript data (you may lose things that were there before, but now have better specificity, i.e. fewer false positives). Make sure you provided protein data from at least two related species to help maintain sensitivity lost form the transcript data. You can also add rejected genes models back in after the fact by using iprscan to identify unsupported models with identifiable protein domains ?> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/

Thanks,
Carson




On Jul 1, 2017, at 5:21 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

So I have assembled my transcriptome with Trinity using the jaccard clip option and I have run maker with and without corrected_est_fusion.

I have then use SNAP to train/filter it with:

maker2zff  specie.all.gff

Here are my results:

Number of gene after maker -> Number of gene after maker2zff

- Without corrected_est_fusion: 21621 -> 13875
- With corrected_est_fusion: 16850 -> 9098

1 )If I understand well how works corrected_est_fusion, because it prevents gene merging, shouldn't be the invert ?
Normally I should find more genes with corrected_est_fusion right ?

2) I think I should find something like 13000-14000 genes for my specie. SHould I go with the "Without corrected_est_fusion" for the 2nd iteration of maker ?

 Thanks for your help



Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 26, 2017 11:38 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Sorry the option is ?> correct_est_fusion

It is in the maker_opts.ctl file.

I would use both SNAP and Augustus on a few large contigs then review the results manually. If one of them is not behaving well, then drop it. If both behave well (i.e. correlate well with evidence alignemnts) then keep them both.

?Carson



On Jun 26, 2017, at 3:48 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Thanks for your answer.

1) Do you think that adding a Augustus training in addition to SNAP at the step 3 and 5 will add more confidence (instead of adding Augustus only for the final round) ?
Because I am using autoAug for this and it tooks a while to compute ..

2) I don't see this option : 'avoid_est_fusion=1' . I have tried to add it but I got this error:

WARNING: Invalid option 'avoid_est_fusion' in control file maker_opts.ctl

(I am using v 2.31.8 )


Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 5, 2017 8:29 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Your plan sounds good. A couple of related notes.

Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.

Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory).

?Carson


On Jun 2, 2017, at 3:56 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hello,

This is my first time running Maker for an insect genome annotation.

I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:


What I have:
- RNA evidence: transcriptome
- Proteine evidence: swissprot/uniprot + busco protein set of insect
- Cegma and busco results of my genome


1) Train SNAP with CEGMA

2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).

3) Create SNAP model from run A.

4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

5) Create SNAP model from run B.

6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

7)  Create SNAP model from run C AND Create Augustus gene model from run C

8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1). + Use keep_preds=1



Does it seems coherent ?

Cheers,

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org







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From dandence at gmail.com  Mon Oct  2 07:17:57 2017
From: dandence at gmail.com (Daniel Ence)
Date: Mon, 2 Oct 2017 09:17:57 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
Message-ID: <F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>

Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink
The fasta headers in this file are different from the fasta header that the file you used has: 
>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1

Let us know if that helps, 
Daniel

> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> I intend to rename genes for Genebank submission
> 
> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
> 
> the output of BLAST RESULT looks like this
> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
> 
> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
> 
> I got the following result
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
> 
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
> 
> What can I do?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
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From michael.s.campbell1 at gmail.com  Mon Oct  2 07:30:43 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 09:30:43 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
Message-ID: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 

Thanks,
Mike


> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hello-
> 
> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
> 
> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
> 
> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
> 
> Thanks for your help,
> 
> Best,
> 
> Chris Willett
> 
>   
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: 2252 Genome Science Building
> phone:
> 919-843-8663
> fax:
> 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:19:51 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:19:51 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
Message-ID: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
> On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi Mike-
> 
> I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?
> 
> Thanks for your help,
> 
> Best,
> 
> Chris
> 
> 
> 
>> On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com <mailto:michael.s.campbell1 at gmail.com>> wrote:
>> 
>> Hi Chris,
>> 
>> This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 
>> 
>> Thanks,
>> Mike
>> 
>> 
>>> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu <mailto:willett4 at email.unc.edu>> wrote:
>>> 
>>> Hello-
>>> 
>>> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
>>> 
>>> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
>>> 
>>> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
>>> 
>>> Thanks for your help,
>>> 
>>> Best,
>>> 
>>> Chris Willett
>>> 
>>>   
>>> 
>>> 
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Research Associate Professor
>>> Department of Biology
>>> CB#3280 Coker Hall
>>> University of North Carolina, Chapel Hill
>>> Chapel Hill, NC, 27599-3280 
>>> 
>>> Office: 2252 Genome Science Building
>>> phone:
>>> 919-843-8663
>>> fax:
>>> 919-962-1625
>>> 
>>> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
> 

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:35:55 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:35:55 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
	<FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
Message-ID: <4C4E3DE7-CE28-4DF7-B234-E88701CAD172@gmail.com>

Hi Chris,

It?s this line here:
model_gff=/proj/willetlb/users/cwillett/MAKER_analyses/dovetail_ann/SDv1.0_est-forward-SDv2.1.gff

Anything passed to model_gff is treated as sacred by MAKER and will be kept regardless of AED. If you pass it in as pred_gff= then it will be subject to the AED filters.

I hope this helps,
Mike
> On Oct 2, 2017, at 3:28 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> <maker_opts.ctl_full8>




From daren.card at gmail.com  Wed Oct  4 09:53:42 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 4 Oct 2017 10:53:42 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
Message-ID: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>

Hi all,

I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?

I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).

Any help would be greatly appreciated.
Daren Card

University of Texas Arlington

###################################################
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=3, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

deleted:0 hits
deleted:0 hits
###################################################




From carsonhh at gmail.com  Wed Oct  4 10:03:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 10:03:52 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
Message-ID: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>

The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.

?Carson


> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi all,
> 
> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
> 
> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
> 
> Any help would be greatly appreciated.
> Daren Card
> 
> University of Texas Arlington
> 
> ###################################################
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
> #-------------------------------#
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=3, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
> #-------------------------------#
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> deleted:0 hits
> deleted:0 hits
> ###################################################
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From qwzhang0601 at gmail.com  Wed Oct  4 16:31:09 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 18:31:09 -0400
Subject: [maker-devel] About eAED
Message-ID: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>

Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I
found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be
the reason of the great difference between AED and eAED. For this gene it
has a very low AED score, is it still a reliable gene model if its eAED
equals 1?

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei
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From xvazquezc at gmail.com  Wed Oct  4 16:35:41 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 5 Oct 2017 09:35:41 +1100
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>

Carson commented on this here
https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:

> Hello:
>
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
> I found there are several hundred genes with eAED 1.
>
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
> be the reason of the great difference between AED and eAED. For this gene
> it has a very low AED score, is it still a reliable gene model if its eAED
> equals 1?
>
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
> QI:75|0|0|1|0|0|2|111|35
>
> Thanks
>
> Best
> Quanwei
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From carsonhh at gmail.com  Wed Oct  4 16:38:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:38:00 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <77155DA5-6454-4B25-BCF6-DE6B077BA548@gmail.com>

eAED is an extended AED calculation that does some inference about the evidence (i.e. checks reading frame and not just overlap, and may infer support for an exon if by splice sites are confirmed etc.). If eAED is 1 that means that while there is evidence supporting the model, the evidence is more likely to be spurious, so it may be a false model.

?Carson

 
> On Oct 4, 2017, at 4:31 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct  4 16:39:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:39:52 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
Message-ID: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>

This one is an even better explanation than the answer I just gave. Thank you.

?Carson

> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> 
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From eennadi at gmail.com  Sun Oct  1 23:03:01 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Oct 2017 06:03:01 +0100
Subject: [maker-devel] Error with Maker_functional_gff
Message-ID: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>

Hello,
I intend to rename genes for Genebank submission

I downloaded swissprot.fa from NCBI and used blast MAKER generated file to
swissprot.

the output of BLAST RESULT looks like this

snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1
49.315  73      37      0       43      115     874     946     2.61e-14
    71.6


I attempted to run maker_funtional_gff using the swissprot.fa downloaded
and the blastp result


I got the following result

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 2897906.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 2897906.

Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin;
AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP;
AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName:
Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1;
Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor



Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 1608599.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 1608599.

Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X
methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase


What can I do?



Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From willett4 at email.unc.edu  Mon Oct  2 09:04:38 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 15:04:38 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
Message-ID: <DBEB554A-5809-4EB8-AC78-8B410E73B0C4@ad.unc.edu>

Hi Mike-

Thanks for getting back to me. I was using the grep -cP '\tgene\t? syntax to count the numbers and it seems to be giving me the same numbers I got before when I was counting either the transcripts or the genes in the fasta output files from our original run. I will have to look at the files a bit more to see if I can find some examples of genes that fit what you are suggesting.

Best,

Chris


On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From willett4 at email.unc.edu  Mon Oct  2 13:28:19 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 19:28:19 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
Message-ID: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>

Hi Mike-

Here is the control file for the last run of MAKER with keep_preds=0 and here is an example of one mRNA retained from the gff file:

Chromosome_6    maker   mRNA    556000  557215  .       +       .       ID=maker-Chromosome_6-exonerate_est2genome-gene-5.3-mRNA-1;Parent=maker-Chromosome_6-exonerate_est2genome-gene-5.3;Name=TCALIF_02833-PA;_AED=1.00;_eAED=1.00;_QI=15|0|0|0|1|1|2|75|338;score=100;Alias=TCALIF_02833-PA

Thanks,

Chris






On Oct 2, 2017, at 3:19 PM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hi Mike-

I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?

Thanks for your help,

Best,

Chris



On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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From qwzhang0601 at gmail.com  Wed Oct  4 20:35:55 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 22:35:55 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
Message-ID: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>

Thank you all.  Most time, the AED is equal to or lower than eAED, but
there are some genes whose eAED is smaller than AED. I feel the eAED is
more stringent than AED. Would you give me an example, under what condition
eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do
you think eAED is a better choice to filter gene models than AED?

Best
Quanwei



2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> This one is an even better explanation than the answer I just gave. Thank
> you.
>
> ?Carson
>
> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
>> Hello:
>>
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
>> I found there are several hundred genes with eAED 1.
>>
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>> be the reason of the great difference between AED and eAED. For this gene
>> it has a very low AED score, is it still a reliable gene model if its eAED
>> equals 1?
>>
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>> QI:75|0|0|1|0|0|2|111|35
>>
>> Thanks
>>
>> Best
>> Quanwei
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From carsonhh at gmail.com  Wed Oct  4 20:38:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:38:25 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
Message-ID: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>

The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

?Carson


> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
> 
> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
> 
> Best
> Quanwei
> 
>  
> 
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> This one is an even better explanation than the answer I just gave. Thank you.
> 
> ?Carson
> 
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>> 
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>> 
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> Hello:
>> 
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>> 
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>> 
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>> 
>> Thanks
>> 
>> Best
>> Quanwei
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
>> 
>> 
>> -- 
>> Xabier V?zquez-Campos, PhD
>> Research Associate
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From carsonhh at gmail.com  Wed Oct  4 20:43:28 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:43:28 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
Message-ID: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>

eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn?t exist, it just means you should spend a little more time deciding if you really believe it or not.

?Carson


> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> 
>> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
>> 
>> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
>> 
>> Best
>> Quanwei
>> 
>>  
>> 
>> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
>> This one is an even better explanation than the answer I just gave. Thank you.
>> 
>> ?Carson
>> 
>>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>>> 
>>> Carson commented on this here
>>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>>> 
>>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>>> Hello:
>>> 
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>>> 
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>>> 
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>>> 
>>> Thanks
>>> 
>>> Best
>>> Quanwei
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Xabier V?zquez-Campos, PhD
>>> Research Associate
>>> NSW Systems Biology Initiative
>>> School of Biotechnology and Biomolecular Sciences
>>> The University of New South Wales
>>> Sydney NSW 2052 AUSTRALIA
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
> 

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From qwzhang0601 at gmail.com  Wed Oct  4 21:25:24 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 23:25:24 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
	<C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
Message-ID: <CAOW6FSKZzHUVFm=b+3V82whb+gWNdAgERfO=e5f1k1HSRGz=kw@mail.gmail.com>

Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> eAED can be better for edge cases, but neither is perfect. Low AED
> generally correlates with better models. But a high AED does not mean the
> model doesn?t exist, it just means you should spend a little more time
> deciding if you really believe it or not.
>
> ?Carson
>
>
>
> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> The previous linked comment explains in detail ?>
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> Basically the middle support of exon is inferred from edge support even
> though no overlap exists (so eAED infers support and AED does not).
>
> ?Carson
>
>
> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Thank you all.  Most time, the AED is equal to or lower than eAED, but
> there are some genes whose eAED is smaller than AED. I feel the eAED is
> more stringent than AED. Would you give me an example, under what condition
> eAED can be smaller than AED?
>
> The default maker2 gene set includes all genes with AED less than 1.  Do
> you think eAED is a better choice to filter gene models than AED?
>
> Best
> Quanwei
>
>
>
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:
>
>> This one is an even better explanation than the answer I just gave. Thank
>> you.
>>
>> ?Carson
>>
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
>> wrote:
>>
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-
>> ko/iC4KTuIitGEJ
>>
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>>> Hello:
>>>
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1).
>>> But I found there are several hundred genes with eAED 1.
>>>
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>>> be the reason of the great difference between AED and eAED. For this gene
>>> it has a very low AED score, is it still a reliable gene model if its eAED
>>> equals 1?
>>>
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>>> QI:75|0|0|1|0|0|2|111|35
>>>
>>> Thanks
>>>
>>> Best
>>> Quanwei
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>> --
>> Xabier V?zquez-Campos, *PhD*
>> *Research Associate*
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
>
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From dandence at gmail.com  Thu Oct  5 08:00:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Thu, 5 Oct 2017 10:00:21 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
	<F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>
	<CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
Message-ID: <ECCCAE79-FEDA-4C6E-B7E4-A8FC0C3AD1C2@gmail.com>

Hi Emmanuel, 

I can?t tell whether it?s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you?ll run after all the blasts are complete. 

Assembly isn?t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. 

How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I?d recommend starting with a  review like this one: http://www.sciencedirect.com/science/article/pii/S1672022912000095 <http://www.sciencedirect.com/science/article/pii/S1672022912000095>

~Daniel

> On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Daniel,
> 
> Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now
> 
> it looks like this
> 
> MUCPR_041061-RA	sp|P10978|POLX_TOBAC	49.315	73	37	0	43	115	874	946	2.95e-14	71.6
> MUCPR_026643-RA	sp|Q00451|PRF1_SOLLC	86.207	87	11	1	243	328	257	343	3.65e-32	126
> 
> Is it ok?
> 
> I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?
> 
> I wish to assemble my sequence into scaffold can you advice on the best software to use?
> 
> I attempted using SSPACE: a new stand-alone scaffolding tool for small and large genomes
> but am having problem with the library. Funny enough the software does not have support to solve problems
> 
> Thanks
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink <http://www.uniprot.org/downloads#uniprotkblink>
> The fasta headers in this file are different from the fasta header that the file you used has: 
> >sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1
> 
> Let us know if that helps, 
> Daniel
> 
>> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Hello,
>> I intend to rename genes for Genebank submission
>> 
>> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
>> 
>> the output of BLAST RESULT looks like this
>> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
>> 
>> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
>> 
>> I got the following result
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
>> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
>> 
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
>> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
>> 
>> What can I do?
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
> 

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From daren.card at gmail.com  Fri Oct  6 06:23:36 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Fri, 6 Oct 2017 07:23:36 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
Message-ID: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>

Dear Carson,

Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.

Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.

Thank you,
Daren Card


################################################
doing repeat masking
re reading repeat masker report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
doing blastx repeats
re reading blast report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
deleted:2 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=NA, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

examining contents of the fasta file and run log
################################################



> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>> 
>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>> 
>> Any help would be greatly appreciated.
>> Daren Card
>> 
>> University of Texas Arlington
>> 
>> ###################################################
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=3, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>> #-------------------------------#
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> deleted:0 hits
>> deleted:0 hits
>> ###################################################
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Sat Oct  7 15:34:46 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sat, 7 Oct 2017 22:34:46 +0100
Subject: [maker-devel] jbrowse not working
Message-ID: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse.

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Sun Oct  8 18:37:12 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 8 Oct 2017 18:37:12 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
Message-ID: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>

MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).

The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/ <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/>

?Carson





> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Dear Carson,
> 
> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
> 
> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
> 
> Thank you,
> Daren Card
> 
> 
> ################################################
> doing repeat masking
> re reading repeat masker report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
> doing blastx repeats
> re reading blast report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
> deleted:2 hits
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=NA, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> examining contents of the fasta file and run log
> ################################################
> 
> 
> 
>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>> 
>> ?Carson
>> 
>> 
>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Hi all,
>>> 
>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>> 
>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>> 
>>> Any help would be greatly appreciated.
>>> Daren Card
>>> 
>>> University of Texas Arlington
>>> 
>>> ###################################################
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>> #-------------------------------#
>>> deleted:0 hits
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=3, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>> #-------------------------------#
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> deleted:0 hits
>>> deleted:0 hits
>>> ###################################################
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 

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From carsonhh at gmail.com  Mon Oct  9 18:35:49 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 9 Oct 2017 18:35:49 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
Message-ID: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>

Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Please,
> I ran the command line
> 
> maker2jbrowse muc1_genome_snap2.all.gff
> 
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
> 
> Please what does it mean? How can I view it in jbrowse. 
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From eennadi at gmail.com  Mon Oct  9 22:42:35 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 10 Oct 2017 05:42:35 +0100
Subject: [maker-devel] jbrowse not working
In-Reply-To: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
Message-ID: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge ?d
dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse
/Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse
-d
/Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log
\-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the
jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31
contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of
> the file? That can happen if you use the -n option with gff3_merge.
> Alternatively it?s possible one of the individual contig gff3 used to build
> the merged gff3 is truncated. If that is the case then gff3_merge should
> have thrown some sort of error or warning when you run it.
>
> Thanks,
> Carson
>
>
>
>
> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Please,
> I ran the command line
>
> maker2jbrowse muc1_genome_snap2.all.gff
>
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
>
> Please what does it mean? How can I view it in jbrowse.
>
> Thanks
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
>
>
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From jacques.dainat at nbis.se  Tue Oct 10 03:24:34 2017
From: jacques.dainat at nbis.se (Jacques Dainat)
Date: Tue, 10 Oct 2017 11:24:34 +0200
Subject: [maker-devel] MAKER annotation submission (EMBLmyGFF3)
Message-ID: <967873FE-D61F-4233-A004-C877A60A2AC1@nbis.se>

Hi MAKER users,

I take advantage to this mailing list to share a tool that I hope will be useful for MAKER's users. One of the steps once we are happy of our wonderful annotation is to submit it to the public archives through one of the three INSDC databases (EMBL-EBI / NCBI / DDBJ).
We developed EMBLmyGFF3, allowing to easily convert any kind of GFF3 annotation to the EMBL flat file format in order to submit to the European Nucleotide Archive (ENA) Database that is part of EMBL-EBI.
It works well, amongst others, with the MAKER annotation output. We hope the tool will ease the submission process of your annotations.

You will find it here:
https://github.com/NBISweden/EMBLmyGFF3

A typical usage case will look like that (where ERSXXXXXX and PRJXXXXXX are the accession number and the project ID provided by EMBL-EBI prior to any submission):
./EMBLmyGFF3.py maker.gff3 maker.fa --data_class STD --topology linear --molecule_type 'genomic DNA' --table 1 --species 'Drosophila melanogaster (fly)' --taxonomy INV --accession ERSXXXXXXX --project_id PRJXXXXXXX --rg MYGROUP -o result.embl

Best regards,

Jacques Dainat, PhD
---------------------------------------
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
---------------------------------------
Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics


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From mcsimenc at gmail.com  Wed Oct 11 08:53:36 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 07:53:36 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons with
 EST only?
Message-ID: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence
supporting gene models in my MAKER annotation where the left side shows
number of genes with EST support only, the right side shows number of genes
with protein support only, and the intersection shows number of genes with
EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be
fraction of exons that overlap an EST alignment and possibly also a protein
alignment. If that is the case then we can't calculate the number of genes
that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to
get this?

Thanks!!!
Matt Simenc
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From michael.s.campbell1 at gmail.com  Wed Oct 11 09:18:54 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Wed, 11 Oct 2017 11:18:54 -0400
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
Message-ID: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> Hey MAKER people,
> 
> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
> 
> QI summary has:
> 
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
> 
> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
> 
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
> 
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 11 09:22:54 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Oct 2017 09:22:54 -0600
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
Message-ID: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>

Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL <https://github.com/The-Sequence-Ontology/GAL>

?Carson


 
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Matt,
> 
> I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.
> 
> To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.
> 
> Hope this helps,
> Mike
> 
>> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>> 
>> Hey MAKER people,
>> 
>> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
>> 
>> QI summary has:
>> 
>> Fraction of exons that overlap an EST alignment
>> Fraction of exons that overlap EST or Protein alignments
>> 
>> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
>> 
>> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
>> 
>> Thanks!!!
>> Matt Simenc
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From mcsimenc at gmail.com  Wed Oct 11 22:19:04 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 21:19:04 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
Message-ID: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Also look at GAL for building GFF3 feature queries ?>
> https://github.com/The-Sequence-Ontology/GAL
>
> ?Carson
>
>
>
>
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <
> michael.s.campbell1 at gmail.com> wrote:
>
> Hi Matt,
>
> I have a hacky way that I?ve done it. It requires running MAKER two more
> times but they are quicker runs.
>
> To identify the genes that have protein support I pass all of the
> annotation back to MAKER using the model_gff option in the maker_opts.ctl
> file. Then I pull out all of the protein2genome features from the big MAKER
> GFF3 file and pass them in using the protein_gff option. I turn off all
> repeat masking and run MAKER. It runs fast because it doesn?t have to run
> any gene finders, align evidence, or repeatmask. In the output any gene
> with an AED less than 1 has protein support. Then I do the same thing with
> est2genome lines from the big GFF3 file and put them in as est_gff. The
> output of that one gives you genes with EST support. Then the genes with an
> AED of less than one in both sets have support from protein and EST.
>
> Hope this helps,
> Mike
>
> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>
> Hey MAKER people,
>
> I would like to make a Venn diagram showing the kinds of evidence
> supporting gene models in my MAKER annotation where the left side shows
> number of genes with EST support only, the right side shows number of genes
> with protein support only, and the intersection shows number of genes with
> EST and protein support.
>
> QI summary has:
>
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
>
> Please correct me if I'm wrong, because I am interpreting the first to be
> fraction of exons that overlap an EST alignment and possibly also a protein
> alignment. If that is the case then we can't calculate the number of genes
> that overlap only EST or (EST and protein) from the QI information.
>
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to
> get this?
>
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From scott at scottcain.net  Thu Oct 12 17:33:05 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:33:05 -0400
Subject: [maker-devel] GMOD hackathon before PAG San Diego in January
Message-ID: <CA+JTaoytocv6efRcY6LqKXRjPZXeqa9JFFStCPxE0VunjmB-Nw@mail.gmail.com>

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From daren.card at gmail.com  Thu Oct 12 20:22:54 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Thu, 12 Oct 2017 21:22:54 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
Message-ID: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>

Hi Carson,

Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.

Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.

I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.

What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.

Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.

Thanks,
Daren


> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
> 
> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
> 
> ?Carson
> 
> 
> 
> 
> 
>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Dear Carson,
>> 
>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>> 
>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>> 
>> Thank you,
>> Daren Card
>> 
>> 
>> ################################################
>> doing repeat masking
>> re reading repeat masker report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>> doing blastx repeats
>> re reading blast report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>> deleted:2 hits
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=NA, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> examining contents of the fasta file and run log
>> ################################################
>> 
>> 
>> 
>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>> 
>>> ?Carson
>>> 
>>> 
>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>> 
>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>> 
>>>> Any help would be greatly appreciated.
>>>> Daren Card
>>>> 
>>>> University of Texas Arlington
>>>> 
>>>> ###################################################
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>> #-------------------------------#
>>>> deleted:0 hits
>>>> collecting blastx repeatmasking
>>>> processing all repeats
>>>> in cluster::shadow_cluster...
>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>> --> rank=3, hostname=moonunit0
>>>> ERROR: Failed while processing all repeats
>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>> #-------------------------------#
>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> deleted:0 hits
>>>> deleted:0 hits
>>>> ###################################################
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
> 




From robert.zimmermann at univie.ac.at  Wed Oct 11 13:42:14 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Wed, 11 Oct 2017 21:42:14 +0200
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
Message-ID: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>

Hello,

I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 

My gene prediction section of the maker_opts.ctl file looks like this:
...
augustus_species=all_combined #Augustus gene prediction species model
...
pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
?

It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.

Thanks for your help!

Bob


From xvazquezc at gmail.com  Thu Oct 12 00:09:32 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 12 Oct 2017 17:09:32 +1100
Subject: [maker-devel] choosing the right gene model
Message-ID: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>

Hi there,

I was visualising the annotations and I realised that in some cases, what
it seems to be a gene is splitted according to one of the gene models,
despite that the other 2, est2genome and prot2genome suggest that it isn't
the case.



Although the opposite also happens.


?
For some reason, the "out of place" model is always (or almost) the one
from Genemark.

How much weight does carry the RNAseq and protein data on this decision (if
any)?
How exactly is the final gene selected?

Cheers,
Xabi

-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From jan.nagel at fabi.up.ac.za  Thu Oct 12 01:37:07 2017
From: jan.nagel at fabi.up.ac.za (Jan FABI)
Date: Thu, 12 Oct 2017 09:37:07 +0200
Subject: [maker-devel] Maker problem
Message-ID: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution
to it online.

I am running maker on a new genome, using BRAKER trained models for
Augustus and GeneMark. This was successful and performed as expected,
except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with
intron models. I have made sure that the input fasta does not contain
characters other than ATCGN or contains "windows"/non-UNIX carriage
returns.

I include the relevant portion of the log below. Could you help me
determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus
--species=Np_2017_braker --UTR=off
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 >
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

-- 
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : jan.nagel at fabi.up.ac.za

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

-- 
This message and attachments are subject to a disclaimer.
Please refer to 
http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf for full 
details.
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From scott at scottcain.net  Thu Oct 12 17:40:33 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:40:33 -0400
Subject: [maker-devel] Call for presentations at GMOD workshop at PAG
Message-ID: <CA+JTaoyZEYHX0RyKMW7+3d+wic+PyshCUUfhzCzeroXnmyVECw@mail.gmail.com>

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From carsonhh at gmail.com  Fri Oct 13 09:37:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:37:25 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
Message-ID: <C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>

So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.

Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi <http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi>

?Carson



> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi Carson,
> 
> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
> 
> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
> 
> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
> 
> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
> 
> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
> 
> Thanks,
> Daren
> 
> 
>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>> 
>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>> 
>> ?Carson
>> 
>> 
>> 
>> 
>> 
>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Dear Carson,
>>> 
>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>> 
>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>> 
>>> Thank you,
>>> Daren Card
>>> 
>>> 
>>> ################################################
>>> doing repeat masking
>>> re reading repeat masker report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>> doing blastx repeats
>>> re reading blast report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>> deleted:2 hits
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=NA, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> examining contents of the fasta file and run log
>>> ################################################
>>> 
>>> 
>>> 
>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> 
>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>> 
>>>> ?Carson
>>>> 
>>>> 
>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>> 
>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>> 
>>>>> Any help would be greatly appreciated.
>>>>> Daren Card
>>>>> 
>>>>> University of Texas Arlington
>>>>> 
>>>>> ###################################################
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>> #-------------------------------#
>>>>> deleted:0 hits
>>>>> collecting blastx repeatmasking
>>>>> processing all repeats
>>>>> in cluster::shadow_cluster...
>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>> --> rank=3, hostname=moonunit0
>>>>> ERROR: Failed while processing all repeats
>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>> #-------------------------------#
>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> deleted:0 hits
>>>>> deleted:0 hits
>>>>> ###################################################
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>> 
>> 
> 

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From carsonhh at gmail.com  Fri Oct 13 09:42:41 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:42:41 -0600
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
In-Reply-To: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
References: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
Message-ID: <947BFB2F-A893-417B-A043-07CE71F6F97E@gmail.com>

Hi Bob,

pred_gff is a way to get models MAKER cannot run into the analysis. Input to pred_gff will not get hints since MAKER is not running the program. Setting augustus_species allows MAKER to run Augustus with and without hints and then those models compete against each other. You cannot just run with hints as the raw model is also used as a filter to help reduce false positive gene models that result from bad hints. If the gff3 you are providing is the same as the MAKER run of Augustus, I would recommend not providing it. If it is different in some way, then you can leave it in.  If you run under MPI (it?s ok to run MPI on a single machine), then MAKER will parallelize the Augustus run by running multiple configs and contig chunks at the same time.

Thanks,
Carson





> On Oct 11, 2017, at 1:42 PM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hello,
> 
> I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 
> 
> My gene prediction section of the maker_opts.ctl file looks like this:
> ...
> augustus_species=all_combined #Augustus gene prediction species model
> ...
> pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
> model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
> est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
> protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
> ?
> 
> It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.
> 
> Thanks for your help!
> 
> Bob
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Fri Oct 13 09:50:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:50:26 -0600
Subject: [maker-devel] Maker problem
In-Reply-To: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
References: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
Message-ID: <FE4BF464-D049-415D-9AC2-D013B0FB727B@gmail.com>

If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example ?> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke (mario.stanke at uni-greifswald.de <mailto:mario.stanke at uni-greifswald.de>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

?Carson


> On Oct 12, 2017, at 1:37 AM, Jan FABI <jan.nagel at fabi.up.ac.za> wrote:
> 
> Dear Maker team
> 
> I am experiencing a problem while running maker and cannot find a solution to it online. 
> 
> I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. 
> 
> This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. 
> 
> I include the relevant portion of the log below. Could you help me determine the cause of this error.
> 
> 
> 
> setting up GFF3 output and fasta chunks
> preparing ab-inits
> running  augustus.
> #--------- command -------------#
> Widget::augustus:
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx-VirtualBox
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 
> 
> -- 
> Regards 
> Jan Nagel
> ----------------------------------------------------------------------
> PhD Genetics student
> Department of Genetics
> Forestry and Agricultural Biotechnology Institute (FABI) 
> FABI 1, Room 1-55
> University of Pretoria
> 74 Lunnon Rd. Hillcrest
> 0002
> Gauteng Province
> South Africa
> 
> Email : jan.nagel at fabi.up.ac.za <mailto:jan.nagel at fabi.up.ac.za>
> 
> Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961 <http://www.fabinet.up.ac.za/index.php/people-profile?profile=961>
> This message and attachments are subject to a disclaimer.
> Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf <http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf> for full details.
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 09:56:43 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:56:43 -0600
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
Message-ID: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>

Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it?s evidence, so it?s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it?s a fungi, I often find GeneMark can have that affect).

?Carson


> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi there,
> 
> I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.
> 
> <split-gene.png>
> 
> Although the opposite also happens.
> 
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one from Genemark.
> 
> How much weight does carry the RNAseq and protein data on this decision (if any)?
> How exactly is the final gene selected?
> 
> Cheers,
> Xabi
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 10:56:30 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 10:56:30 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
	<CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
Message-ID: <2D6E11BC-6853-458D-AEB1-12EF74D041A3@gmail.com>

The master_datastore_index.log file has a list of failed and finished contigs.  You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.

Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it?s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).

You will need to see if you can identify which contig file is truncated and rerun it.

?Carson






> On Oct 9, 2017, at 10:42 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> Thanks for the reply
> 
> I generated the off with this command gff3_merge ?d dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
> I had to rerun browse with the following command
> 
> maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb
> 
> Although its showing
> 
> WARNING: No matching features found for mRNA I don't know what it means
> 
> I don't understand what it means
> 
> 
> Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host
> 
> 
> The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?
> 
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.
> 
> Thanks,
> Carson
> 
> 
> 
> 
>> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Please,
>> I ran the command line
>> 
>> maker2jbrowse muc1_genome_snap2.all.gff
>> 
>> The command created some folders. However, at the end it read
>> No reference sequences defined in configuration, nothing to do.
>> 
>> Please what does it mean? How can I view it in jbrowse. 
>> 
>> Thanks
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> 

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From xvazquezc at gmail.com  Fri Oct 13 14:26:40 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Sat, 14 Oct 2017 07:26:40 +1100
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
	<821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
Message-ID: <CAL0hg4Hxgrfhbah+7euuQV0YSCjYkV+WqxVu4_QYyf38pYts3Q@mail.gmail.com>

Actually, it's a fungal genome. Although not very typical, almost half of
it are repeats. Worth mention that Genemark generates a lot of predictions
that overlap LTRs and other complex repeats, something that neither SNAP or
Augustus do. Have you seen this before?

On 14 Oct. 2017 02:56, "Carson Holt" <carsonhh at gmail.com> wrote:

> Both transcript and protein evidence will go into the AED calculation for
> overlap support. So in both cases the chosen model had better overlap
> (protein evidence will not count toward the eAED overlap calculation if it
> is out of frame with the model it is supposed to be supporting). The larger
> merged model generates a clutering affect on it?s evidence, so it?s
> evidence set for AED calculation is slightly different than the SNAP and
> Augustus model would generate. In both cases, I think GeneMark is hurting
> more than it is helping. You may want to just drop it from the analysis
> (unless it?s a fungi, I often find GeneMark can have that affect).
>
> ?Carson
>
>
> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Hi there,
>
> I was visualising the annotations and I realised that in some cases, what
> it seems to be a gene is splitted according to one of the gene models,
> despite that the other 2, est2genome and prot2genome suggest that it isn't
> the case.
>
> <split-gene.png>
>
> Although the opposite also happens.
>
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one
> from Genemark.
>
> How much weight does carry the RNAseq and protein data on this decision
> (if any)?
> How exactly is the final gene selected?
>
> Cheers,
> Xabi
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From z2.stewart at qut.edu.au  Sat Oct 14 23:02:08 2017
From: z2.stewart at qut.edu.au (ZACHARY STEWART)
Date: Sun, 15 Oct 2017 05:02:08 +0000
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
Message-ID: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>

Hello MAKER team,


I am hoping I could have a bit of your time if that isn't a problem. I am currently performing the advanced repeat library construction as described on the MAKER wiki, and everything appears to work as expected until I reach "2.1.5 Building examplars". At this point I encounter a problem previously documented in the Google group (title: advanced repeat masking library constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta" and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify what you meant by simplifying the sequence names. The genomic contig names are in a format such as ">001676F" and I modified the MITE library to have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]" which I have not tried changing since I suspect the name is important for later reassociation. If you could point me in the right direction that would be very appreciated.


Regards,

Zac.
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From eennadi at gmail.com  Sun Oct 15 15:32:10 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sun, 15 Oct 2017 22:32:10 +0100
Subject: [maker-devel] Backlash running through my sequence
Message-ID: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>

Hi all,
I am trying to running annotation on some of my sequences but noticed that
i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From xvazquezc at gmail.com  Mon Oct 16 01:26:56 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Mon, 16 Oct 2017 18:26:56 +1100
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
In-Reply-To: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
References: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
Message-ID: <CAL0hg4Gz=vfaDkQEb3J-JPDw0TiRsmH2Fae2YsKX5AtZe0YYjA@mail.gmail.com>

Hi Zac,
The contig names you indicate shouldn't give any problems. And if you
changed the names of MITE.lib right after creation and before using it
downstream, it shouldn't be an issue.

Have you confirmed if the prior blastx output has any results?

Also, be sure you use the same version of makeblastdb and blastx/blastn. I
remember reading before running the protocol for first time that in some
cases, switching versions could give problems.
And be careful if you copy/paste from the wiki page, there are a few typos
and dashes instead of minus characters in the command line option flags,
all of which will result in errors

Xabi

On 15 October 2017 at 16:02, ZACHARY STEWART <z2.stewart at qut.edu.au> wrote:

> Hello MAKER team,
>
>
> I am hoping I could have a bit of your time if that isn't a problem. I am
> currently performing the advanced repeat library construction as described
> on the MAKER wiki, and everything appears to work as expected until I reach
> "2.1.5 Building examplars". At this point I encounter a problem previously
> documented in the Google group (title: advanced repeat masking library
> constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta"
> and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify
> what you meant by simplifying the sequence names. The genomic contig names
> are in a format such as ">001676F" and I modified the MITE library to
> have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta
> has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]"
> which I have not tried changing since I suspect the name is important for
> later reassociation. If you could point me in the right direction that
> would be very appreciated.
>
>
> Regards,
>
> Zac.
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From yuejiaxing at gmail.com  Mon Oct 16 02:54:42 2017
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Mon, 16 Oct 2017 10:54:42 +0200
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>

Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning
message about uninitialized value (see the warning message below) although
still finished the installation.

[jxyue at paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/bu
ild/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm
line 3082.
Use of uninitialized value $line in substitution (s///) at
/home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/
cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors
about cannot find my specified snaphmm model for the annotation, despite
that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the
"maker_opts.ctl" file and this configuration information has been
successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap
/home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm
/tmp/maker_m8TVEQ/chrI.abinit_masked.0 >
/tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap
S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta >
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening
file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot
about the path to  my specified hmm file and instead looks for this file in
its default installation location)

It is worth noting that the parallel installation and run with
maker-3.00.0-beta finish smoothly without any problem. So I suspect both
the installation warning and the executing error are caused by the changes
during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check
about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker
(e.g. 3.00.0-beta in this particular case) when the user finish the
registration in the maker download page? This will help users to roll back
to older version when needed.  Also this helps for the version control when
other developers develop annotation pipelines that use maker as a
dependency package. Thanks for the consideration!


Best,
Jia-Xing

-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Facult? de M?decine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/
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From carsonhh at gmail.com  Mon Oct 16 10:20:32 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 16 Oct 2017 10:20:32 -0600
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
Message-ID: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



> On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi all,
> I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
>  I attached the sequence
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications><sample_1.fasta>

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From cjfields at illinois.edu  Tue Oct 17 13:11:39 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 17 Oct 2017 19:11:39 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
Message-ID: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson Holt <carsonhh at gmail.com>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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From carsonhh at gmail.com  Tue Oct 17 13:33:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Oct 2017 13:33:26 -0600
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
	<CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
Message-ID: <30F2FDFE-3B4E-4951-89D8-63C2FC772B63@gmail.com>

Thanks. The map_fasta_ids script was empty in the bin directory for some reason, so the installer through an error because it could not find the #!/usr/bin/perl line. I have put it back in the bin directory where it was supposed to be and the issue goes away for the install.

For the second issue, I think I found it and have updated a new tar ball to the website.

Also here is a link to download the old 3.00-beta, although I would not recommend making it part of a pipeline because version 3 is still beta and still has bugs (you should use 2.31.9 instead for piplines).  ?> http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz <http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz>

?Carson


 
> On Oct 16, 2017, at 2:54 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
> 
> Dear maker developers,
> 
> I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation. 
> 
> [jxyue at paralog src]$ ./Build install
> Building MAKER
> Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
> Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
> Installing MAKER...
> Building MAKER
> ...
> 
> Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
> #-------------------------------#
> 
> # (my comment: up to now everything looks fine)
> ....
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
> /maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
> #-------------------------------#
> ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
> ZOE library version 2017-03-01
> ERROR: Snap failed
> --> rank=NA, hostname=paralog.itc.unipi.it <http://paralog.itc.unipi.it/>
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chrI
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chrI
> 
> examining contents of the fasta file and run log
> 
> # (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)
> 
> It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!
> 
> Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!
> 
> 
> Best,
> Jia-Xing
> 
> -- 
> Jia-Xing Yue 
> 
> Population Genomics and Complex Traits Group
> Tour Pasteur 8eme etage
> Facult? de M?decine
> Institute for Research on Cancer and Aging, Nice (IRCAN)
> CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
> 28 Avenue de Valombrose
> 06107 NICE Cedex 2
> France
> 
> Personal website: http://www.iamphioxus.org/ <http://www.iamphioxus.org/>
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From patrick.tranvan at unil.ch  Wed Oct 18 05:47:35 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Wed, 18 Oct 2017 11:47:35 +0000
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>,
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <1508327278733.19140@unil.ch>

Hi Carson,


1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?


2) I am trying to annotate a 1GB specie but it's superslow.

I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ?

Cheers,

Patrick Tran Van


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From carsonhh at gmail.com  Wed Oct 18 09:09:10 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 18 Oct 2017 09:09:10 -0600
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <1508327278733.19140@unil.ch>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
	<1508327278733.19140@unil.ch>
Message-ID: <486FE3D5-0902-4B05-A3E1-96642C68E422@gmail.com>

MAKER can coordinate parallelization under MPI in a way it can?t even with multiple simultaneous runs. Because processes can comunicate among themselves under MPI, MAKER can break larger contigs into chunks or even pull off individual steps and pass them onto another processor, then receive the results back from that processor. So multiple BLAST, RepeatMasker, Exonerate, and prediction processes can all run at the same time for the same contig. Then they all pass their result back to the parent process so it can produce output for that contig. MPI was chosen as the parallelization framework rather than threads because it works both within a single machine as well as across multiple machines, so you can scale up to hundreds of processes if needed.

?Carson


> On Oct 18, 2017, at 5:47 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi Carson, 
> 
> 1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?
> 
> 2) I am trying to annotate a 1GB specie but it's superslow.
> I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ? 
> 
> Cheers,
> 
> Patrick Tran Van
> 
> 

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From jhumann at wsu.edu  Wed Oct 18 14:38:41 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Wed, 18 Oct 2017 20:38:41 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
Message-ID: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>

Hello,

I was wondering if there was any way to enable the '-fix_nucleotides' option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu


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From robert.zimmermann at univie.ac.at  Thu Oct 19 09:25:08 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:25:08 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
Message-ID: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>

Hi Maker Developers,

I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.

Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?

Thanks for your help!

Best,
Bob

?

Department of Molecular Evolution and Development
Universit?t Wien
Althanstra?e 14 (UZA I), Zimmer 2.019 
1090 Vienna
Austria

+43 1 427757002




From robert.zimmermann at univie.ac.at  Thu Oct 19 09:28:17 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:28:17 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
Message-ID: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>

Correction to the above numbers, the median lengths are 1414 and 1256.

> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hi Maker Developers,
> 
> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
> 
> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
> 
> Thanks for your help!
> 
> Best,
> Bob
> 
> ?
> 
> Department of Molecular Evolution and Development
> Universit?t Wien
> Althanstra?e 14 (UZA I), Zimmer 2.019 
> 1090 Vienna
> Austria
> 
> +43 1 427757002
> 




From carsonhh at gmail.com  Thu Oct 19 09:44:07 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 09:44:07 -0600
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
	<CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
Message-ID: <62F04A76-F3F1-4044-B4AD-129B15A9EEB2@gmail.com>

You should look at both in a browser to get a better idea of what?s going on. What MAKER does is take the evidence given, clusters it (strand specific clustering) then uses the transcript evidence as intron hints to the predictors and protein alignments as exon hints (will also use polished protein hints to generate intron hints in the absence of transcript intron hints). Finally it uses overlapping transcript evidence to generate UTR. So look at it in a browser. See if the apparent overlap clusters are different in extent, also look for mRNA-seq evidence being merged. If the cluster is falsely merging between two loci because the mRNA-seq is merged, one of two things will happen you will get multiple models since the predictor can?t make a single model work within the cluster using the hints, or you will get a model with a really long UTR that is blocking other models from existing in the region. Also as depending on the mRNA-seq evidence coming in, you may be generating false models because of noise in the data. Essentially everything is transcribed at a basal level, so as you get more and more mRNA-seq, you generate more and more spurious alignments. So more evidence might gernate fewer long alignments for true loci or by falsely merging genes while simultaneously adding a number of very short spurious results.

?Carson



> On Oct 19, 2017, at 9:28 AM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Correction to the above numbers, the median lengths are 1414 and 1256.
> 
>> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
>> 
>> Hi Maker Developers,
>> 
>> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
>> 
>> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
>> 
>> Thanks for your help!
>> 
>> Best,
>> Bob
>> 
>> ?
>> 
>> Department of Molecular Evolution and Development
>> Universit?t Wien
>> Althanstra?e 14 (UZA I), Zimmer 2.019 
>> 1090 Vienna
>> Austria
>> 
>> +43 1 427757002
>> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Thu Oct 19 11:32:44 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 11:32:44 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Oct 19 12:46:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 12:46:17 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
	<SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <052F801C-3B37-4B0F-B40A-A905F5F2B1CE@gmail.com>

Yes. That is the current version.

?Carson

> On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?
>  
> Jodi
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Thursday, October 19, 2017 10:33 AM
> To: Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] fix nucleotides option on MWAS
>  
> Hi Jodi,
>  
> I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).
>  
> Somewhere inside the script there will be a line like this ?>
>  $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
>  
> You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.
>  
> Thanks,
> Carson
>  
>  
> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>> wrote:
>  
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>
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From jhumann at wsu.edu  Thu Oct 19 12:45:43 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Thu, 19 Oct 2017 18:45:43 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
Message-ID: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?

Jodi

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <jhumann at wsu.edu>
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] fix nucleotides option on MWAS

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu<mailto:jhumann at wsu.edu>> wrote:

Hello,

I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu<mailto:jhumann at wsu.edu>


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>

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From eennadi at gmail.com  Mon Oct 23 07:30:07 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 23 Oct 2017 14:30:07 +0100
Subject: [maker-devel] Contamination report from NCBI
Message-ID: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>

Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this
contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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SUBID     	BioProject	BioSample	Organism
--------------------------------------------------------
SUB3124577	PRJNA414658	SAMN07821433	Mucuna pruriens

[] We ran your sequences through our Contamination Screen. The screen found 
contigs that need to be trimmed and/or excluded. Please adjust the 
sequences appropriately and then resubmit your sequences. After you remove the 
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

Note that hits in eukaryotic genomes to mitochondrial sequences can be ignored 
when specific criteria are met. Those criteria are explained below.

Note that mismatches between the name of the adaptor/primer identified in the screen 
and the sequencing technology used to generate the sequencing data should not be used 
to discount the validity of the screen results as the adaptors/primers of many 
different sequencing platforms share sequence similarity.



[] Some of the sequences hit primers or adaptors used in Illumina or 
454 or other sequencing strategies or platforms.  Primers at the 
end of a sequence should be removed. However, if primers are 
present within sequences then you should strongly consider 
splitting the sequences at the primers because the primer sequence 
could have been the region of overlap, causing a misassembly.


Screened 26,016 sequences, 396,641,426 bp.
Note: 5,610 sequences with runs of Ns 10 bp or longer (or those longer that 20 MB) were split before screening.
428 sequences with locations to mask/trim
(31 split spans to exclude, 397 split spans with locations to mask/trim)

Trim:
Sequence name, length, span(s), apparent source
contig_10109	13138	13078..13138	adaptor:NGB00847.1
contig_10200	20270	1..76	adaptor:NGB00847.1
contig_10202	22517	1..44	adaptor:NGB00360.1
contig_10218	55661	55592..55661	adaptor:NGB00847.1
contig_10283	11575	1..79	adaptor:NGB00847.1
contig_1038	91134	91073..91134	adaptor:NGB00360.1
contig_104	10061	10005..10061	adaptor:NGB00360.1
contig_10405	24076	1..43	adaptor:NGB00847.1
contig_10425	16694	16639..16694	adaptor:NGB00360.1
contig_10447	37445	37233..37445	adaptor:NGB00360.1
contig_10466	19368	1..52	adaptor:NGB00847.1
contig_10576	12053	12003..12053	adaptor:NGB00360.1
contig_1059	34516	34457..34516	adaptor:NGB00847.1
contig_106	49997	1..45	adaptor:NGB00360.1
contig_10695	27664	1..38	adaptor:NGB01029.1
contig_10753	12481	12413..12481	adaptor:NGB00847.1
contig_10822	33522	33441..33522	adaptor:NGB00847.1
contig_1083	10637	1..23	adaptor:NGB01096.1
contig_10851	36752	36682..36752	adaptor:NGB00360.1
contig_10878	27925	27848..27925	adaptor:NGB00360.1
contig_10965	23597	1..57	adaptor:NGB00360.1
contig_10968	7413	1..40	adaptor:NGB00847.1
contig_1099	35847	1..70	adaptor:NGB00360.1
contig_11034	10224	10166..10224	adaptor:NGB00360.1
contig_11058	32994	1..23	adaptor:NGB01088.1
contig_11138	17426	1..73	adaptor:NGB00847.1
contig_11166	6306	6266..6306	adaptor:NGB00360.1
contig_11182	26558	1..30	adaptor:NGB01096.1
contig_11216	15160	1..59	adaptor:NGB00847.1
contig_11269	14732	14655..14732	adaptor:NGB00847.1
contig_11306	28246	28199..28246	adaptor:NGB00360.1
contig_1136	28186	1..73	adaptor:NGB00847.1
contig_1141	58119	58028..58119	adaptor:NGB00847.1
contig_11416	8561	8539..8561	adaptor:NGB01088.1
contig_11504	8890	8840..8890	adaptor:NGB00360.1
contig_1158	17422	17398..17422	adaptor:NGB01088.1
contig_11647	7021	1..69	adaptor:NGB00847.1
contig_11684	17442	17418..17442	adaptor:NGB01096.1
contig_11752	38337	38314..38337	adaptor:NGB01088.1
contig_11767	6366	6324..6366	adaptor:NGB00847.1
contig_11791	22415	1..43	adaptor:NGB00847.1
contig_11792	58260	1..29	adaptor:NGB01096.1
contig_1187	39501	39462..39501	adaptor:NGB01029.1
contig_12059	10094	1..72	adaptor:NGB00360.1
contig_12130	13210	13164..13210	adaptor:NGB00360.1
contig_12164	17561	17539..17561	adaptor:NGB01096.1
contig_12169	14178	139..196	adaptor:NGB00360.1
contig_12183	15822	61..112	adaptor:NGB00360.1
contig_12266	11704	11640..11704	adaptor:NGB00360.1
contig_12300	9550	9360..9550	adaptor:NGB01088.1
contig_12324	49997	49891..49997	adaptor:NGB00847.1
contig_12423	45971	45860..45918	adaptor:NGB00360.1
contig_12441	15141	1..42	adaptor:NGB00847.1
contig_12514	14655	1..69	adaptor:NGB00847.1
contig_12515	5355	5326..5355	adaptor:NGB01088.1
contig_12535	22496	22458..22496	adaptor:NGB01029.1
contig_12544	19615	19559..19615	adaptor:NGB00360.1
contig_12558	20026	20007..20026	adaptor:NGB01088.1
contig_12613	6880	6793..6880	adaptor:NGB00847.1
contig_12701	18439	18330..18382	adaptor:NGB00360.1
contig_12713	13341	13274..13341	adaptor:NGB00360.1
contig_12723	17913	1..38	adaptor:NGB01088.1
contig_12730	55277	55249..55277	adaptor:NGB01096.1
contig_12739	6792	1..48	adaptor:NGB00360.1
contig_12787	30950	1..19	adaptor:NGB01096.1
contig_1279	18699	18670..18699	adaptor:NGB01088.1
contig_12815	5168	5091..5168	adaptor:NGB00847.1
contig_12846	20753	1..70	adaptor:NGB00360.1
contig_1288	34784	1..31	adaptor:NGB01096.1
contig_12888	12204	1..23	adaptor:NGB01096.1
contig_12919	10315	1..71	adaptor:NGB00360.1
contig_13031	8972	8938..8972	adaptor:NGB01093.1
contig_13088	6275	1..22	adaptor:NGB01088.1
contig_13140	36197	1..48	adaptor:NGB00360.1
contig_13233	16414	16355..16414	adaptor:NGB00847.1
contig_1330	33261	1..44	adaptor:NGB00847.1
contig_13319	19747	1..20	adaptor:NGB01096.1
contig_13367	36004	35868..35931	adaptor:NGB00847.1
contig_13395	5338	1..79	adaptor:NGB00360.1
contig_1341	30756	30734..30756	adaptor:NGB01088.1
contig_13481	9637	9600..9637	adaptor:NGB00360.1
contig_13506	5704	5662..5704	adaptor:NGB00360.1
contig_13548	5814	79..121	adaptor:NGB00360.1
contig_13567	21576	1..47	adaptor:NGB00847.1
contig_13669	8336	1..24	adaptor:NGB01088.1
contig_13718	23500	1..25	adaptor:NGB01096.1
contig_13783	18720	1..41	adaptor:NGB00847.1
contig_13830	32395	32367..32395	adaptor:NGB01096.1
contig_13845	15572	15493..15572	adaptor:NGB00360.1
contig_13854	10932	1..48	adaptor:NGB00360.1
contig_13943	37701	37674..37701	adaptor:NGB01096.1
contig_13957	7159	1..30	adaptor:NGB01096.1
contig_14014	29735	29672..29735	adaptor:NGB00360.1
contig_14027	21418	21340..21418	adaptor:NGB00360.1
contig_14032	47642	1..53	adaptor:NGB00847.1
contig_14047	26936	1..28	adaptor:NGB01088.1
contig_14048	45832	1..22	adaptor:NGB01088.1
contig_14061	11471	1..179	adaptor:NGB01096.1
contig_14113	17661	1..67	adaptor:NGB00360.1
contig_14173	17601	1..41	adaptor:NGB00847.1
contig_1418	31840	1..248	adaptor:NGB00847.1
contig_14194	7456	7294..7456	adaptor:NGB01096.1
contig_14210	8814	1971..2025	adaptor:NGB00360.1
contig_14223	12513	12489..12513	adaptor:NGB01096.1
contig_14317	21472	21410..21472	adaptor:NGB00360.1
contig_14424	6040	5973..6040	adaptor:NGB00360.1
contig_14425	6404	6379..6404	adaptor:NGB01096.1
contig_14426	31457	31398..31457	adaptor:NGB00847.1
contig_14458	6814	6623..6814	adaptor:NGB01088.1
contig_14524	9488	9431..9488	adaptor:NGB00847.1
contig_14584	20433	1..96	adaptor:NGB00847.1
contig_1459	32979	1..32	adaptor:NGB01096.1
contig_14601	19077	1..28	adaptor:NGB01096.1
contig_14641	21747	1..45	adaptor:NGB00847.1
contig_14664	48155	48118..48155	adaptor:NGB00360.1
contig_14711	11854	11827..11854	adaptor:NGB01096.1
contig_14736	21360	1..37	adaptor:NGB01029.1
contig_14749	12830	1..33	adaptor:NGB01093.1
contig_14966	9962	9891..9962	adaptor:NGB00360.1
contig_14999	5248	1..41	adaptor:NGB00360.1
contig_15010	17976	1..43	adaptor:NGB00360.1
contig_15011	26484	26462..26484	adaptor:NGB01096.1
contig_15017	9331	9291..9331	adaptor:NGB00360.1
contig_1503	63533	1..33	adaptor:NGB01096.1
contig_15032	32240	32157..32240	adaptor:NGB00847.1
contig_15060	15050	15010..15050	adaptor:NGB00847.1
contig_15065	13062	12996..13062	adaptor:NGB00360.1
contig_15070	29943	1..29	adaptor:NGB01096.1
contig_15132	20431	1..71	adaptor:NGB00847.1
contig_15169	7086	7051..7086	adaptor:NGB00846.1
contig_15174	19921	1..23	adaptor:NGB01096.1
contig_15194	16100	16039..16100	adaptor:NGB00847.1
contig_15212	9272	1..50	adaptor:NGB00847.1
contig_15215	15591	1..58	adaptor:NGB00360.1
contig_15271	37699	37647..37699	adaptor:NGB00847.1
contig_15276	11087	11031..11087	adaptor:NGB00847.1
contig_15309	10118	1..42	adaptor:NGB00847.1
contig_15320	7963	7901..7963	adaptor:NGB00847.1
contig_15334	5683	1..36	adaptor:NGB00846.1
contig_15364	17306	76..139	adaptor:NGB00847.1
contig_15374	28301	28263..28301	adaptor:NGB00360.1
contig_15377	10470	10428..10470	adaptor:NGB00360.1
contig_15398	24069	23999..24069	adaptor:NGB00847.1
contig_15500	9289	9271..9289	adaptor:NGB01096.1
contig_15507	25565	1..22	adaptor:NGB01088.1
contig_15523	5782	5762..5782	adaptor:NGB01088.1
contig_15529	10225	10143..10225	adaptor:NGB00360.1
contig_15569	9645	9612..9645	adaptor:NGB01090.1
contig_15596	7163	1..42	adaptor:NGB00360.1
contig_15605	18521	1..31	adaptor:NGB01096.1
contig_15672	8446	1..213	adaptor:NGB01088.1
contig_15686	22141	58..90	adaptor:NGB00847.1
contig_15708	18098	17996..18098	adaptor:NGB00847.1
contig_15736	18284	18252..18284	adaptor:NGB01096.1
contig_15777	17192	1..45	adaptor:NGB00360.1
contig_15812	8602	1..77	adaptor:NGB00360.1
contig_15959	10936	10913..10936	adaptor:NGB01096.1
contig_15972	11324	1..71	adaptor:NGB00360.1
contig_15974	24312	24243..24312	adaptor:NGB00847.1
contig_16057	8838	8775..8838	adaptor:NGB00847.1
contig_16088	7608	1..71	adaptor:NGB00360.1
contig_16142	10392	1..53	adaptor:NGB00847.1
contig_1617	14870	255..310	adaptor:NGB00360.1
contig_16183	9226	9205..9226	adaptor:NGB01088.1
contig_16188	62666	62586..62666	adaptor:NGB00847.1
contig_16370	7868	1..42	adaptor:NGB00847.1
contig_16416	19512	1..21	adaptor:NGB01088.1
contig_1645	25016	24951..25016	adaptor:NGB00360.1
contig_16510	31845	31776..31845	adaptor:NGB00847.1
contig_16529	17342	1..45	adaptor:NGB00360.1
contig_16558	9338	9097..9338	adaptor:NGB00360.1
contig_16573	6590	6521..6590	adaptor:NGB00847.1
contig_16608	7397	7324..7397	adaptor:NGB00847.1
contig_16631	11055	1..50	adaptor:NGB00360.1
contig_16641	5482	1..190	adaptor:NGB01088.1
contig_1667	35244	35200..35244	adaptor:NGB01029.1
contig_16682	14500	1..71	adaptor:NGB00847.1
contig_16699	6216	6148..6216	adaptor:NGB00360.1
contig_16734	12674	12625..12674	adaptor:NGB00360.1
contig_16790	6341	1..51	adaptor:NGB00360.1
contig_16807	7512	1..36	adaptor:NGB01096.1
contig_16817	20743	1..155	adaptor:NGB01088.1
contig_16839	6969	1..69	adaptor:multiple
contig_16870	10948	1..49	adaptor:NGB00847.1
contig_16880	5622	5549..5622	adaptor:NGB00360.1
contig_16889	9182	1..40	adaptor:NGB00360.1
contig_16911	6691	1..28	adaptor:NGB01088.1
contig_16921	9432	9358..9432	adaptor:NGB00360.1
contig_16951	14285	14262..14285	adaptor:NGB01088.1
contig_17021	12242	1..75	adaptor:NGB00360.1
contig_17092	22712	1..64	adaptor:NGB00360.1
contig_17147	7706	7685..7706	adaptor:NGB01096.1
contig_17195	15668	15643..15668	adaptor:NGB01096.1
contig_17214	7881	7819..7881	adaptor:NGB00847.1
contig_17299	7861	7830..7861	adaptor:NGB01088.1
contig_17344	8915	8765..8823	adaptor:NGB00360.1
contig_17361	8425	1..26	adaptor:NGB01096.1
contig_17422	11017	10964..11017	adaptor:NGB00360.1
contig_17471	5988	5964..5988	adaptor:NGB01096.1
contig_17505	10208	1..74	adaptor:NGB00360.1
contig_17506	6091	1..61	adaptor:NGB00360.1
contig_17520	6084	6028..6084	adaptor:NGB00360.1
contig_17538	5796	5766..5796	adaptor:NGB01096.1
contig_17558	7066	6837..7066	adaptor:NGB01080.1
contig_17561	15165	1..206	adaptor:NGB01083.1
contig_17594	6976	1..26	adaptor:NGB01088.1
contig_17655	14371	14177..14371	adaptor:NGB01088.1
contig_17671	17801	1..50	adaptor:NGB00847.1
contig_17680	5752	5693..5752	adaptor:NGB00847.1
contig_17738	6456	1..44	adaptor:NGB00360.1
contig_17741	10917	10889..10917	adaptor:NGB01096.1
contig_17775	5928	1..79	adaptor:NGB00847.1
contig_17804	11597	11562..11597	adaptor:NGB00846.1
contig_17872	11319	11278..11319	adaptor:NGB00847.1
contig_17876	5647	5613..5647	adaptor:NGB01083.1
contig_17925	9923	1..22	adaptor:NGB01088.1
contig_17938	5246	1..23	adaptor:NGB01088.1
contig_18016	8044	1..29	adaptor:NGB01096.1
contig_18017	6668	6647..6668	adaptor:NGB01096.1
contig_18044	11330	11299..11330	adaptor:NGB01096.1
contig_18049	10560	1..88	adaptor:NGB00847.1
contig_18173	12243	1..159	adaptor:NGB01096.1
contig_18175	8788	8765..8788	adaptor:NGB01096.1
contig_18177	11418	11340..11418	adaptor:multiple
contig_18182	11901	11832..11901	adaptor:NGB00847.1
contig_18201	6059	6038..6059	adaptor:NGB01096.1
contig_18222	11216	11136..11216	adaptor:NGB00847.1
contig_18228	8386	8361..8386	adaptor:NGB01088.1
contig_18321	5922	5897..5922	adaptor:NGB01096.1
contig_18370	5400	5085..5116	adaptor:NGB00747.1
contig_18453	5849	1..38	adaptor:NGB00360.1
contig_1846	23210	1..64	adaptor:NGB00360.1
contig_18479	5209	1..44	adaptor:NGB00360.1
contig_18486	5749	5726..5749	adaptor:NGB01088.1
contig_18488	5217	1..19	adaptor:NGB01088.1
contig_1969	65776	1..60	adaptor:NGB00360.1
contig_197	9215	1..83	adaptor:NGB00847.1
contig_1977	13765	1..35	adaptor:NGB01093.1
contig_1999	53427	53398..53427	adaptor:NGB01096.1
contig_2125	11803	11769..11803	adaptor:NGB01083.1
contig_2151	9544	1..37	adaptor:NGB01029.1
contig_2179	38972	1..67	adaptor:NGB00360.1
contig_2186	31110	30935..31110	adaptor:NGB01096.1
contig_2203	60314	60124..60187	adaptor:NGB00847.1
contig_2278	33271	1..36	adaptor:NGB01090.1
contig_2305	17957	1..58	adaptor:NGB00360.1
contig_2361	48816	48764..48816	adaptor:NGB00847.1
contig_242	49604	49535..49604	adaptor:NGB00360.1
contig_2429	76318	76242..76318	adaptor:NGB00847.1
contig_2430	70439	70373..70439	adaptor:NGB00847.1
contig_2459	63920	1..96	adaptor:NGB00847.1
contig_2485	31300	31260..31300	adaptor:NGB00360.1
contig_2508	25152	25095..25152	adaptor:NGB00847.1
contig_2650	36583	1..58	adaptor:NGB00847.1
contig_2668	22089	22052..22089	adaptor:NGB01029.1
contig_2735	13614	1..19	adaptor:NGB01088.1
contig_2781	50403	1..70	adaptor:NGB00847.1
contig_2800	30768	22802..22846	adaptor:NGB00360.1
contig_2824	44109	1..38	adaptor:NGB00847.1
contig_2888	19121	1..89	adaptor:NGB00360.1
contig_2900	36871	1..32	adaptor:NGB01088.1
contig_2949	25959	25916..25959	adaptor:NGB00360.1
contig_2970	20833	1..46	adaptor:NGB00360.1
contig_2986	16429	1..43	adaptor:NGB00360.1
contig_3069	38956	38904..38956	adaptor:NGB00847.1
contig_3106	9135	1..87	adaptor:NGB00847.1
contig_3124	70101	70072..70101	adaptor:NGB01088.1
contig_3129	30402	30379..30402	adaptor:NGB01088.1
contig_3147	10611	10586..10611	adaptor:NGB01096.1
contig_3190	117726	117687..117726	adaptor:NGB01029.1
contig_3243	44291	44273..44291	adaptor:NGB01096.1
contig_3276	57911	1..42	adaptor:NGB00360.1
contig_341	67008	1..22	adaptor:NGB01096.1
contig_3542	16855	1..60	adaptor:NGB00847.1
contig_3595	29288	1..79	adaptor:NGB00847.1
contig_3712	73078	1..78	adaptor:NGB00847.1
contig_3840	40472	40414..40472	adaptor:NGB00360.1
contig_3868	33875	33819..33875	adaptor:NGB00360.1
contig_3903	40080	40010..40080	adaptor:NGB00847.1
contig_3996	44010	43970..44010	adaptor:NGB00360.1
contig_4001	26085	1..73	adaptor:NGB00847.1
contig_4014	30676	30590..30676	adaptor:NGB00360.1
contig_4019	49543	1..76	adaptor:NGB00360.1
contig_4036	58848	58696..58848	adaptor:NGB00846.1
contig_4084	41308	41210..41308	adaptor:NGB00360.1
contig_4095	24801	1..70	adaptor:NGB00847.1
contig_4098	27393	1..189	adaptor:NGB01096.1
contig_410	57740	57678..57740	adaptor:NGB00360.1
contig_4172	20870	9717..9749	adaptor:NGB01096.1
contig_4318	55870	55805..55870	adaptor:NGB00360.1
contig_432	58593	58569..58593	adaptor:NGB01088.1
contig_4323	87370	87304..87370	adaptor:NGB00847.1
contig_4365	27401	27350..27401	adaptor:NGB00847.1
contig_4516	14480	1..98	adaptor:NGB00847.1
contig_452	34031	1..23	adaptor:NGB01096.1
contig_4530	63069	63006..63069	adaptor:NGB00360.1
contig_4651	67570	67518..67570	adaptor:NGB00847.1
contig_4679	20970	1..38	adaptor:NGB00360.1
contig_4686	7411	1..24	adaptor:NGB01096.1
contig_4743	37926	1..79	adaptor:NGB00360.1
contig_4765	11248	11167..11248	adaptor:NGB00360.1
contig_4801	91339	1..50	adaptor:NGB00360.1
contig_4812	37300	37121..37300	adaptor:NGB01093.1
contig_4820	80899	80862..80899	adaptor:NGB00360.1
contig_4904	9220	1..52	adaptor:NGB00847.1
contig_4916	29759	29718..29759	adaptor:NGB00847.1
contig_4924	19015	1..49	adaptor:NGB00847.1
contig_4939	23620	23574..23620	adaptor:NGB01029.1
contig_4956	40890	1..24	adaptor:NGB01088.1
contig_4994	71509	71447..71509	adaptor:NGB00847.1
contig_501	34157	34116..34157	adaptor:NGB00847.1
contig_5036	13162	1..77	adaptor:NGB00360.1
contig_5052	64212	1..170	adaptor:NGB01096.1
contig_5063	35265	35243..35265	adaptor:NGB01096.1
contig_5090	27510	27441..27510	adaptor:NGB00847.1
contig_5157	5988	5805..5988	adaptor:NGB00847.1
contig_5168	6086	6051..6086	adaptor:NGB00846.1
contig_5176	9131	1..41	adaptor:NGB00360.1
contig_5243	44178	1..88	adaptor:NGB00847.1
contig_5270	39229	39177..39229	adaptor:NGB00847.1
contig_5452	30446	1..36	adaptor:NGB00846.1
contig_5576	58918	1..34	adaptor:NGB01096.1
contig_5582	108611	1..87	adaptor:NGB00847.1
contig_5590	55235	55210..55235	adaptor:NGB01088.1
contig_5700	8246	1..82	adaptor:NGB00847.1
contig_5815	99837	1..63	adaptor:NGB00847.1
contig_5820	11616	1..202	adaptor:NGB00847.1
contig_5878	55755	1..26	adaptor:NGB01096.1
contig_59	12390	1..24	adaptor:NGB01096.1
contig_5959	11737	11532..11737	adaptor:NGB01096.1
contig_6065	11492	1..32	adaptor:NGB01088.1
contig_6067	19311	1..39	adaptor:NGB01029.1
contig_6092	14700	1..37	adaptor:NGB01029.1
contig_6194	32760	1..19	adaptor:NGB01088.1
contig_620	10761	1..206	adaptor:NGB01029.1
contig_6259	83001	1..50	adaptor:NGB00360.1
contig_6321	29279	29260..29279	adaptor:NGB01096.1
contig_6408	14690	1..74	adaptor:NGB00360.1
contig_6455	68530	68497..68530	adaptor:NGB01090.1
contig_6513	12061	11986..12061	adaptor:NGB00847.1
contig_6542	45321	1..41	adaptor:NGB00360.1
contig_6569	19579	19500..19579	adaptor:NGB00847.1
contig_6628	13125	13107..13125	adaptor:NGB01096.1
contig_6673	6733	6699..6733	adaptor:NGB01088.1
contig_6676	13298	13265..13298	adaptor:NGB01088.1
contig_6692	17411	1..43	adaptor:NGB00847.1
contig_6703	57771	1..63	adaptor:NGB00360.1
contig_6785	8258	8237..8258	adaptor:NGB01088.1
contig_6908	53004	52732..52792	adaptor:NGB00847.1
contig_6940	18777	18580..18777	adaptor:NGB00360.1
contig_6941	42032	41980..42032	adaptor:NGB00847.1
contig_6945	53258	1..71	adaptor:NGB00360.1
contig_6986	49101	1..21	adaptor:NGB01088.1
contig_701	57358	1..28	adaptor:NGB01096.1
contig_7017	41786	1..88	adaptor:NGB00360.1
contig_7035	53503	53477..53503	adaptor:NGB01096.1
contig_7046	12860	12812..12860	adaptor:NGB00360.1
contig_7081	27746	1..78	adaptor:NGB00847.1
contig_7082	26783	1..73	adaptor:NGB00847.1
contig_7083	44465	1..70	adaptor:NGB00847.1
contig_7117	33739	33661..33739	adaptor:NGB00360.1
contig_7197	5439	5361..5439	adaptor:NGB00360.1
contig_720	34826	34755..34826	adaptor:NGB00360.1
contig_7210	16719	1..30	adaptor:NGB01096.1
contig_7225	51589	51483..51519	adaptor:NGB01090.1
contig_7228	37410	1..64	adaptor:NGB00360.1
contig_7296	6652	1..80	adaptor:NGB00847.1
contig_7317	11682	1..30	adaptor:NGB01088.1
contig_7323	47612	47560..47612	adaptor:NGB00847.1
contig_7353	50534	50506..50534	adaptor:NGB01096.1
contig_7478	44000	43977..44000	adaptor:NGB01088.1
contig_7510	11029	1..22	adaptor:NGB01096.1
contig_7540	12614	12566..12614	adaptor:NGB00360.1
contig_7587	74260	74065..74260	adaptor:NGB00847.1
contig_7607	14652	1..31	adaptor:NGB01088.1
contig_7612	27455	27299..27354	adaptor:NGB00360.1
contig_7705	39772	1..49	adaptor:NGB00360.1
contig_7729	22305	1..172	adaptor:NGB00360.1
contig_7747	11568	11502..11568	adaptor:NGB00847.1
contig_7750	52785	52748..52785	adaptor:NGB01029.1
contig_7800	20628	20588..20628	adaptor:NGB00360.1
contig_7851	53514	53439..53514	adaptor:NGB00360.1
contig_7989	51399	1..97	adaptor:NGB00847.1
contig_7992	9120	9035..9120	adaptor:NGB00360.1
contig_7995	103073	103034..103073	adaptor:NGB00360.1
contig_8000	16924	1..85	adaptor:NGB00847.1
contig_8071	73728	73657..73728	adaptor:NGB00360.1
contig_809	20474	20399..20474	adaptor:NGB00360.1
contig_8139	33627	1..25	adaptor:NGB01088.1
contig_8165	17003	16958..17003	adaptor:NGB00847.1
contig_8207	30300	30275..30300	adaptor:NGB01096.1
contig_821	111683	111656..111683	adaptor:NGB01096.1
contig_8236	30705	1..70	adaptor:NGB00360.1
contig_8261	49091	1..181	adaptor:NGB00847.1
contig_8265	28139	27940..28139	adaptor:NGB00360.1
contig_8307	32654	32591..32654	adaptor:NGB00360.1
contig_8340	12953	12925..12953	adaptor:NGB01096.1
contig_8389	19738	1..75	adaptor:NGB00847.1
contig_8399	35159	1..147	adaptor:NGB01096.1
contig_8569	19455	1..38	adaptor:multiple
contig_8735	42362	42335..42362	adaptor:NGB01088.1
contig_8737	22308	1..70	adaptor:NGB00360.1
contig_8790	14216	14198..14216	adaptor:NGB01096.1
contig_8797	6889	1..95	adaptor:NGB00847.1
contig_8815	39194	1..80	adaptor:NGB00360.1
contig_886	10028	1..76	adaptor:NGB00360.1
contig_8861	12192	12145..12192	adaptor:NGB00360.1
contig_8909	11109	11042..11109	adaptor:NGB00360.1
contig_8932	8331	8281..8331	adaptor:NGB00847.1
contig_8975	8730	8671..8730	adaptor:NGB00847.1
contig_8992	12682	12661..12682	adaptor:NGB01088.1
contig_8994	7982	7950..7982	adaptor:NGB01096.1
contig_9017	8069	7896..8069	adaptor:NGB00360.1
contig_9045	35343	535..598	adaptor:NGB00847.1
contig_9082	10766	1..28	adaptor:NGB01096.1
contig_9271	17773	17750..17773	adaptor:NGB01096.1
contig_9273	12180	1..180	adaptor:NGB01096.1
contig_9287	6067	1..77	adaptor:NGB00847.1
contig_9474	33382	33060..33111	adaptor:NGB00360.1
contig_9495	19348	19274..19348	adaptor:NGB00847.1
contig_9540	30855	30836..30855	adaptor:NGB01088.1
contig_9591	10604	1..41	adaptor:NGB00847.1
contig_9628	15083	1..34	adaptor:NGB01096.1
contig_9677	5510	5486..5510	adaptor:NGB01088.1
contig_9693	9823	1..84	adaptor:NGB00847.1
contig_9825	54363	54309..54363	adaptor:NGB00847.1
contig_9863	14033	14013..14033	adaptor:NGB01088.1
contig_9993	35388	1..26	adaptor:NGB01096.1


From xvazquezc at gmail.com  Mon Oct 23 16:02:47 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Tue, 24 Oct 2017 09:02:47 +1100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's
actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the
contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the
"Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a
different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com> wrote:

> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this
> contamination report.
>
> Please how do I use maker to effect the correction
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From cjfields at illinois.edu  Mon Oct 23 17:21:06 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 23 Oct 2017 23:21:06 +0000
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
Message-ID: <8B4331B5-9D10-478A-91A5-80AF702CD9CD@illinois.edu>

It looks like the adapter is primarily at the ends, which is easy to remove.  However, I agree, removing these and redoing the assembly may improve the assembly quality.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Xabier V?zquez-Campos <xvazquezc at gmail.com>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>, "Ence, daniel" <d.ence at ufl.edu>
Subject: Re: [maker-devel] Contamination report from NCBI

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations
Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
Xabier V?zquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From mmokrejs at gmail.com  Tue Oct 24 04:23:38 2017
From: mmokrejs at gmail.com (=?UTF-8?Q?Martin_MOKREJ=c5=a0?=)
Date: Tue, 24 Oct 2017 12:23:38 +0200
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>

Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
> 
> Good day.
> 
> Please I submitted my sequence to NCBI and they sent back this contamination report.
> 
> Please how do I use maker to effect the correction

-- 
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/



From eennadi at gmail.com  Tue Oct 24 04:44:20 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 24 Oct 2017 11:44:20 +0100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
Message-ID: <CAOXM=CX=AiSo-u8gQ7de1KrgZLUbBZ2GXPbdU6kG3hjrUBjE1A@mail.gmail.com>

Thanks!
Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications



On Oct 24, 2017 11:23 AM, "Martin MOKREJ?" <mmokrejs at gmail.com> wrote:

> Hi Emmanuel,
>   use trimmomatic or cutadapt to remove the adapters and check the output
> file for unremoved cases. Once they are all removed redo the assembly.
> Martin
>
> Emmanuel Nnadi wrote:
> > Hello
> >
> > Good day.
> >
> > Please I submitted my sequence to NCBI and they sent back this
> contamination report.
> >
> > Please how do I use maker to effect the correction
>
> --
> Martin Mokrejs, Ph.D.
> Adapter/artefact removal from datasets based on the following technologies:
>   454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
> http://www.bioinformatics.cz/software/supported-protocols/
>
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From qwzhang0601 at gmail.com  Tue Oct 24 10:54:13 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Tue, 24 Oct 2017 12:54:13 -0400
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
Message-ID: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>

Dear Carson:

Thank you again for your suggestions. I just get the new genome assembly of
NMR and start to do gene annotation. I understand you ideas about this. But
can I simply use the old genome transcripts as transcript evidence, and
just following the standard Maker2 pipeline? I set est2genome=1 and provide
the mRNA sequences in the fasta format for the first round training of SNAP.

For transcripts I have the following choices. I think the first choice is
more reliable and better, right?
(1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded
those sequences in fasta format.
(2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by
trinity for each sample and then get the transcripts. But I think most of
the RNA-seq should have been submitted to NCBI.

BTW, if we use the RefSeq data from NCBI, we can download the mRNA
sequences, coding sequences or protein sequences. I wonder which type of
data are the best to train the SNAP? For Augustus, we will use BUSCO to
train it.

Many thanks.

Best
Quanwei




2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> You can try using the est2genome=1 option to map the old models forward
> onto the new assembly as if they were ESTs (add a line that says
> est_forward=1 to the control file to maintain old naming and set est=1 to
> the old model transcript file). Then provide the final models as a pred_gff
> for a subsuquent run (i.e. a traditional MAKER run where you are annotating
> the new assembly with transcript and protein evidence and ab initio
> predictors). Don?t supply the old models to est= on that run.
>
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will
> change. So by doing it this way, you will at least be able to move many
> models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are
> just letting old models compete against new annotations. They will be
> rejected if they have no evidence support, or can be kept if they score
> better than alternate models from SNAP/Augustus. That way you have the
> chance to integrate old models while at the same time rejecting some old
> models that have no evidence overlap.
>
> ?Carson
>
>
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been
> assembled and annotated a few years ago. We can download the gene
> annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder
> how can I fully make use of existing annotations. On the other hand, since
> the previous genome is not very well assemblies, some genes annotation
> maybe false positives. I hope those false positive genes in previous
> annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Tue Oct 24 16:26:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 24 Oct 2017 16:26:00 -0600
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
	<CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
Message-ID: <C02680FC-A5ED-4CD9-8517-3018CA1A0D69@gmail.com>

Yes. If you use est2genome it will just align the model, and then find the longest ORF. So it is a quick way to jsut align old models to the new assembly. Alternatively you can just do de novo annotation.

?Carson



> On Oct 24, 2017, at 10:54 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Dear Carson:
> 
> Thank you again for your suggestions. I just get the new genome assembly of NMR and start to do gene annotation. I understand you ideas about this. But can I simply use the old genome transcripts as transcript evidence, and just following the standard Maker2 pipeline? I set est2genome=1 and provide the mRNA sequences in the fasta format for the first round training of SNAP.
> 
> For transcripts I have the following choices. I think the first choice is more reliable and better, right?
> (1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded those sequences in fasta format.
> (2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by trinity for each sample and then get the transcripts. But I think most of the RNA-seq should have been submitted to NCBI. 
> 
> BTW, if we use the RefSeq data from NCBI, we can download the mRNA sequences, coding sequences or protein sequences. I wonder which type of data are the best to train the SNAP? For Augustus, we will use BUSCO to train it. 
> 
> Many thanks. 
> 
> Best
> Quanwei
> 
> 
> 
> 
> 2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> You can try using the est2genome=1 option to map the old models forward onto the new assembly as if they were ESTs (add a line that says est_forward=1 to the control file to maintain old naming and set est=1 to the old model transcript file). Then provide the final models as a pred_gff for a subsuquent run (i.e. a traditional MAKER run where you are annotating the new assembly with transcript and protein evidence and ab initio predictors). Don?t supply the old models to est= on that run.
> 
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will change. So by doing it this way, you will at least be able to move many models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are just letting old models compete against new annotations. They will be rejected if they have no evidence support, or can be kept if they score better than alternate models from SNAP/Augustus. That way you have the chance to integrate old models while at the same time rejecting some old models that have no evidence overlap.
> 
> ?Carson
> 
> 
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been assembled and annotated a few years ago. We can download the gene annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder how can I fully make use of existing annotations. On the other hand, since the previous genome is not very well assemblies, some genes annotation maybe false positives. I hope those false positive genes in previous annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From daren.card at gmail.com  Wed Oct 25 06:17:13 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 25 Oct 2017 07:17:13 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
	<C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>
	<97656D7C-3613-4B0B-9D99-0441AC28ABCC@gmail.com>
	<49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
Message-ID: <0406D4C3-9C43-4198-B2EA-241C6C504425@gmail.com>

Hi Carson (and CCed MAKER list for the record),

Thanks for troubleshooting my issue further. Good to hear that the run should ultimately work, but strange it isn?t for me. I?ll keep playing with it and will hopefully get it sorted out by running through the list you suggested. 

Thanks again for the help,
Daren


> On Oct 24, 2017, at 11:27 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> I cannot seem to replicate this. I ran with MAKER 2.31.8 and 2.31.9, both with and without the GFF3 file (total of 4 runs). It succeeded without issues in every case.
> 
> The only things I can think to try are.
> 1. Reinstall BLAST+. Even though you have 2.6.0, just try it anyways. Also Install rmblast 2.6.0 for use wth RepeatMasker (requires that you install from source).
> 2. Maker sure you run ./configure inside RepeatMasker to let it know about the new rmblast installation.
> 3. Change the location of blast and related scripts in maker_exe.ctl otherwise MAKER won?t know to use your new installation.
> 4. delete the mpi_blastdb directory under MAKER?s output directory tp force it to rebuild all BLAST indexes.
> 5. delete any fle with a ?.db? extension in the maker output directory to force it to rebuld all GFF3 indexes.
> 6. Update BioPerl to the current CPAN version.
> 
> Also here is a link to the results I got for your contig (version 2.31.8 using the repeat masking GFF3 file) ?> http://weatherby.genetics.utah.edu/data/scaffold-1.tgz
> 
> ?Carson
> 
> 
> 
>> On Oct 17, 2017, at 6:46 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi Carson,
>> 
>> Thanks for offering to take a further look at this. I?ve uploaded all the files that I think you?d need to run MAKER on your systems, but let me know if you need anything else. My username is ?guest_5038?. 
>> 
>> Repeat annotations GFF is from RepeatModeler, with simple repeats filtered away. Transcript evidence was from Trinity assembly of several RNAseq libraries. Several sets of protein evidence from related species. Also have augustus HMM trained based on the genome assembly using BUSCO with retraining turned on. 
>> 
>> The command I?ve used is below, and here are the software versions I?m working with: 
>> 
>> Maker - 2.31.8
>> BLAST - 2.6.0
>> Augustus - 3.2.3
>> RepeatMasker - 4.0.6
>> 
>> mpiexec -n 12 maker -base CroVir_rnd1_chr1 round1_maker_opts.chr1.ctl maker_bopts.ctl maker_exe.ctl
>> 
>> Thanks again!
>> Daren
>> 
>> 
>>> On Oct 13, 2017, at 10:37 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.
>>> 
>>> Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>>> 
>>> ?Carson
>>> 
>>> 
>>> 
>>>> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi Carson,
>>>> 
>>>> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
>>>> 
>>>> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
>>>> 
>>>> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
>>>> 
>>>> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
>>>> 
>>>> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
>>>> 
>>>> Thanks,
>>>> Daren
>>>> 
>>>> 
>>>>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>>>>> 
>>>>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>>>>> 
>>>>> ?Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>> 
>>>>>> Dear Carson,
>>>>>> 
>>>>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>>>>> 
>>>>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>>>>> 
>>>>>> Thank you,
>>>>>> Daren Card
>>>>>> 
>>>>>> 
>>>>>> ################################################
>>>>>> doing repeat masking
>>>>>> re reading repeat masker report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>>>>> doing blastx repeats
>>>>>> re reading blast report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>>>>> deleted:2 hits
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> collecting blastx repeatmasking
>>>>>> processing all repeats
>>>>>> in cluster::shadow_cluster...
>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>> --> rank=NA, hostname=moonunit0
>>>>>> ERROR: Failed while processing all repeats
>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> examining contents of the fasta file and run log
>>>>>> ################################################
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>>>> 
>>>>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>>>>> 
>>>>>>> ?Carson
>>>>>>> 
>>>>>>> 
>>>>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>>>> 
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>>>>> 
>>>>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>>>>> 
>>>>>>>> Any help would be greatly appreciated.
>>>>>>>> Daren Card
>>>>>>>> 
>>>>>>>> University of Texas Arlington
>>>>>>>> 
>>>>>>>> ###################################################
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> deleted:0 hits
>>>>>>>> collecting blastx repeatmasking
>>>>>>>> processing all repeats
>>>>>>>> in cluster::shadow_cluster...
>>>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>>>> --> rank=3, hostname=moonunit0
>>>>>>>> ERROR: Failed while processing all repeats
>>>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> deleted:0 hits
>>>>>>>> deleted:0 hits
>>>>>>>> ###################################################
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 




From venyao at qq.com  Wed Oct 25 01:25:25 2017
From: venyao at qq.com (=?ISO-8859-1?B?V2VuIFlhbw==?=)
Date: Wed, 25 Oct 2017 15:25:25 +0800
Subject: [maker-devel] NNN in maker output transcript
Message-ID: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>

Dear guys,


Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.


Thanks!


Wen Yao
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From dandence at gmail.com  Wed Oct 25 09:42:04 2017
From: dandence at gmail.com (Daniel Ence)
Date: Wed, 25 Oct 2017 11:42:04 -0400
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <4913D7BA-CD9B-4B7F-83EF-B8072B4950A6@gmail.com>

Hi Wen Yao, 

Do you mean that some of the transcript sequences contain ?N? characters or that an entire transcript sequence is ?NNN??  



> On Oct 25, 2017, at 3:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:42:34 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:42:34 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>

The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.

?Carson




> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:43:37 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:43:37 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
	<96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
Message-ID: <F55EEB1B-9F79-474A-8AE4-5232566D7380@gmail.com>

Also you can check the source of the model by looking a the name. i.e. does it have, augustus, snap, or est2genome in the name?

?Carson

> On Oct 25, 2017, at 9:42 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.
> 
> ?Carson
> 
> 
> 
> 
>> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
>> 
>> Dear guys,
>> 
>> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
>> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
>> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
>> 
>> Thanks!
>> 
>> Wen Yao
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Thu Oct 26 15:34:33 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Thu, 26 Oct 2017 22:34:33 +0100
Subject: [maker-devel] How to remove contigs from GFF file
Message-ID: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>

Hello,

I need to remove sequences from my GFF file can someone help me with
command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in
gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>
 [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ:
gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From bmoore at genetics.utah.edu  Fri Oct 27 07:17:41 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:17:41 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <98FAE3F3-7C52-4EDA-8FBB-5F43DB7D54C9@umail.utah.edu>

Those look suspiciously like the remnants of end-of-line control characters.  Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I?d look at the upstream path of where your files come from and how they?ve been processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server).  One bizarre example we?ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted to MS format.  Good luck?

Barry

On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From bmoore at genetics.utah.edu  Fri Oct 27 07:24:44 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:24:44 +0000
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
	<CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
Message-ID: <FB1F1E37-1246-4A10-BD9A-BF0644528F15@umail.utah.edu>

Also, you could probably build these overlap sets on the command line by subsetting the MAKER GFF3 file and then using BedTools intersect for overlap queries.

Barry

On Oct 11, 2017, at 10:19 PM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL

?Carson



On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?

Thanks!!!
Matt Simenc
_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
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From dandence at gmail.com  Fri Oct 27 08:51:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Fri, 27 Oct 2017 10:51:21 -0400
Subject: [maker-devel] How to remove contigs from GFF file
In-Reply-To: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
References: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
Message-ID: <D0CA7ADF-64A3-4B15-ACA3-26FA95B1C5F9@gmail.com>

Hi Emmanuel, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this ?grep -v ?scaffold_name? gff3_file?. 

~Daniel



> On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> 
> I need to remove sequences from my GFF file can someone help me with command line for such removal
> 
> ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
> ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 27 16:00:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Oct 2017 16:00:17 -0600
Subject: [maker-devel] "ALRM" isn't numeric in exit - MAKER warning
 message
In-Reply-To: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
References: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
Message-ID: <399AB5BD-2FC5-45F4-9AC8-1665CCFEA0D1@gmail.com>

Hi Marivi,

The only time MAKER uses the ALRM signal is during exit. Sometimes MPI_Finalize can freeze (it has to do with the fact it is being called from Perl). So we set an alarm just in case. Then if it takes to long we assume it is frozen and let things exit in a less than graceful way rather than let it block forever (it is already finished after all). The complaint you get may be because your system doesn?t support the alarm signal or forks.pm (which tries to intercept signals) is having an issue. Or it may just be ugliness related to parts of the process being killed with other parts still being active (it is an ungraceful exit after all). Or it may be another source of the ALRM all together (but I assume it is the MAKER ALRM given that it happens right after MAKER says it is finished). 

Thanks,
Carson



> On Oct 27, 2017, at 1:03 PM, Marivi Colle <collemar at msu.edu> wrote:
> 
> Hi Carson,
> 
> After running MAKER, I checked my std output and here's the message at the end of the file. I was wondering what this warning message means?
> 
> 
> Start_time: 1508465182
> End_time:   1508950543
> Elapsed:    485361
> 
> 
> Maker is now finished!!!
> 
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184
> 
> 
> Thank you.
> Marivi
> 
> 
> -- 
> Marivi G. Colle
> Research Associate
> Department of Horticulture
> Michigan State University
> 1066 Bogue St., East Lansing
> Michigan 48824-1325, USA

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From patrick.tranvan at unil.ch  Sat Oct 28 08:14:59 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Sat, 28 Oct 2017 14:14:59 +0000
Subject: [maker-devel] Advice on my pipeline
In-Reply-To: <651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
References: <6b029690bace4d3fbae77c0bb1bddce8@prdexch02.ad.unil.ch>
	<A39F4213-70A8-4E07-AB13-00C427E4F244@gmail.com>
	<1498470630221.84642@unil.ch>
	<696C51C6-5606-4ECB-A8B8-9C077182FFFA@gmail.com>
	<1498908228256.16549@unil.ch>
	<58E904BF-9AB8-4AC7-B10B-C902F414E03D@gmail.com>
	<1505986013492.52354@unil.ch>,
	<651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
Message-ID: <1509200133044.96929@unil.ch>

Hi Carson,


If I want to look for alternative splicing variant, can I just add the option


alt_splice=1


only at the last round of maker or do I have to set it since the beggining ? (and perform the 4 rounds with this option).

Cheers,

Patrick


________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: Friday, September 22, 2017 10:08 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Advice on my pipeline

The gff3 passthrough options are there to help users get old data into MAKER when they have lost access to the original files. But for iterative running of the pipeline, it is more effective just to rerun in place so MAKER can access the raw alignment reports. The raw reports from the alignments have more detail than what is stored in the GFF3. Details that are lost when trying to use the GFF3 as input.

?Carson


On Sep 21, 2017, at 3:26 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hi Carson,

I have a doubt for the round 2, so in a previous reply you said:

" Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory). "



Does it means that I don't need to modify the section :

#-----Re-annotation Using MAKER Derived GFF3

?

If I let everything by default such as :


altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no


It will not look again for repeat and protein + transcriptome alignment ?

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, July 3, 2017 10:50 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

maker2zff is just for SNAP training and not for gene filtering (please do not use it for filtering, it does not do what you think).

So the final annotation set after maker with correct_est_fusion is 16,850. To decide which set is better, look at them in a browser (gene counts are not useful for guaging result). A well annotated genome will have evidence clusters that closely match the final models. A poorly annoted genome will have evidence clusters that are split or merged by the models.

The corrected_est_fusion does two things. It trims long overlapping UTR fragments, and it stops evidence clusters from being merged on BLASTP evidence alone (so gene predictors will get unmerged hint regions if clusters are split).

You may also find that using jaccard_clip with Trinity has reduced sensitivity for the transcript data (you may lose things that were there before, but now have better specificity, i.e. fewer false positives). Make sure you provided protein data from at least two related species to help maintain sensitivity lost form the transcript data. You can also add rejected genes models back in after the fact by using iprscan to identify unsupported models with identifiable protein domains ?> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/

Thanks,
Carson




On Jul 1, 2017, at 5:21 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

So I have assembled my transcriptome with Trinity using the jaccard clip option and I have run maker with and without corrected_est_fusion.

I have then use SNAP to train/filter it with:

maker2zff  specie.all.gff

Here are my results:

Number of gene after maker -> Number of gene after maker2zff

- Without corrected_est_fusion: 21621 -> 13875
- With corrected_est_fusion: 16850 -> 9098

1 )If I understand well how works corrected_est_fusion, because it prevents gene merging, shouldn't be the invert ?
Normally I should find more genes with corrected_est_fusion right ?

2) I think I should find something like 13000-14000 genes for my specie. SHould I go with the "Without corrected_est_fusion" for the 2nd iteration of maker ?

 Thanks for your help



Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 26, 2017 11:38 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Sorry the option is ?> correct_est_fusion

It is in the maker_opts.ctl file.

I would use both SNAP and Augustus on a few large contigs then review the results manually. If one of them is not behaving well, then drop it. If both behave well (i.e. correlate well with evidence alignemnts) then keep them both.

?Carson



On Jun 26, 2017, at 3:48 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Thanks for your answer.

1) Do you think that adding a Augustus training in addition to SNAP at the step 3 and 5 will add more confidence (instead of adding Augustus only for the final round) ?
Because I am using autoAug for this and it tooks a while to compute ..

2) I don't see this option : 'avoid_est_fusion=1' . I have tried to add it but I got this error:

WARNING: Invalid option 'avoid_est_fusion' in control file maker_opts.ctl

(I am using v 2.31.8 )


Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 5, 2017 8:29 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Your plan sounds good. A couple of related notes.

Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.

Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory).

?Carson


On Jun 2, 2017, at 3:56 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hello,

This is my first time running Maker for an insect genome annotation.

I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:


What I have:
- RNA evidence: transcriptome
- Proteine evidence: swissprot/uniprot + busco protein set of insect
- Cegma and busco results of my genome


1) Train SNAP with CEGMA

2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).

3) Create SNAP model from run A.

4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

5) Create SNAP model from run B.

6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

7)  Create SNAP model from run C AND Create Augustus gene model from run C

8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1). + Use keep_preds=1



Does it seems coherent ?

Cheers,

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org







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From dandence at gmail.com  Mon Oct  2 07:17:57 2017
From: dandence at gmail.com (Daniel Ence)
Date: Mon, 2 Oct 2017 09:17:57 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
Message-ID: <F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>

Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink
The fasta headers in this file are different from the fasta header that the file you used has: 
>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1

Let us know if that helps, 
Daniel

> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> I intend to rename genes for Genebank submission
> 
> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
> 
> the output of BLAST RESULT looks like this
> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
> 
> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
> 
> I got the following result
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
> 
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
> 
> What can I do?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
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From michael.s.campbell1 at gmail.com  Mon Oct  2 07:30:43 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 09:30:43 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
Message-ID: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 

Thanks,
Mike


> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hello-
> 
> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
> 
> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
> 
> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
> 
> Thanks for your help,
> 
> Best,
> 
> Chris Willett
> 
>   
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: 2252 Genome Science Building
> phone:
> 919-843-8663
> fax:
> 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:19:51 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:19:51 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
Message-ID: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
> On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi Mike-
> 
> I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?
> 
> Thanks for your help,
> 
> Best,
> 
> Chris
> 
> 
> 
>> On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com <mailto:michael.s.campbell1 at gmail.com>> wrote:
>> 
>> Hi Chris,
>> 
>> This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 
>> 
>> Thanks,
>> Mike
>> 
>> 
>>> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu <mailto:willett4 at email.unc.edu>> wrote:
>>> 
>>> Hello-
>>> 
>>> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
>>> 
>>> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
>>> 
>>> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
>>> 
>>> Thanks for your help,
>>> 
>>> Best,
>>> 
>>> Chris Willett
>>> 
>>>   
>>> 
>>> 
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Research Associate Professor
>>> Department of Biology
>>> CB#3280 Coker Hall
>>> University of North Carolina, Chapel Hill
>>> Chapel Hill, NC, 27599-3280 
>>> 
>>> Office: 2252 Genome Science Building
>>> phone:
>>> 919-843-8663
>>> fax:
>>> 919-962-1625
>>> 
>>> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
> 

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:35:55 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:35:55 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
	<FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
Message-ID: <4C4E3DE7-CE28-4DF7-B234-E88701CAD172@gmail.com>

Hi Chris,

It?s this line here:
model_gff=/proj/willetlb/users/cwillett/MAKER_analyses/dovetail_ann/SDv1.0_est-forward-SDv2.1.gff

Anything passed to model_gff is treated as sacred by MAKER and will be kept regardless of AED. If you pass it in as pred_gff= then it will be subject to the AED filters.

I hope this helps,
Mike
> On Oct 2, 2017, at 3:28 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> <maker_opts.ctl_full8>




From daren.card at gmail.com  Wed Oct  4 09:53:42 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 4 Oct 2017 10:53:42 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
Message-ID: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>

Hi all,

I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?

I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).

Any help would be greatly appreciated.
Daren Card

University of Texas Arlington

###################################################
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=3, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

deleted:0 hits
deleted:0 hits
###################################################




From carsonhh at gmail.com  Wed Oct  4 10:03:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 10:03:52 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
Message-ID: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>

The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.

?Carson


> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi all,
> 
> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
> 
> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
> 
> Any help would be greatly appreciated.
> Daren Card
> 
> University of Texas Arlington
> 
> ###################################################
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
> #-------------------------------#
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=3, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
> #-------------------------------#
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> deleted:0 hits
> deleted:0 hits
> ###################################################
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From qwzhang0601 at gmail.com  Wed Oct  4 16:31:09 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 18:31:09 -0400
Subject: [maker-devel] About eAED
Message-ID: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>

Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I
found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be
the reason of the great difference between AED and eAED. For this gene it
has a very low AED score, is it still a reliable gene model if its eAED
equals 1?

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei
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From xvazquezc at gmail.com  Wed Oct  4 16:35:41 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 5 Oct 2017 09:35:41 +1100
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>

Carson commented on this here
https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:

> Hello:
>
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
> I found there are several hundred genes with eAED 1.
>
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
> be the reason of the great difference between AED and eAED. For this gene
> it has a very low AED score, is it still a reliable gene model if its eAED
> equals 1?
>
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
> QI:75|0|0|1|0|0|2|111|35
>
> Thanks
>
> Best
> Quanwei
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From carsonhh at gmail.com  Wed Oct  4 16:38:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:38:00 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <77155DA5-6454-4B25-BCF6-DE6B077BA548@gmail.com>

eAED is an extended AED calculation that does some inference about the evidence (i.e. checks reading frame and not just overlap, and may infer support for an exon if by splice sites are confirmed etc.). If eAED is 1 that means that while there is evidence supporting the model, the evidence is more likely to be spurious, so it may be a false model.

?Carson

 
> On Oct 4, 2017, at 4:31 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct  4 16:39:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:39:52 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
Message-ID: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>

This one is an even better explanation than the answer I just gave. Thank you.

?Carson

> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> 
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From eennadi at gmail.com  Sun Oct  1 23:03:01 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Oct 2017 06:03:01 +0100
Subject: [maker-devel] Error with Maker_functional_gff
Message-ID: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>

Hello,
I intend to rename genes for Genebank submission

I downloaded swissprot.fa from NCBI and used blast MAKER generated file to
swissprot.

the output of BLAST RESULT looks like this

snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1
49.315  73      37      0       43      115     874     946     2.61e-14
    71.6


I attempted to run maker_funtional_gff using the swissprot.fa downloaded
and the blastp result


I got the following result

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 2897906.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 2897906.

Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin;
AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP;
AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName:
Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1;
Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor



Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 1608599.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 1608599.

Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X
methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase


What can I do?



Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From willett4 at email.unc.edu  Mon Oct  2 09:04:38 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 15:04:38 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
Message-ID: <DBEB554A-5809-4EB8-AC78-8B410E73B0C4@ad.unc.edu>

Hi Mike-

Thanks for getting back to me. I was using the grep -cP '\tgene\t? syntax to count the numbers and it seems to be giving me the same numbers I got before when I was counting either the transcripts or the genes in the fasta output files from our original run. I will have to look at the files a bit more to see if I can find some examples of genes that fit what you are suggesting.

Best,

Chris


On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From willett4 at email.unc.edu  Mon Oct  2 13:28:19 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 19:28:19 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
Message-ID: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>

Hi Mike-

Here is the control file for the last run of MAKER with keep_preds=0 and here is an example of one mRNA retained from the gff file:

Chromosome_6    maker   mRNA    556000  557215  .       +       .       ID=maker-Chromosome_6-exonerate_est2genome-gene-5.3-mRNA-1;Parent=maker-Chromosome_6-exonerate_est2genome-gene-5.3;Name=TCALIF_02833-PA;_AED=1.00;_eAED=1.00;_QI=15|0|0|0|1|1|2|75|338;score=100;Alias=TCALIF_02833-PA

Thanks,

Chris






On Oct 2, 2017, at 3:19 PM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hi Mike-

I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?

Thanks for your help,

Best,

Chris



On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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From qwzhang0601 at gmail.com  Wed Oct  4 20:35:55 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 22:35:55 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
Message-ID: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>

Thank you all.  Most time, the AED is equal to or lower than eAED, but
there are some genes whose eAED is smaller than AED. I feel the eAED is
more stringent than AED. Would you give me an example, under what condition
eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do
you think eAED is a better choice to filter gene models than AED?

Best
Quanwei



2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> This one is an even better explanation than the answer I just gave. Thank
> you.
>
> ?Carson
>
> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
>> Hello:
>>
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
>> I found there are several hundred genes with eAED 1.
>>
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>> be the reason of the great difference between AED and eAED. For this gene
>> it has a very low AED score, is it still a reliable gene model if its eAED
>> equals 1?
>>
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>> QI:75|0|0|1|0|0|2|111|35
>>
>> Thanks
>>
>> Best
>> Quanwei
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From carsonhh at gmail.com  Wed Oct  4 20:38:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:38:25 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
Message-ID: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>

The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

?Carson


> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
> 
> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
> 
> Best
> Quanwei
> 
>  
> 
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> This one is an even better explanation than the answer I just gave. Thank you.
> 
> ?Carson
> 
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>> 
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>> 
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> Hello:
>> 
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>> 
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>> 
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>> 
>> Thanks
>> 
>> Best
>> Quanwei
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
>> 
>> 
>> -- 
>> Xabier V?zquez-Campos, PhD
>> Research Associate
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From carsonhh at gmail.com  Wed Oct  4 20:43:28 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:43:28 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
Message-ID: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>

eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn?t exist, it just means you should spend a little more time deciding if you really believe it or not.

?Carson


> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> 
>> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
>> 
>> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
>> 
>> Best
>> Quanwei
>> 
>>  
>> 
>> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
>> This one is an even better explanation than the answer I just gave. Thank you.
>> 
>> ?Carson
>> 
>>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>>> 
>>> Carson commented on this here
>>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>>> 
>>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>>> Hello:
>>> 
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>>> 
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>>> 
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>>> 
>>> Thanks
>>> 
>>> Best
>>> Quanwei
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Xabier V?zquez-Campos, PhD
>>> Research Associate
>>> NSW Systems Biology Initiative
>>> School of Biotechnology and Biomolecular Sciences
>>> The University of New South Wales
>>> Sydney NSW 2052 AUSTRALIA
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
> 

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From qwzhang0601 at gmail.com  Wed Oct  4 21:25:24 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 23:25:24 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
	<C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
Message-ID: <CAOW6FSKZzHUVFm=b+3V82whb+gWNdAgERfO=e5f1k1HSRGz=kw@mail.gmail.com>

Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> eAED can be better for edge cases, but neither is perfect. Low AED
> generally correlates with better models. But a high AED does not mean the
> model doesn?t exist, it just means you should spend a little more time
> deciding if you really believe it or not.
>
> ?Carson
>
>
>
> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> The previous linked comment explains in detail ?>
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> Basically the middle support of exon is inferred from edge support even
> though no overlap exists (so eAED infers support and AED does not).
>
> ?Carson
>
>
> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Thank you all.  Most time, the AED is equal to or lower than eAED, but
> there are some genes whose eAED is smaller than AED. I feel the eAED is
> more stringent than AED. Would you give me an example, under what condition
> eAED can be smaller than AED?
>
> The default maker2 gene set includes all genes with AED less than 1.  Do
> you think eAED is a better choice to filter gene models than AED?
>
> Best
> Quanwei
>
>
>
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:
>
>> This one is an even better explanation than the answer I just gave. Thank
>> you.
>>
>> ?Carson
>>
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
>> wrote:
>>
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-
>> ko/iC4KTuIitGEJ
>>
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>>> Hello:
>>>
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1).
>>> But I found there are several hundred genes with eAED 1.
>>>
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>>> be the reason of the great difference between AED and eAED. For this gene
>>> it has a very low AED score, is it still a reliable gene model if its eAED
>>> equals 1?
>>>
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>>> QI:75|0|0|1|0|0|2|111|35
>>>
>>> Thanks
>>>
>>> Best
>>> Quanwei
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>> --
>> Xabier V?zquez-Campos, *PhD*
>> *Research Associate*
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
>
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From dandence at gmail.com  Thu Oct  5 08:00:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Thu, 5 Oct 2017 10:00:21 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
	<F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>
	<CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
Message-ID: <ECCCAE79-FEDA-4C6E-B7E4-A8FC0C3AD1C2@gmail.com>

Hi Emmanuel, 

I can?t tell whether it?s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you?ll run after all the blasts are complete. 

Assembly isn?t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. 

How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I?d recommend starting with a  review like this one: http://www.sciencedirect.com/science/article/pii/S1672022912000095 <http://www.sciencedirect.com/science/article/pii/S1672022912000095>

~Daniel

> On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Daniel,
> 
> Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now
> 
> it looks like this
> 
> MUCPR_041061-RA	sp|P10978|POLX_TOBAC	49.315	73	37	0	43	115	874	946	2.95e-14	71.6
> MUCPR_026643-RA	sp|Q00451|PRF1_SOLLC	86.207	87	11	1	243	328	257	343	3.65e-32	126
> 
> Is it ok?
> 
> I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?
> 
> I wish to assemble my sequence into scaffold can you advice on the best software to use?
> 
> I attempted using SSPACE: a new stand-alone scaffolding tool for small and large genomes
> but am having problem with the library. Funny enough the software does not have support to solve problems
> 
> Thanks
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink <http://www.uniprot.org/downloads#uniprotkblink>
> The fasta headers in this file are different from the fasta header that the file you used has: 
> >sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1
> 
> Let us know if that helps, 
> Daniel
> 
>> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Hello,
>> I intend to rename genes for Genebank submission
>> 
>> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
>> 
>> the output of BLAST RESULT looks like this
>> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
>> 
>> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
>> 
>> I got the following result
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
>> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
>> 
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
>> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
>> 
>> What can I do?
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
> 

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From daren.card at gmail.com  Fri Oct  6 06:23:36 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Fri, 6 Oct 2017 07:23:36 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
Message-ID: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>

Dear Carson,

Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.

Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.

Thank you,
Daren Card


################################################
doing repeat masking
re reading repeat masker report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
doing blastx repeats
re reading blast report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
deleted:2 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=NA, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

examining contents of the fasta file and run log
################################################



> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>> 
>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>> 
>> Any help would be greatly appreciated.
>> Daren Card
>> 
>> University of Texas Arlington
>> 
>> ###################################################
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=3, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>> #-------------------------------#
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> deleted:0 hits
>> deleted:0 hits
>> ###################################################
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Sat Oct  7 15:34:46 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sat, 7 Oct 2017 22:34:46 +0100
Subject: [maker-devel] jbrowse not working
Message-ID: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse.

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Sun Oct  8 18:37:12 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 8 Oct 2017 18:37:12 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
Message-ID: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>

MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).

The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/ <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/>

?Carson





> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Dear Carson,
> 
> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
> 
> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
> 
> Thank you,
> Daren Card
> 
> 
> ################################################
> doing repeat masking
> re reading repeat masker report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
> doing blastx repeats
> re reading blast report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
> deleted:2 hits
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=NA, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> examining contents of the fasta file and run log
> ################################################
> 
> 
> 
>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>> 
>> ?Carson
>> 
>> 
>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Hi all,
>>> 
>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>> 
>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>> 
>>> Any help would be greatly appreciated.
>>> Daren Card
>>> 
>>> University of Texas Arlington
>>> 
>>> ###################################################
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>> #-------------------------------#
>>> deleted:0 hits
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=3, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>> #-------------------------------#
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> deleted:0 hits
>>> deleted:0 hits
>>> ###################################################
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 

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From carsonhh at gmail.com  Mon Oct  9 18:35:49 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 9 Oct 2017 18:35:49 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
Message-ID: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>

Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Please,
> I ran the command line
> 
> maker2jbrowse muc1_genome_snap2.all.gff
> 
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
> 
> Please what does it mean? How can I view it in jbrowse. 
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From eennadi at gmail.com  Mon Oct  9 22:42:35 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 10 Oct 2017 05:42:35 +0100
Subject: [maker-devel] jbrowse not working
In-Reply-To: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
Message-ID: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge ?d
dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse
/Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse
-d
/Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log
\-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the
jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31
contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of
> the file? That can happen if you use the -n option with gff3_merge.
> Alternatively it?s possible one of the individual contig gff3 used to build
> the merged gff3 is truncated. If that is the case then gff3_merge should
> have thrown some sort of error or warning when you run it.
>
> Thanks,
> Carson
>
>
>
>
> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Please,
> I ran the command line
>
> maker2jbrowse muc1_genome_snap2.all.gff
>
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
>
> Please what does it mean? How can I view it in jbrowse.
>
> Thanks
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
>
>
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From jacques.dainat at nbis.se  Tue Oct 10 03:24:34 2017
From: jacques.dainat at nbis.se (Jacques Dainat)
Date: Tue, 10 Oct 2017 11:24:34 +0200
Subject: [maker-devel] MAKER annotation submission (EMBLmyGFF3)
Message-ID: <967873FE-D61F-4233-A004-C877A60A2AC1@nbis.se>

Hi MAKER users,

I take advantage to this mailing list to share a tool that I hope will be useful for MAKER's users. One of the steps once we are happy of our wonderful annotation is to submit it to the public archives through one of the three INSDC databases (EMBL-EBI / NCBI / DDBJ).
We developed EMBLmyGFF3, allowing to easily convert any kind of GFF3 annotation to the EMBL flat file format in order to submit to the European Nucleotide Archive (ENA) Database that is part of EMBL-EBI.
It works well, amongst others, with the MAKER annotation output. We hope the tool will ease the submission process of your annotations.

You will find it here:
https://github.com/NBISweden/EMBLmyGFF3

A typical usage case will look like that (where ERSXXXXXX and PRJXXXXXX are the accession number and the project ID provided by EMBL-EBI prior to any submission):
./EMBLmyGFF3.py maker.gff3 maker.fa --data_class STD --topology linear --molecule_type 'genomic DNA' --table 1 --species 'Drosophila melanogaster (fly)' --taxonomy INV --accession ERSXXXXXXX --project_id PRJXXXXXXX --rg MYGROUP -o result.embl

Best regards,

Jacques Dainat, PhD
---------------------------------------
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
---------------------------------------
Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics


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From mcsimenc at gmail.com  Wed Oct 11 08:53:36 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 07:53:36 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons with
 EST only?
Message-ID: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence
supporting gene models in my MAKER annotation where the left side shows
number of genes with EST support only, the right side shows number of genes
with protein support only, and the intersection shows number of genes with
EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be
fraction of exons that overlap an EST alignment and possibly also a protein
alignment. If that is the case then we can't calculate the number of genes
that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to
get this?

Thanks!!!
Matt Simenc
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From michael.s.campbell1 at gmail.com  Wed Oct 11 09:18:54 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Wed, 11 Oct 2017 11:18:54 -0400
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
Message-ID: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> Hey MAKER people,
> 
> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
> 
> QI summary has:
> 
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
> 
> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
> 
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
> 
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 11 09:22:54 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Oct 2017 09:22:54 -0600
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
Message-ID: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>

Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL <https://github.com/The-Sequence-Ontology/GAL>

?Carson


 
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Matt,
> 
> I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.
> 
> To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.
> 
> Hope this helps,
> Mike
> 
>> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>> 
>> Hey MAKER people,
>> 
>> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
>> 
>> QI summary has:
>> 
>> Fraction of exons that overlap an EST alignment
>> Fraction of exons that overlap EST or Protein alignments
>> 
>> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
>> 
>> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
>> 
>> Thanks!!!
>> Matt Simenc
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From mcsimenc at gmail.com  Wed Oct 11 22:19:04 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 21:19:04 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
Message-ID: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Also look at GAL for building GFF3 feature queries ?>
> https://github.com/The-Sequence-Ontology/GAL
>
> ?Carson
>
>
>
>
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <
> michael.s.campbell1 at gmail.com> wrote:
>
> Hi Matt,
>
> I have a hacky way that I?ve done it. It requires running MAKER two more
> times but they are quicker runs.
>
> To identify the genes that have protein support I pass all of the
> annotation back to MAKER using the model_gff option in the maker_opts.ctl
> file. Then I pull out all of the protein2genome features from the big MAKER
> GFF3 file and pass them in using the protein_gff option. I turn off all
> repeat masking and run MAKER. It runs fast because it doesn?t have to run
> any gene finders, align evidence, or repeatmask. In the output any gene
> with an AED less than 1 has protein support. Then I do the same thing with
> est2genome lines from the big GFF3 file and put them in as est_gff. The
> output of that one gives you genes with EST support. Then the genes with an
> AED of less than one in both sets have support from protein and EST.
>
> Hope this helps,
> Mike
>
> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>
> Hey MAKER people,
>
> I would like to make a Venn diagram showing the kinds of evidence
> supporting gene models in my MAKER annotation where the left side shows
> number of genes with EST support only, the right side shows number of genes
> with protein support only, and the intersection shows number of genes with
> EST and protein support.
>
> QI summary has:
>
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
>
> Please correct me if I'm wrong, because I am interpreting the first to be
> fraction of exons that overlap an EST alignment and possibly also a protein
> alignment. If that is the case then we can't calculate the number of genes
> that overlap only EST or (EST and protein) from the QI information.
>
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to
> get this?
>
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From scott at scottcain.net  Thu Oct 12 17:33:05 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:33:05 -0400
Subject: [maker-devel] GMOD hackathon before PAG San Diego in January
Message-ID: <CA+JTaoytocv6efRcY6LqKXRjPZXeqa9JFFStCPxE0VunjmB-Nw@mail.gmail.com>

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From daren.card at gmail.com  Thu Oct 12 20:22:54 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Thu, 12 Oct 2017 21:22:54 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
Message-ID: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>

Hi Carson,

Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.

Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.

I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.

What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.

Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.

Thanks,
Daren


> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
> 
> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
> 
> ?Carson
> 
> 
> 
> 
> 
>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Dear Carson,
>> 
>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>> 
>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>> 
>> Thank you,
>> Daren Card
>> 
>> 
>> ################################################
>> doing repeat masking
>> re reading repeat masker report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>> doing blastx repeats
>> re reading blast report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>> deleted:2 hits
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=NA, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> examining contents of the fasta file and run log
>> ################################################
>> 
>> 
>> 
>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>> 
>>> ?Carson
>>> 
>>> 
>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>> 
>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>> 
>>>> Any help would be greatly appreciated.
>>>> Daren Card
>>>> 
>>>> University of Texas Arlington
>>>> 
>>>> ###################################################
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>> #-------------------------------#
>>>> deleted:0 hits
>>>> collecting blastx repeatmasking
>>>> processing all repeats
>>>> in cluster::shadow_cluster...
>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>> --> rank=3, hostname=moonunit0
>>>> ERROR: Failed while processing all repeats
>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>> #-------------------------------#
>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> deleted:0 hits
>>>> deleted:0 hits
>>>> ###################################################
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
> 




From robert.zimmermann at univie.ac.at  Wed Oct 11 13:42:14 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Wed, 11 Oct 2017 21:42:14 +0200
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
Message-ID: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>

Hello,

I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 

My gene prediction section of the maker_opts.ctl file looks like this:
...
augustus_species=all_combined #Augustus gene prediction species model
...
pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
?

It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.

Thanks for your help!

Bob


From xvazquezc at gmail.com  Thu Oct 12 00:09:32 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 12 Oct 2017 17:09:32 +1100
Subject: [maker-devel] choosing the right gene model
Message-ID: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>

Hi there,

I was visualising the annotations and I realised that in some cases, what
it seems to be a gene is splitted according to one of the gene models,
despite that the other 2, est2genome and prot2genome suggest that it isn't
the case.



Although the opposite also happens.


?
For some reason, the "out of place" model is always (or almost) the one
from Genemark.

How much weight does carry the RNAseq and protein data on this decision (if
any)?
How exactly is the final gene selected?

Cheers,
Xabi

-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From jan.nagel at fabi.up.ac.za  Thu Oct 12 01:37:07 2017
From: jan.nagel at fabi.up.ac.za (Jan FABI)
Date: Thu, 12 Oct 2017 09:37:07 +0200
Subject: [maker-devel] Maker problem
Message-ID: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution
to it online.

I am running maker on a new genome, using BRAKER trained models for
Augustus and GeneMark. This was successful and performed as expected,
except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with
intron models. I have made sure that the input fasta does not contain
characters other than ATCGN or contains "windows"/non-UNIX carriage
returns.

I include the relevant portion of the log below. Could you help me
determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus
--species=Np_2017_braker --UTR=off
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 >
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

-- 
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : jan.nagel at fabi.up.ac.za

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

-- 
This message and attachments are subject to a disclaimer.
Please refer to 
http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf for full 
details.
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From scott at scottcain.net  Thu Oct 12 17:40:33 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:40:33 -0400
Subject: [maker-devel] Call for presentations at GMOD workshop at PAG
Message-ID: <CA+JTaoyZEYHX0RyKMW7+3d+wic+PyshCUUfhzCzeroXnmyVECw@mail.gmail.com>

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From carsonhh at gmail.com  Fri Oct 13 09:37:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:37:25 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
Message-ID: <C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>

So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.

Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi <http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi>

?Carson



> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi Carson,
> 
> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
> 
> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
> 
> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
> 
> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
> 
> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
> 
> Thanks,
> Daren
> 
> 
>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>> 
>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>> 
>> ?Carson
>> 
>> 
>> 
>> 
>> 
>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Dear Carson,
>>> 
>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>> 
>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>> 
>>> Thank you,
>>> Daren Card
>>> 
>>> 
>>> ################################################
>>> doing repeat masking
>>> re reading repeat masker report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>> doing blastx repeats
>>> re reading blast report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>> deleted:2 hits
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=NA, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> examining contents of the fasta file and run log
>>> ################################################
>>> 
>>> 
>>> 
>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> 
>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>> 
>>>> ?Carson
>>>> 
>>>> 
>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>> 
>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>> 
>>>>> Any help would be greatly appreciated.
>>>>> Daren Card
>>>>> 
>>>>> University of Texas Arlington
>>>>> 
>>>>> ###################################################
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>> #-------------------------------#
>>>>> deleted:0 hits
>>>>> collecting blastx repeatmasking
>>>>> processing all repeats
>>>>> in cluster::shadow_cluster...
>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>> --> rank=3, hostname=moonunit0
>>>>> ERROR: Failed while processing all repeats
>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>> #-------------------------------#
>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> deleted:0 hits
>>>>> deleted:0 hits
>>>>> ###################################################
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>> 
>> 
> 

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From carsonhh at gmail.com  Fri Oct 13 09:42:41 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:42:41 -0600
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
In-Reply-To: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
References: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
Message-ID: <947BFB2F-A893-417B-A043-07CE71F6F97E@gmail.com>

Hi Bob,

pred_gff is a way to get models MAKER cannot run into the analysis. Input to pred_gff will not get hints since MAKER is not running the program. Setting augustus_species allows MAKER to run Augustus with and without hints and then those models compete against each other. You cannot just run with hints as the raw model is also used as a filter to help reduce false positive gene models that result from bad hints. If the gff3 you are providing is the same as the MAKER run of Augustus, I would recommend not providing it. If it is different in some way, then you can leave it in.  If you run under MPI (it?s ok to run MPI on a single machine), then MAKER will parallelize the Augustus run by running multiple configs and contig chunks at the same time.

Thanks,
Carson





> On Oct 11, 2017, at 1:42 PM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hello,
> 
> I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 
> 
> My gene prediction section of the maker_opts.ctl file looks like this:
> ...
> augustus_species=all_combined #Augustus gene prediction species model
> ...
> pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
> model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
> est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
> protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
> ?
> 
> It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.
> 
> Thanks for your help!
> 
> Bob
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Fri Oct 13 09:50:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:50:26 -0600
Subject: [maker-devel] Maker problem
In-Reply-To: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
References: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
Message-ID: <FE4BF464-D049-415D-9AC2-D013B0FB727B@gmail.com>

If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example ?> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke (mario.stanke at uni-greifswald.de <mailto:mario.stanke at uni-greifswald.de>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

?Carson


> On Oct 12, 2017, at 1:37 AM, Jan FABI <jan.nagel at fabi.up.ac.za> wrote:
> 
> Dear Maker team
> 
> I am experiencing a problem while running maker and cannot find a solution to it online. 
> 
> I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. 
> 
> This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. 
> 
> I include the relevant portion of the log below. Could you help me determine the cause of this error.
> 
> 
> 
> setting up GFF3 output and fasta chunks
> preparing ab-inits
> running  augustus.
> #--------- command -------------#
> Widget::augustus:
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx-VirtualBox
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 
> 
> -- 
> Regards 
> Jan Nagel
> ----------------------------------------------------------------------
> PhD Genetics student
> Department of Genetics
> Forestry and Agricultural Biotechnology Institute (FABI) 
> FABI 1, Room 1-55
> University of Pretoria
> 74 Lunnon Rd. Hillcrest
> 0002
> Gauteng Province
> South Africa
> 
> Email : jan.nagel at fabi.up.ac.za <mailto:jan.nagel at fabi.up.ac.za>
> 
> Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961 <http://www.fabinet.up.ac.za/index.php/people-profile?profile=961>
> This message and attachments are subject to a disclaimer.
> Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf <http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf> for full details.
> _______________________________________________
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From carsonhh at gmail.com  Fri Oct 13 09:56:43 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:56:43 -0600
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
Message-ID: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>

Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it?s evidence, so it?s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it?s a fungi, I often find GeneMark can have that affect).

?Carson


> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi there,
> 
> I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.
> 
> <split-gene.png>
> 
> Although the opposite also happens.
> 
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one from Genemark.
> 
> How much weight does carry the RNAseq and protein data on this decision (if any)?
> How exactly is the final gene selected?
> 
> Cheers,
> Xabi
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 10:56:30 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 10:56:30 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
	<CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
Message-ID: <2D6E11BC-6853-458D-AEB1-12EF74D041A3@gmail.com>

The master_datastore_index.log file has a list of failed and finished contigs.  You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.

Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it?s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).

You will need to see if you can identify which contig file is truncated and rerun it.

?Carson






> On Oct 9, 2017, at 10:42 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> Thanks for the reply
> 
> I generated the off with this command gff3_merge ?d dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
> I had to rerun browse with the following command
> 
> maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb
> 
> Although its showing
> 
> WARNING: No matching features found for mRNA I don't know what it means
> 
> I don't understand what it means
> 
> 
> Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host
> 
> 
> The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?
> 
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.
> 
> Thanks,
> Carson
> 
> 
> 
> 
>> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Please,
>> I ran the command line
>> 
>> maker2jbrowse muc1_genome_snap2.all.gff
>> 
>> The command created some folders. However, at the end it read
>> No reference sequences defined in configuration, nothing to do.
>> 
>> Please what does it mean? How can I view it in jbrowse. 
>> 
>> Thanks
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> 

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From xvazquezc at gmail.com  Fri Oct 13 14:26:40 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Sat, 14 Oct 2017 07:26:40 +1100
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
	<821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
Message-ID: <CAL0hg4Hxgrfhbah+7euuQV0YSCjYkV+WqxVu4_QYyf38pYts3Q@mail.gmail.com>

Actually, it's a fungal genome. Although not very typical, almost half of
it are repeats. Worth mention that Genemark generates a lot of predictions
that overlap LTRs and other complex repeats, something that neither SNAP or
Augustus do. Have you seen this before?

On 14 Oct. 2017 02:56, "Carson Holt" <carsonhh at gmail.com> wrote:

> Both transcript and protein evidence will go into the AED calculation for
> overlap support. So in both cases the chosen model had better overlap
> (protein evidence will not count toward the eAED overlap calculation if it
> is out of frame with the model it is supposed to be supporting). The larger
> merged model generates a clutering affect on it?s evidence, so it?s
> evidence set for AED calculation is slightly different than the SNAP and
> Augustus model would generate. In both cases, I think GeneMark is hurting
> more than it is helping. You may want to just drop it from the analysis
> (unless it?s a fungi, I often find GeneMark can have that affect).
>
> ?Carson
>
>
> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Hi there,
>
> I was visualising the annotations and I realised that in some cases, what
> it seems to be a gene is splitted according to one of the gene models,
> despite that the other 2, est2genome and prot2genome suggest that it isn't
> the case.
>
> <split-gene.png>
>
> Although the opposite also happens.
>
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one
> from Genemark.
>
> How much weight does carry the RNAseq and protein data on this decision
> (if any)?
> How exactly is the final gene selected?
>
> Cheers,
> Xabi
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From z2.stewart at qut.edu.au  Sat Oct 14 23:02:08 2017
From: z2.stewart at qut.edu.au (ZACHARY STEWART)
Date: Sun, 15 Oct 2017 05:02:08 +0000
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
Message-ID: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>

Hello MAKER team,


I am hoping I could have a bit of your time if that isn't a problem. I am currently performing the advanced repeat library construction as described on the MAKER wiki, and everything appears to work as expected until I reach "2.1.5 Building examplars". At this point I encounter a problem previously documented in the Google group (title: advanced repeat masking library constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta" and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify what you meant by simplifying the sequence names. The genomic contig names are in a format such as ">001676F" and I modified the MITE library to have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]" which I have not tried changing since I suspect the name is important for later reassociation. If you could point me in the right direction that would be very appreciated.


Regards,

Zac.
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From eennadi at gmail.com  Sun Oct 15 15:32:10 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sun, 15 Oct 2017 22:32:10 +0100
Subject: [maker-devel] Backlash running through my sequence
Message-ID: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>

Hi all,
I am trying to running annotation on some of my sequences but noticed that
i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From xvazquezc at gmail.com  Mon Oct 16 01:26:56 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Mon, 16 Oct 2017 18:26:56 +1100
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
In-Reply-To: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
References: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
Message-ID: <CAL0hg4Gz=vfaDkQEb3J-JPDw0TiRsmH2Fae2YsKX5AtZe0YYjA@mail.gmail.com>

Hi Zac,
The contig names you indicate shouldn't give any problems. And if you
changed the names of MITE.lib right after creation and before using it
downstream, it shouldn't be an issue.

Have you confirmed if the prior blastx output has any results?

Also, be sure you use the same version of makeblastdb and blastx/blastn. I
remember reading before running the protocol for first time that in some
cases, switching versions could give problems.
And be careful if you copy/paste from the wiki page, there are a few typos
and dashes instead of minus characters in the command line option flags,
all of which will result in errors

Xabi

On 15 October 2017 at 16:02, ZACHARY STEWART <z2.stewart at qut.edu.au> wrote:

> Hello MAKER team,
>
>
> I am hoping I could have a bit of your time if that isn't a problem. I am
> currently performing the advanced repeat library construction as described
> on the MAKER wiki, and everything appears to work as expected until I reach
> "2.1.5 Building examplars". At this point I encounter a problem previously
> documented in the Google group (title: advanced repeat masking library
> constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta"
> and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify
> what you meant by simplifying the sequence names. The genomic contig names
> are in a format such as ">001676F" and I modified the MITE library to
> have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta
> has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]"
> which I have not tried changing since I suspect the name is important for
> later reassociation. If you could point me in the right direction that
> would be very appreciated.
>
>
> Regards,
>
> Zac.
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From yuejiaxing at gmail.com  Mon Oct 16 02:54:42 2017
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Mon, 16 Oct 2017 10:54:42 +0200
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>

Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning
message about uninitialized value (see the warning message below) although
still finished the installation.

[jxyue at paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/bu
ild/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm
line 3082.
Use of uninitialized value $line in substitution (s///) at
/home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/
cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors
about cannot find my specified snaphmm model for the annotation, despite
that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the
"maker_opts.ctl" file and this configuration information has been
successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap
/home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm
/tmp/maker_m8TVEQ/chrI.abinit_masked.0 >
/tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap
S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta >
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening
file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot
about the path to  my specified hmm file and instead looks for this file in
its default installation location)

It is worth noting that the parallel installation and run with
maker-3.00.0-beta finish smoothly without any problem. So I suspect both
the installation warning and the executing error are caused by the changes
during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check
about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker
(e.g. 3.00.0-beta in this particular case) when the user finish the
registration in the maker download page? This will help users to roll back
to older version when needed.  Also this helps for the version control when
other developers develop annotation pipelines that use maker as a
dependency package. Thanks for the consideration!


Best,
Jia-Xing

-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Facult? de M?decine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/
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From carsonhh at gmail.com  Mon Oct 16 10:20:32 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 16 Oct 2017 10:20:32 -0600
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
Message-ID: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



> On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi all,
> I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
>  I attached the sequence
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications><sample_1.fasta>

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From cjfields at illinois.edu  Tue Oct 17 13:11:39 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 17 Oct 2017 19:11:39 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
Message-ID: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson Holt <carsonhh at gmail.com>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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From carsonhh at gmail.com  Tue Oct 17 13:33:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Oct 2017 13:33:26 -0600
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
	<CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
Message-ID: <30F2FDFE-3B4E-4951-89D8-63C2FC772B63@gmail.com>

Thanks. The map_fasta_ids script was empty in the bin directory for some reason, so the installer through an error because it could not find the #!/usr/bin/perl line. I have put it back in the bin directory where it was supposed to be and the issue goes away for the install.

For the second issue, I think I found it and have updated a new tar ball to the website.

Also here is a link to download the old 3.00-beta, although I would not recommend making it part of a pipeline because version 3 is still beta and still has bugs (you should use 2.31.9 instead for piplines).  ?> http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz <http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz>

?Carson


 
> On Oct 16, 2017, at 2:54 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
> 
> Dear maker developers,
> 
> I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation. 
> 
> [jxyue at paralog src]$ ./Build install
> Building MAKER
> Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
> Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
> Installing MAKER...
> Building MAKER
> ...
> 
> Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
> #-------------------------------#
> 
> # (my comment: up to now everything looks fine)
> ....
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
> /maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
> #-------------------------------#
> ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
> ZOE library version 2017-03-01
> ERROR: Snap failed
> --> rank=NA, hostname=paralog.itc.unipi.it <http://paralog.itc.unipi.it/>
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chrI
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chrI
> 
> examining contents of the fasta file and run log
> 
> # (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)
> 
> It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!
> 
> Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!
> 
> 
> Best,
> Jia-Xing
> 
> -- 
> Jia-Xing Yue 
> 
> Population Genomics and Complex Traits Group
> Tour Pasteur 8eme etage
> Facult? de M?decine
> Institute for Research on Cancer and Aging, Nice (IRCAN)
> CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
> 28 Avenue de Valombrose
> 06107 NICE Cedex 2
> France
> 
> Personal website: http://www.iamphioxus.org/ <http://www.iamphioxus.org/>
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From patrick.tranvan at unil.ch  Wed Oct 18 05:47:35 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Wed, 18 Oct 2017 11:47:35 +0000
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>,
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <1508327278733.19140@unil.ch>

Hi Carson,


1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?


2) I am trying to annotate a 1GB specie but it's superslow.

I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ?

Cheers,

Patrick Tran Van


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From carsonhh at gmail.com  Wed Oct 18 09:09:10 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 18 Oct 2017 09:09:10 -0600
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <1508327278733.19140@unil.ch>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
	<1508327278733.19140@unil.ch>
Message-ID: <486FE3D5-0902-4B05-A3E1-96642C68E422@gmail.com>

MAKER can coordinate parallelization under MPI in a way it can?t even with multiple simultaneous runs. Because processes can comunicate among themselves under MPI, MAKER can break larger contigs into chunks or even pull off individual steps and pass them onto another processor, then receive the results back from that processor. So multiple BLAST, RepeatMasker, Exonerate, and prediction processes can all run at the same time for the same contig. Then they all pass their result back to the parent process so it can produce output for that contig. MPI was chosen as the parallelization framework rather than threads because it works both within a single machine as well as across multiple machines, so you can scale up to hundreds of processes if needed.

?Carson


> On Oct 18, 2017, at 5:47 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi Carson, 
> 
> 1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?
> 
> 2) I am trying to annotate a 1GB specie but it's superslow.
> I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ? 
> 
> Cheers,
> 
> Patrick Tran Van
> 
> 

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From jhumann at wsu.edu  Wed Oct 18 14:38:41 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Wed, 18 Oct 2017 20:38:41 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
Message-ID: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>

Hello,

I was wondering if there was any way to enable the '-fix_nucleotides' option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu


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From robert.zimmermann at univie.ac.at  Thu Oct 19 09:25:08 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:25:08 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
Message-ID: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>

Hi Maker Developers,

I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.

Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?

Thanks for your help!

Best,
Bob

?

Department of Molecular Evolution and Development
Universit?t Wien
Althanstra?e 14 (UZA I), Zimmer 2.019 
1090 Vienna
Austria

+43 1 427757002




From robert.zimmermann at univie.ac.at  Thu Oct 19 09:28:17 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:28:17 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
Message-ID: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>

Correction to the above numbers, the median lengths are 1414 and 1256.

> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hi Maker Developers,
> 
> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
> 
> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
> 
> Thanks for your help!
> 
> Best,
> Bob
> 
> ?
> 
> Department of Molecular Evolution and Development
> Universit?t Wien
> Althanstra?e 14 (UZA I), Zimmer 2.019 
> 1090 Vienna
> Austria
> 
> +43 1 427757002
> 




From carsonhh at gmail.com  Thu Oct 19 09:44:07 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 09:44:07 -0600
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
	<CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
Message-ID: <62F04A76-F3F1-4044-B4AD-129B15A9EEB2@gmail.com>

You should look at both in a browser to get a better idea of what?s going on. What MAKER does is take the evidence given, clusters it (strand specific clustering) then uses the transcript evidence as intron hints to the predictors and protein alignments as exon hints (will also use polished protein hints to generate intron hints in the absence of transcript intron hints). Finally it uses overlapping transcript evidence to generate UTR. So look at it in a browser. See if the apparent overlap clusters are different in extent, also look for mRNA-seq evidence being merged. If the cluster is falsely merging between two loci because the mRNA-seq is merged, one of two things will happen you will get multiple models since the predictor can?t make a single model work within the cluster using the hints, or you will get a model with a really long UTR that is blocking other models from existing in the region. Also as depending on the mRNA-seq evidence coming in, you may be generating false models because of noise in the data. Essentially everything is transcribed at a basal level, so as you get more and more mRNA-seq, you generate more and more spurious alignments. So more evidence might gernate fewer long alignments for true loci or by falsely merging genes while simultaneously adding a number of very short spurious results.

?Carson



> On Oct 19, 2017, at 9:28 AM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Correction to the above numbers, the median lengths are 1414 and 1256.
> 
>> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
>> 
>> Hi Maker Developers,
>> 
>> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
>> 
>> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
>> 
>> Thanks for your help!
>> 
>> Best,
>> Bob
>> 
>> ?
>> 
>> Department of Molecular Evolution and Development
>> Universit?t Wien
>> Althanstra?e 14 (UZA I), Zimmer 2.019 
>> 1090 Vienna
>> Austria
>> 
>> +43 1 427757002
>> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Thu Oct 19 11:32:44 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 11:32:44 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Oct 19 12:46:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 12:46:17 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
	<SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <052F801C-3B37-4B0F-B40A-A905F5F2B1CE@gmail.com>

Yes. That is the current version.

?Carson

> On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?
>  
> Jodi
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Thursday, October 19, 2017 10:33 AM
> To: Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] fix nucleotides option on MWAS
>  
> Hi Jodi,
>  
> I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).
>  
> Somewhere inside the script there will be a line like this ?>
>  $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
>  
> You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.
>  
> Thanks,
> Carson
>  
>  
> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>> wrote:
>  
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>
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From jhumann at wsu.edu  Thu Oct 19 12:45:43 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Thu, 19 Oct 2017 18:45:43 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
Message-ID: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?

Jodi

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <jhumann at wsu.edu>
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] fix nucleotides option on MWAS

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu<mailto:jhumann at wsu.edu>> wrote:

Hello,

I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu<mailto:jhumann at wsu.edu>


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>

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From eennadi at gmail.com  Mon Oct 23 07:30:07 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 23 Oct 2017 14:30:07 +0100
Subject: [maker-devel] Contamination report from NCBI
Message-ID: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>

Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this
contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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SUBID     	BioProject	BioSample	Organism
--------------------------------------------------------
SUB3124577	PRJNA414658	SAMN07821433	Mucuna pruriens

[] We ran your sequences through our Contamination Screen. The screen found 
contigs that need to be trimmed and/or excluded. Please adjust the 
sequences appropriately and then resubmit your sequences. After you remove the 
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

Note that hits in eukaryotic genomes to mitochondrial sequences can be ignored 
when specific criteria are met. Those criteria are explained below.

Note that mismatches between the name of the adaptor/primer identified in the screen 
and the sequencing technology used to generate the sequencing data should not be used 
to discount the validity of the screen results as the adaptors/primers of many 
different sequencing platforms share sequence similarity.



[] Some of the sequences hit primers or adaptors used in Illumina or 
454 or other sequencing strategies or platforms.  Primers at the 
end of a sequence should be removed. However, if primers are 
present within sequences then you should strongly consider 
splitting the sequences at the primers because the primer sequence 
could have been the region of overlap, causing a misassembly.


Screened 26,016 sequences, 396,641,426 bp.
Note: 5,610 sequences with runs of Ns 10 bp or longer (or those longer that 20 MB) were split before screening.
428 sequences with locations to mask/trim
(31 split spans to exclude, 397 split spans with locations to mask/trim)

Trim:
Sequence name, length, span(s), apparent source
contig_10109	13138	13078..13138	adaptor:NGB00847.1
contig_10200	20270	1..76	adaptor:NGB00847.1
contig_10202	22517	1..44	adaptor:NGB00360.1
contig_10218	55661	55592..55661	adaptor:NGB00847.1
contig_10283	11575	1..79	adaptor:NGB00847.1
contig_1038	91134	91073..91134	adaptor:NGB00360.1
contig_104	10061	10005..10061	adaptor:NGB00360.1
contig_10405	24076	1..43	adaptor:NGB00847.1
contig_10425	16694	16639..16694	adaptor:NGB00360.1
contig_10447	37445	37233..37445	adaptor:NGB00360.1
contig_10466	19368	1..52	adaptor:NGB00847.1
contig_10576	12053	12003..12053	adaptor:NGB00360.1
contig_1059	34516	34457..34516	adaptor:NGB00847.1
contig_106	49997	1..45	adaptor:NGB00360.1
contig_10695	27664	1..38	adaptor:NGB01029.1
contig_10753	12481	12413..12481	adaptor:NGB00847.1
contig_10822	33522	33441..33522	adaptor:NGB00847.1
contig_1083	10637	1..23	adaptor:NGB01096.1
contig_10851	36752	36682..36752	adaptor:NGB00360.1
contig_10878	27925	27848..27925	adaptor:NGB00360.1
contig_10965	23597	1..57	adaptor:NGB00360.1
contig_10968	7413	1..40	adaptor:NGB00847.1
contig_1099	35847	1..70	adaptor:NGB00360.1
contig_11034	10224	10166..10224	adaptor:NGB00360.1
contig_11058	32994	1..23	adaptor:NGB01088.1
contig_11138	17426	1..73	adaptor:NGB00847.1
contig_11166	6306	6266..6306	adaptor:NGB00360.1
contig_11182	26558	1..30	adaptor:NGB01096.1
contig_11216	15160	1..59	adaptor:NGB00847.1
contig_11269	14732	14655..14732	adaptor:NGB00847.1
contig_11306	28246	28199..28246	adaptor:NGB00360.1
contig_1136	28186	1..73	adaptor:NGB00847.1
contig_1141	58119	58028..58119	adaptor:NGB00847.1
contig_11416	8561	8539..8561	adaptor:NGB01088.1
contig_11504	8890	8840..8890	adaptor:NGB00360.1
contig_1158	17422	17398..17422	adaptor:NGB01088.1
contig_11647	7021	1..69	adaptor:NGB00847.1
contig_11684	17442	17418..17442	adaptor:NGB01096.1
contig_11752	38337	38314..38337	adaptor:NGB01088.1
contig_11767	6366	6324..6366	adaptor:NGB00847.1
contig_11791	22415	1..43	adaptor:NGB00847.1
contig_11792	58260	1..29	adaptor:NGB01096.1
contig_1187	39501	39462..39501	adaptor:NGB01029.1
contig_12059	10094	1..72	adaptor:NGB00360.1
contig_12130	13210	13164..13210	adaptor:NGB00360.1
contig_12164	17561	17539..17561	adaptor:NGB01096.1
contig_12169	14178	139..196	adaptor:NGB00360.1
contig_12183	15822	61..112	adaptor:NGB00360.1
contig_12266	11704	11640..11704	adaptor:NGB00360.1
contig_12300	9550	9360..9550	adaptor:NGB01088.1
contig_12324	49997	49891..49997	adaptor:NGB00847.1
contig_12423	45971	45860..45918	adaptor:NGB00360.1
contig_12441	15141	1..42	adaptor:NGB00847.1
contig_12514	14655	1..69	adaptor:NGB00847.1
contig_12515	5355	5326..5355	adaptor:NGB01088.1
contig_12535	22496	22458..22496	adaptor:NGB01029.1
contig_12544	19615	19559..19615	adaptor:NGB00360.1
contig_12558	20026	20007..20026	adaptor:NGB01088.1
contig_12613	6880	6793..6880	adaptor:NGB00847.1
contig_12701	18439	18330..18382	adaptor:NGB00360.1
contig_12713	13341	13274..13341	adaptor:NGB00360.1
contig_12723	17913	1..38	adaptor:NGB01088.1
contig_12730	55277	55249..55277	adaptor:NGB01096.1
contig_12739	6792	1..48	adaptor:NGB00360.1
contig_12787	30950	1..19	adaptor:NGB01096.1
contig_1279	18699	18670..18699	adaptor:NGB01088.1
contig_12815	5168	5091..5168	adaptor:NGB00847.1
contig_12846	20753	1..70	adaptor:NGB00360.1
contig_1288	34784	1..31	adaptor:NGB01096.1
contig_12888	12204	1..23	adaptor:NGB01096.1
contig_12919	10315	1..71	adaptor:NGB00360.1
contig_13031	8972	8938..8972	adaptor:NGB01093.1
contig_13088	6275	1..22	adaptor:NGB01088.1
contig_13140	36197	1..48	adaptor:NGB00360.1
contig_13233	16414	16355..16414	adaptor:NGB00847.1
contig_1330	33261	1..44	adaptor:NGB00847.1
contig_13319	19747	1..20	adaptor:NGB01096.1
contig_13367	36004	35868..35931	adaptor:NGB00847.1
contig_13395	5338	1..79	adaptor:NGB00360.1
contig_1341	30756	30734..30756	adaptor:NGB01088.1
contig_13481	9637	9600..9637	adaptor:NGB00360.1
contig_13506	5704	5662..5704	adaptor:NGB00360.1
contig_13548	5814	79..121	adaptor:NGB00360.1
contig_13567	21576	1..47	adaptor:NGB00847.1
contig_13669	8336	1..24	adaptor:NGB01088.1
contig_13718	23500	1..25	adaptor:NGB01096.1
contig_13783	18720	1..41	adaptor:NGB00847.1
contig_13830	32395	32367..32395	adaptor:NGB01096.1
contig_13845	15572	15493..15572	adaptor:NGB00360.1
contig_13854	10932	1..48	adaptor:NGB00360.1
contig_13943	37701	37674..37701	adaptor:NGB01096.1
contig_13957	7159	1..30	adaptor:NGB01096.1
contig_14014	29735	29672..29735	adaptor:NGB00360.1
contig_14027	21418	21340..21418	adaptor:NGB00360.1
contig_14032	47642	1..53	adaptor:NGB00847.1
contig_14047	26936	1..28	adaptor:NGB01088.1
contig_14048	45832	1..22	adaptor:NGB01088.1
contig_14061	11471	1..179	adaptor:NGB01096.1
contig_14113	17661	1..67	adaptor:NGB00360.1
contig_14173	17601	1..41	adaptor:NGB00847.1
contig_1418	31840	1..248	adaptor:NGB00847.1
contig_14194	7456	7294..7456	adaptor:NGB01096.1
contig_14210	8814	1971..2025	adaptor:NGB00360.1
contig_14223	12513	12489..12513	adaptor:NGB01096.1
contig_14317	21472	21410..21472	adaptor:NGB00360.1
contig_14424	6040	5973..6040	adaptor:NGB00360.1
contig_14425	6404	6379..6404	adaptor:NGB01096.1
contig_14426	31457	31398..31457	adaptor:NGB00847.1
contig_14458	6814	6623..6814	adaptor:NGB01088.1
contig_14524	9488	9431..9488	adaptor:NGB00847.1
contig_14584	20433	1..96	adaptor:NGB00847.1
contig_1459	32979	1..32	adaptor:NGB01096.1
contig_14601	19077	1..28	adaptor:NGB01096.1
contig_14641	21747	1..45	adaptor:NGB00847.1
contig_14664	48155	48118..48155	adaptor:NGB00360.1
contig_14711	11854	11827..11854	adaptor:NGB01096.1
contig_14736	21360	1..37	adaptor:NGB01029.1
contig_14749	12830	1..33	adaptor:NGB01093.1
contig_14966	9962	9891..9962	adaptor:NGB00360.1
contig_14999	5248	1..41	adaptor:NGB00360.1
contig_15010	17976	1..43	adaptor:NGB00360.1
contig_15011	26484	26462..26484	adaptor:NGB01096.1
contig_15017	9331	9291..9331	adaptor:NGB00360.1
contig_1503	63533	1..33	adaptor:NGB01096.1
contig_15032	32240	32157..32240	adaptor:NGB00847.1
contig_15060	15050	15010..15050	adaptor:NGB00847.1
contig_15065	13062	12996..13062	adaptor:NGB00360.1
contig_15070	29943	1..29	adaptor:NGB01096.1
contig_15132	20431	1..71	adaptor:NGB00847.1
contig_15169	7086	7051..7086	adaptor:NGB00846.1
contig_15174	19921	1..23	adaptor:NGB01096.1
contig_15194	16100	16039..16100	adaptor:NGB00847.1
contig_15212	9272	1..50	adaptor:NGB00847.1
contig_15215	15591	1..58	adaptor:NGB00360.1
contig_15271	37699	37647..37699	adaptor:NGB00847.1
contig_15276	11087	11031..11087	adaptor:NGB00847.1
contig_15309	10118	1..42	adaptor:NGB00847.1
contig_15320	7963	7901..7963	adaptor:NGB00847.1
contig_15334	5683	1..36	adaptor:NGB00846.1
contig_15364	17306	76..139	adaptor:NGB00847.1
contig_15374	28301	28263..28301	adaptor:NGB00360.1
contig_15377	10470	10428..10470	adaptor:NGB00360.1
contig_15398	24069	23999..24069	adaptor:NGB00847.1
contig_15500	9289	9271..9289	adaptor:NGB01096.1
contig_15507	25565	1..22	adaptor:NGB01088.1
contig_15523	5782	5762..5782	adaptor:NGB01088.1
contig_15529	10225	10143..10225	adaptor:NGB00360.1
contig_15569	9645	9612..9645	adaptor:NGB01090.1
contig_15596	7163	1..42	adaptor:NGB00360.1
contig_15605	18521	1..31	adaptor:NGB01096.1
contig_15672	8446	1..213	adaptor:NGB01088.1
contig_15686	22141	58..90	adaptor:NGB00847.1
contig_15708	18098	17996..18098	adaptor:NGB00847.1
contig_15736	18284	18252..18284	adaptor:NGB01096.1
contig_15777	17192	1..45	adaptor:NGB00360.1
contig_15812	8602	1..77	adaptor:NGB00360.1
contig_15959	10936	10913..10936	adaptor:NGB01096.1
contig_15972	11324	1..71	adaptor:NGB00360.1
contig_15974	24312	24243..24312	adaptor:NGB00847.1
contig_16057	8838	8775..8838	adaptor:NGB00847.1
contig_16088	7608	1..71	adaptor:NGB00360.1
contig_16142	10392	1..53	adaptor:NGB00847.1
contig_1617	14870	255..310	adaptor:NGB00360.1
contig_16183	9226	9205..9226	adaptor:NGB01088.1
contig_16188	62666	62586..62666	adaptor:NGB00847.1
contig_16370	7868	1..42	adaptor:NGB00847.1
contig_16416	19512	1..21	adaptor:NGB01088.1
contig_1645	25016	24951..25016	adaptor:NGB00360.1
contig_16510	31845	31776..31845	adaptor:NGB00847.1
contig_16529	17342	1..45	adaptor:NGB00360.1
contig_16558	9338	9097..9338	adaptor:NGB00360.1
contig_16573	6590	6521..6590	adaptor:NGB00847.1
contig_16608	7397	7324..7397	adaptor:NGB00847.1
contig_16631	11055	1..50	adaptor:NGB00360.1
contig_16641	5482	1..190	adaptor:NGB01088.1
contig_1667	35244	35200..35244	adaptor:NGB01029.1
contig_16682	14500	1..71	adaptor:NGB00847.1
contig_16699	6216	6148..6216	adaptor:NGB00360.1
contig_16734	12674	12625..12674	adaptor:NGB00360.1
contig_16790	6341	1..51	adaptor:NGB00360.1
contig_16807	7512	1..36	adaptor:NGB01096.1
contig_16817	20743	1..155	adaptor:NGB01088.1
contig_16839	6969	1..69	adaptor:multiple
contig_16870	10948	1..49	adaptor:NGB00847.1
contig_16880	5622	5549..5622	adaptor:NGB00360.1
contig_16889	9182	1..40	adaptor:NGB00360.1
contig_16911	6691	1..28	adaptor:NGB01088.1
contig_16921	9432	9358..9432	adaptor:NGB00360.1
contig_16951	14285	14262..14285	adaptor:NGB01088.1
contig_17021	12242	1..75	adaptor:NGB00360.1
contig_17092	22712	1..64	adaptor:NGB00360.1
contig_17147	7706	7685..7706	adaptor:NGB01096.1
contig_17195	15668	15643..15668	adaptor:NGB01096.1
contig_17214	7881	7819..7881	adaptor:NGB00847.1
contig_17299	7861	7830..7861	adaptor:NGB01088.1
contig_17344	8915	8765..8823	adaptor:NGB00360.1
contig_17361	8425	1..26	adaptor:NGB01096.1
contig_17422	11017	10964..11017	adaptor:NGB00360.1
contig_17471	5988	5964..5988	adaptor:NGB01096.1
contig_17505	10208	1..74	adaptor:NGB00360.1
contig_17506	6091	1..61	adaptor:NGB00360.1
contig_17520	6084	6028..6084	adaptor:NGB00360.1
contig_17538	5796	5766..5796	adaptor:NGB01096.1
contig_17558	7066	6837..7066	adaptor:NGB01080.1
contig_17561	15165	1..206	adaptor:NGB01083.1
contig_17594	6976	1..26	adaptor:NGB01088.1
contig_17655	14371	14177..14371	adaptor:NGB01088.1
contig_17671	17801	1..50	adaptor:NGB00847.1
contig_17680	5752	5693..5752	adaptor:NGB00847.1
contig_17738	6456	1..44	adaptor:NGB00360.1
contig_17741	10917	10889..10917	adaptor:NGB01096.1
contig_17775	5928	1..79	adaptor:NGB00847.1
contig_17804	11597	11562..11597	adaptor:NGB00846.1
contig_17872	11319	11278..11319	adaptor:NGB00847.1
contig_17876	5647	5613..5647	adaptor:NGB01083.1
contig_17925	9923	1..22	adaptor:NGB01088.1
contig_17938	5246	1..23	adaptor:NGB01088.1
contig_18016	8044	1..29	adaptor:NGB01096.1
contig_18017	6668	6647..6668	adaptor:NGB01096.1
contig_18044	11330	11299..11330	adaptor:NGB01096.1
contig_18049	10560	1..88	adaptor:NGB00847.1
contig_18173	12243	1..159	adaptor:NGB01096.1
contig_18175	8788	8765..8788	adaptor:NGB01096.1
contig_18177	11418	11340..11418	adaptor:multiple
contig_18182	11901	11832..11901	adaptor:NGB00847.1
contig_18201	6059	6038..6059	adaptor:NGB01096.1
contig_18222	11216	11136..11216	adaptor:NGB00847.1
contig_18228	8386	8361..8386	adaptor:NGB01088.1
contig_18321	5922	5897..5922	adaptor:NGB01096.1
contig_18370	5400	5085..5116	adaptor:NGB00747.1
contig_18453	5849	1..38	adaptor:NGB00360.1
contig_1846	23210	1..64	adaptor:NGB00360.1
contig_18479	5209	1..44	adaptor:NGB00360.1
contig_18486	5749	5726..5749	adaptor:NGB01088.1
contig_18488	5217	1..19	adaptor:NGB01088.1
contig_1969	65776	1..60	adaptor:NGB00360.1
contig_197	9215	1..83	adaptor:NGB00847.1
contig_1977	13765	1..35	adaptor:NGB01093.1
contig_1999	53427	53398..53427	adaptor:NGB01096.1
contig_2125	11803	11769..11803	adaptor:NGB01083.1
contig_2151	9544	1..37	adaptor:NGB01029.1
contig_2179	38972	1..67	adaptor:NGB00360.1
contig_2186	31110	30935..31110	adaptor:NGB01096.1
contig_2203	60314	60124..60187	adaptor:NGB00847.1
contig_2278	33271	1..36	adaptor:NGB01090.1
contig_2305	17957	1..58	adaptor:NGB00360.1
contig_2361	48816	48764..48816	adaptor:NGB00847.1
contig_242	49604	49535..49604	adaptor:NGB00360.1
contig_2429	76318	76242..76318	adaptor:NGB00847.1
contig_2430	70439	70373..70439	adaptor:NGB00847.1
contig_2459	63920	1..96	adaptor:NGB00847.1
contig_2485	31300	31260..31300	adaptor:NGB00360.1
contig_2508	25152	25095..25152	adaptor:NGB00847.1
contig_2650	36583	1..58	adaptor:NGB00847.1
contig_2668	22089	22052..22089	adaptor:NGB01029.1
contig_2735	13614	1..19	adaptor:NGB01088.1
contig_2781	50403	1..70	adaptor:NGB00847.1
contig_2800	30768	22802..22846	adaptor:NGB00360.1
contig_2824	44109	1..38	adaptor:NGB00847.1
contig_2888	19121	1..89	adaptor:NGB00360.1
contig_2900	36871	1..32	adaptor:NGB01088.1
contig_2949	25959	25916..25959	adaptor:NGB00360.1
contig_2970	20833	1..46	adaptor:NGB00360.1
contig_2986	16429	1..43	adaptor:NGB00360.1
contig_3069	38956	38904..38956	adaptor:NGB00847.1
contig_3106	9135	1..87	adaptor:NGB00847.1
contig_3124	70101	70072..70101	adaptor:NGB01088.1
contig_3129	30402	30379..30402	adaptor:NGB01088.1
contig_3147	10611	10586..10611	adaptor:NGB01096.1
contig_3190	117726	117687..117726	adaptor:NGB01029.1
contig_3243	44291	44273..44291	adaptor:NGB01096.1
contig_3276	57911	1..42	adaptor:NGB00360.1
contig_341	67008	1..22	adaptor:NGB01096.1
contig_3542	16855	1..60	adaptor:NGB00847.1
contig_3595	29288	1..79	adaptor:NGB00847.1
contig_3712	73078	1..78	adaptor:NGB00847.1
contig_3840	40472	40414..40472	adaptor:NGB00360.1
contig_3868	33875	33819..33875	adaptor:NGB00360.1
contig_3903	40080	40010..40080	adaptor:NGB00847.1
contig_3996	44010	43970..44010	adaptor:NGB00360.1
contig_4001	26085	1..73	adaptor:NGB00847.1
contig_4014	30676	30590..30676	adaptor:NGB00360.1
contig_4019	49543	1..76	adaptor:NGB00360.1
contig_4036	58848	58696..58848	adaptor:NGB00846.1
contig_4084	41308	41210..41308	adaptor:NGB00360.1
contig_4095	24801	1..70	adaptor:NGB00847.1
contig_4098	27393	1..189	adaptor:NGB01096.1
contig_410	57740	57678..57740	adaptor:NGB00360.1
contig_4172	20870	9717..9749	adaptor:NGB01096.1
contig_4318	55870	55805..55870	adaptor:NGB00360.1
contig_432	58593	58569..58593	adaptor:NGB01088.1
contig_4323	87370	87304..87370	adaptor:NGB00847.1
contig_4365	27401	27350..27401	adaptor:NGB00847.1
contig_4516	14480	1..98	adaptor:NGB00847.1
contig_452	34031	1..23	adaptor:NGB01096.1
contig_4530	63069	63006..63069	adaptor:NGB00360.1
contig_4651	67570	67518..67570	adaptor:NGB00847.1
contig_4679	20970	1..38	adaptor:NGB00360.1
contig_4686	7411	1..24	adaptor:NGB01096.1
contig_4743	37926	1..79	adaptor:NGB00360.1
contig_4765	11248	11167..11248	adaptor:NGB00360.1
contig_4801	91339	1..50	adaptor:NGB00360.1
contig_4812	37300	37121..37300	adaptor:NGB01093.1
contig_4820	80899	80862..80899	adaptor:NGB00360.1
contig_4904	9220	1..52	adaptor:NGB00847.1
contig_4916	29759	29718..29759	adaptor:NGB00847.1
contig_4924	19015	1..49	adaptor:NGB00847.1
contig_4939	23620	23574..23620	adaptor:NGB01029.1
contig_4956	40890	1..24	adaptor:NGB01088.1
contig_4994	71509	71447..71509	adaptor:NGB00847.1
contig_501	34157	34116..34157	adaptor:NGB00847.1
contig_5036	13162	1..77	adaptor:NGB00360.1
contig_5052	64212	1..170	adaptor:NGB01096.1
contig_5063	35265	35243..35265	adaptor:NGB01096.1
contig_5090	27510	27441..27510	adaptor:NGB00847.1
contig_5157	5988	5805..5988	adaptor:NGB00847.1
contig_5168	6086	6051..6086	adaptor:NGB00846.1
contig_5176	9131	1..41	adaptor:NGB00360.1
contig_5243	44178	1..88	adaptor:NGB00847.1
contig_5270	39229	39177..39229	adaptor:NGB00847.1
contig_5452	30446	1..36	adaptor:NGB00846.1
contig_5576	58918	1..34	adaptor:NGB01096.1
contig_5582	108611	1..87	adaptor:NGB00847.1
contig_5590	55235	55210..55235	adaptor:NGB01088.1
contig_5700	8246	1..82	adaptor:NGB00847.1
contig_5815	99837	1..63	adaptor:NGB00847.1
contig_5820	11616	1..202	adaptor:NGB00847.1
contig_5878	55755	1..26	adaptor:NGB01096.1
contig_59	12390	1..24	adaptor:NGB01096.1
contig_5959	11737	11532..11737	adaptor:NGB01096.1
contig_6065	11492	1..32	adaptor:NGB01088.1
contig_6067	19311	1..39	adaptor:NGB01029.1
contig_6092	14700	1..37	adaptor:NGB01029.1
contig_6194	32760	1..19	adaptor:NGB01088.1
contig_620	10761	1..206	adaptor:NGB01029.1
contig_6259	83001	1..50	adaptor:NGB00360.1
contig_6321	29279	29260..29279	adaptor:NGB01096.1
contig_6408	14690	1..74	adaptor:NGB00360.1
contig_6455	68530	68497..68530	adaptor:NGB01090.1
contig_6513	12061	11986..12061	adaptor:NGB00847.1
contig_6542	45321	1..41	adaptor:NGB00360.1
contig_6569	19579	19500..19579	adaptor:NGB00847.1
contig_6628	13125	13107..13125	adaptor:NGB01096.1
contig_6673	6733	6699..6733	adaptor:NGB01088.1
contig_6676	13298	13265..13298	adaptor:NGB01088.1
contig_6692	17411	1..43	adaptor:NGB00847.1
contig_6703	57771	1..63	adaptor:NGB00360.1
contig_6785	8258	8237..8258	adaptor:NGB01088.1
contig_6908	53004	52732..52792	adaptor:NGB00847.1
contig_6940	18777	18580..18777	adaptor:NGB00360.1
contig_6941	42032	41980..42032	adaptor:NGB00847.1
contig_6945	53258	1..71	adaptor:NGB00360.1
contig_6986	49101	1..21	adaptor:NGB01088.1
contig_701	57358	1..28	adaptor:NGB01096.1
contig_7017	41786	1..88	adaptor:NGB00360.1
contig_7035	53503	53477..53503	adaptor:NGB01096.1
contig_7046	12860	12812..12860	adaptor:NGB00360.1
contig_7081	27746	1..78	adaptor:NGB00847.1
contig_7082	26783	1..73	adaptor:NGB00847.1
contig_7083	44465	1..70	adaptor:NGB00847.1
contig_7117	33739	33661..33739	adaptor:NGB00360.1
contig_7197	5439	5361..5439	adaptor:NGB00360.1
contig_720	34826	34755..34826	adaptor:NGB00360.1
contig_7210	16719	1..30	adaptor:NGB01096.1
contig_7225	51589	51483..51519	adaptor:NGB01090.1
contig_7228	37410	1..64	adaptor:NGB00360.1
contig_7296	6652	1..80	adaptor:NGB00847.1
contig_7317	11682	1..30	adaptor:NGB01088.1
contig_7323	47612	47560..47612	adaptor:NGB00847.1
contig_7353	50534	50506..50534	adaptor:NGB01096.1
contig_7478	44000	43977..44000	adaptor:NGB01088.1
contig_7510	11029	1..22	adaptor:NGB01096.1
contig_7540	12614	12566..12614	adaptor:NGB00360.1
contig_7587	74260	74065..74260	adaptor:NGB00847.1
contig_7607	14652	1..31	adaptor:NGB01088.1
contig_7612	27455	27299..27354	adaptor:NGB00360.1
contig_7705	39772	1..49	adaptor:NGB00360.1
contig_7729	22305	1..172	adaptor:NGB00360.1
contig_7747	11568	11502..11568	adaptor:NGB00847.1
contig_7750	52785	52748..52785	adaptor:NGB01029.1
contig_7800	20628	20588..20628	adaptor:NGB00360.1
contig_7851	53514	53439..53514	adaptor:NGB00360.1
contig_7989	51399	1..97	adaptor:NGB00847.1
contig_7992	9120	9035..9120	adaptor:NGB00360.1
contig_7995	103073	103034..103073	adaptor:NGB00360.1
contig_8000	16924	1..85	adaptor:NGB00847.1
contig_8071	73728	73657..73728	adaptor:NGB00360.1
contig_809	20474	20399..20474	adaptor:NGB00360.1
contig_8139	33627	1..25	adaptor:NGB01088.1
contig_8165	17003	16958..17003	adaptor:NGB00847.1
contig_8207	30300	30275..30300	adaptor:NGB01096.1
contig_821	111683	111656..111683	adaptor:NGB01096.1
contig_8236	30705	1..70	adaptor:NGB00360.1
contig_8261	49091	1..181	adaptor:NGB00847.1
contig_8265	28139	27940..28139	adaptor:NGB00360.1
contig_8307	32654	32591..32654	adaptor:NGB00360.1
contig_8340	12953	12925..12953	adaptor:NGB01096.1
contig_8389	19738	1..75	adaptor:NGB00847.1
contig_8399	35159	1..147	adaptor:NGB01096.1
contig_8569	19455	1..38	adaptor:multiple
contig_8735	42362	42335..42362	adaptor:NGB01088.1
contig_8737	22308	1..70	adaptor:NGB00360.1
contig_8790	14216	14198..14216	adaptor:NGB01096.1
contig_8797	6889	1..95	adaptor:NGB00847.1
contig_8815	39194	1..80	adaptor:NGB00360.1
contig_886	10028	1..76	adaptor:NGB00360.1
contig_8861	12192	12145..12192	adaptor:NGB00360.1
contig_8909	11109	11042..11109	adaptor:NGB00360.1
contig_8932	8331	8281..8331	adaptor:NGB00847.1
contig_8975	8730	8671..8730	adaptor:NGB00847.1
contig_8992	12682	12661..12682	adaptor:NGB01088.1
contig_8994	7982	7950..7982	adaptor:NGB01096.1
contig_9017	8069	7896..8069	adaptor:NGB00360.1
contig_9045	35343	535..598	adaptor:NGB00847.1
contig_9082	10766	1..28	adaptor:NGB01096.1
contig_9271	17773	17750..17773	adaptor:NGB01096.1
contig_9273	12180	1..180	adaptor:NGB01096.1
contig_9287	6067	1..77	adaptor:NGB00847.1
contig_9474	33382	33060..33111	adaptor:NGB00360.1
contig_9495	19348	19274..19348	adaptor:NGB00847.1
contig_9540	30855	30836..30855	adaptor:NGB01088.1
contig_9591	10604	1..41	adaptor:NGB00847.1
contig_9628	15083	1..34	adaptor:NGB01096.1
contig_9677	5510	5486..5510	adaptor:NGB01088.1
contig_9693	9823	1..84	adaptor:NGB00847.1
contig_9825	54363	54309..54363	adaptor:NGB00847.1
contig_9863	14033	14013..14033	adaptor:NGB01088.1
contig_9993	35388	1..26	adaptor:NGB01096.1



From xvazquezc at gmail.com  Mon Oct 23 16:02:47 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Tue, 24 Oct 2017 09:02:47 +1100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's
actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the
contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the
"Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a
different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com> wrote:

> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this
> contamination report.
>
> Please how do I use maker to effect the correction
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From cjfields at illinois.edu  Mon Oct 23 17:21:06 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 23 Oct 2017 23:21:06 +0000
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
Message-ID: <8B4331B5-9D10-478A-91A5-80AF702CD9CD@illinois.edu>

It looks like the adapter is primarily at the ends, which is easy to remove.  However, I agree, removing these and redoing the assembly may improve the assembly quality.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Xabier V?zquez-Campos <xvazquezc at gmail.com>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>, "Ence, daniel" <d.ence at ufl.edu>
Subject: Re: [maker-devel] Contamination report from NCBI

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations
Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
Xabier V?zquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From mmokrejs at gmail.com  Tue Oct 24 04:23:38 2017
From: mmokrejs at gmail.com (=?UTF-8?Q?Martin_MOKREJ=c5=a0?=)
Date: Tue, 24 Oct 2017 12:23:38 +0200
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>

Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
> 
> Good day.
> 
> Please I submitted my sequence to NCBI and they sent back this contamination report.
> 
> Please how do I use maker to effect the correction

-- 
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/



From eennadi at gmail.com  Tue Oct 24 04:44:20 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 24 Oct 2017 11:44:20 +0100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
Message-ID: <CAOXM=CX=AiSo-u8gQ7de1KrgZLUbBZ2GXPbdU6kG3hjrUBjE1A@mail.gmail.com>

Thanks!
Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications



On Oct 24, 2017 11:23 AM, "Martin MOKREJ?" <mmokrejs at gmail.com> wrote:

> Hi Emmanuel,
>   use trimmomatic or cutadapt to remove the adapters and check the output
> file for unremoved cases. Once they are all removed redo the assembly.
> Martin
>
> Emmanuel Nnadi wrote:
> > Hello
> >
> > Good day.
> >
> > Please I submitted my sequence to NCBI and they sent back this
> contamination report.
> >
> > Please how do I use maker to effect the correction
>
> --
> Martin Mokrejs, Ph.D.
> Adapter/artefact removal from datasets based on the following technologies:
>   454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
> http://www.bioinformatics.cz/software/supported-protocols/
>
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From qwzhang0601 at gmail.com  Tue Oct 24 10:54:13 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Tue, 24 Oct 2017 12:54:13 -0400
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
Message-ID: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>

Dear Carson:

Thank you again for your suggestions. I just get the new genome assembly of
NMR and start to do gene annotation. I understand you ideas about this. But
can I simply use the old genome transcripts as transcript evidence, and
just following the standard Maker2 pipeline? I set est2genome=1 and provide
the mRNA sequences in the fasta format for the first round training of SNAP.

For transcripts I have the following choices. I think the first choice is
more reliable and better, right?
(1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded
those sequences in fasta format.
(2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by
trinity for each sample and then get the transcripts. But I think most of
the RNA-seq should have been submitted to NCBI.

BTW, if we use the RefSeq data from NCBI, we can download the mRNA
sequences, coding sequences or protein sequences. I wonder which type of
data are the best to train the SNAP? For Augustus, we will use BUSCO to
train it.

Many thanks.

Best
Quanwei




2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> You can try using the est2genome=1 option to map the old models forward
> onto the new assembly as if they were ESTs (add a line that says
> est_forward=1 to the control file to maintain old naming and set est=1 to
> the old model transcript file). Then provide the final models as a pred_gff
> for a subsuquent run (i.e. a traditional MAKER run where you are annotating
> the new assembly with transcript and protein evidence and ab initio
> predictors). Don?t supply the old models to est= on that run.
>
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will
> change. So by doing it this way, you will at least be able to move many
> models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are
> just letting old models compete against new annotations. They will be
> rejected if they have no evidence support, or can be kept if they score
> better than alternate models from SNAP/Augustus. That way you have the
> chance to integrate old models while at the same time rejecting some old
> models that have no evidence overlap.
>
> ?Carson
>
>
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been
> assembled and annotated a few years ago. We can download the gene
> annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder
> how can I fully make use of existing annotations. On the other hand, since
> the previous genome is not very well assemblies, some genes annotation
> maybe false positives. I hope those false positive genes in previous
> annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Tue Oct 24 16:26:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 24 Oct 2017 16:26:00 -0600
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
	<CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
Message-ID: <C02680FC-A5ED-4CD9-8517-3018CA1A0D69@gmail.com>

Yes. If you use est2genome it will just align the model, and then find the longest ORF. So it is a quick way to jsut align old models to the new assembly. Alternatively you can just do de novo annotation.

?Carson



> On Oct 24, 2017, at 10:54 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Dear Carson:
> 
> Thank you again for your suggestions. I just get the new genome assembly of NMR and start to do gene annotation. I understand you ideas about this. But can I simply use the old genome transcripts as transcript evidence, and just following the standard Maker2 pipeline? I set est2genome=1 and provide the mRNA sequences in the fasta format for the first round training of SNAP.
> 
> For transcripts I have the following choices. I think the first choice is more reliable and better, right?
> (1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded those sequences in fasta format.
> (2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by trinity for each sample and then get the transcripts. But I think most of the RNA-seq should have been submitted to NCBI. 
> 
> BTW, if we use the RefSeq data from NCBI, we can download the mRNA sequences, coding sequences or protein sequences. I wonder which type of data are the best to train the SNAP? For Augustus, we will use BUSCO to train it. 
> 
> Many thanks. 
> 
> Best
> Quanwei
> 
> 
> 
> 
> 2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> You can try using the est2genome=1 option to map the old models forward onto the new assembly as if they were ESTs (add a line that says est_forward=1 to the control file to maintain old naming and set est=1 to the old model transcript file). Then provide the final models as a pred_gff for a subsuquent run (i.e. a traditional MAKER run where you are annotating the new assembly with transcript and protein evidence and ab initio predictors). Don?t supply the old models to est= on that run.
> 
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will change. So by doing it this way, you will at least be able to move many models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are just letting old models compete against new annotations. They will be rejected if they have no evidence support, or can be kept if they score better than alternate models from SNAP/Augustus. That way you have the chance to integrate old models while at the same time rejecting some old models that have no evidence overlap.
> 
> ?Carson
> 
> 
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been assembled and annotated a few years ago. We can download the gene annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder how can I fully make use of existing annotations. On the other hand, since the previous genome is not very well assemblies, some genes annotation maybe false positives. I hope those false positive genes in previous annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From daren.card at gmail.com  Wed Oct 25 06:17:13 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 25 Oct 2017 07:17:13 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
	<C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>
	<97656D7C-3613-4B0B-9D99-0441AC28ABCC@gmail.com>
	<49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
Message-ID: <0406D4C3-9C43-4198-B2EA-241C6C504425@gmail.com>

Hi Carson (and CCed MAKER list for the record),

Thanks for troubleshooting my issue further. Good to hear that the run should ultimately work, but strange it isn?t for me. I?ll keep playing with it and will hopefully get it sorted out by running through the list you suggested. 

Thanks again for the help,
Daren


> On Oct 24, 2017, at 11:27 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> I cannot seem to replicate this. I ran with MAKER 2.31.8 and 2.31.9, both with and without the GFF3 file (total of 4 runs). It succeeded without issues in every case.
> 
> The only things I can think to try are.
> 1. Reinstall BLAST+. Even though you have 2.6.0, just try it anyways. Also Install rmblast 2.6.0 for use wth RepeatMasker (requires that you install from source).
> 2. Maker sure you run ./configure inside RepeatMasker to let it know about the new rmblast installation.
> 3. Change the location of blast and related scripts in maker_exe.ctl otherwise MAKER won?t know to use your new installation.
> 4. delete the mpi_blastdb directory under MAKER?s output directory tp force it to rebuild all BLAST indexes.
> 5. delete any fle with a ?.db? extension in the maker output directory to force it to rebuld all GFF3 indexes.
> 6. Update BioPerl to the current CPAN version.
> 
> Also here is a link to the results I got for your contig (version 2.31.8 using the repeat masking GFF3 file) ?> http://weatherby.genetics.utah.edu/data/scaffold-1.tgz
> 
> ?Carson
> 
> 
> 
>> On Oct 17, 2017, at 6:46 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi Carson,
>> 
>> Thanks for offering to take a further look at this. I?ve uploaded all the files that I think you?d need to run MAKER on your systems, but let me know if you need anything else. My username is ?guest_5038?. 
>> 
>> Repeat annotations GFF is from RepeatModeler, with simple repeats filtered away. Transcript evidence was from Trinity assembly of several RNAseq libraries. Several sets of protein evidence from related species. Also have augustus HMM trained based on the genome assembly using BUSCO with retraining turned on. 
>> 
>> The command I?ve used is below, and here are the software versions I?m working with: 
>> 
>> Maker - 2.31.8
>> BLAST - 2.6.0
>> Augustus - 3.2.3
>> RepeatMasker - 4.0.6
>> 
>> mpiexec -n 12 maker -base CroVir_rnd1_chr1 round1_maker_opts.chr1.ctl maker_bopts.ctl maker_exe.ctl
>> 
>> Thanks again!
>> Daren
>> 
>> 
>>> On Oct 13, 2017, at 10:37 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.
>>> 
>>> Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>>> 
>>> ?Carson
>>> 
>>> 
>>> 
>>>> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi Carson,
>>>> 
>>>> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
>>>> 
>>>> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
>>>> 
>>>> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
>>>> 
>>>> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
>>>> 
>>>> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
>>>> 
>>>> Thanks,
>>>> Daren
>>>> 
>>>> 
>>>>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>>>>> 
>>>>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>>>>> 
>>>>> ?Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>> 
>>>>>> Dear Carson,
>>>>>> 
>>>>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>>>>> 
>>>>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>>>>> 
>>>>>> Thank you,
>>>>>> Daren Card
>>>>>> 
>>>>>> 
>>>>>> ################################################
>>>>>> doing repeat masking
>>>>>> re reading repeat masker report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>>>>> doing blastx repeats
>>>>>> re reading blast report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>>>>> deleted:2 hits
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> collecting blastx repeatmasking
>>>>>> processing all repeats
>>>>>> in cluster::shadow_cluster...
>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>> --> rank=NA, hostname=moonunit0
>>>>>> ERROR: Failed while processing all repeats
>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> examining contents of the fasta file and run log
>>>>>> ################################################
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>>>> 
>>>>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>>>>> 
>>>>>>> ?Carson
>>>>>>> 
>>>>>>> 
>>>>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>>>> 
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>>>>> 
>>>>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>>>>> 
>>>>>>>> Any help would be greatly appreciated.
>>>>>>>> Daren Card
>>>>>>>> 
>>>>>>>> University of Texas Arlington
>>>>>>>> 
>>>>>>>> ###################################################
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> deleted:0 hits
>>>>>>>> collecting blastx repeatmasking
>>>>>>>> processing all repeats
>>>>>>>> in cluster::shadow_cluster...
>>>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>>>> --> rank=3, hostname=moonunit0
>>>>>>>> ERROR: Failed while processing all repeats
>>>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> deleted:0 hits
>>>>>>>> deleted:0 hits
>>>>>>>> ###################################################
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 




From venyao at qq.com  Wed Oct 25 01:25:25 2017
From: venyao at qq.com (=?ISO-8859-1?B?V2VuIFlhbw==?=)
Date: Wed, 25 Oct 2017 15:25:25 +0800
Subject: [maker-devel] NNN in maker output transcript
Message-ID: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>

Dear guys,


Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.


Thanks!


Wen Yao
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From dandence at gmail.com  Wed Oct 25 09:42:04 2017
From: dandence at gmail.com (Daniel Ence)
Date: Wed, 25 Oct 2017 11:42:04 -0400
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <4913D7BA-CD9B-4B7F-83EF-B8072B4950A6@gmail.com>

Hi Wen Yao, 

Do you mean that some of the transcript sequences contain ?N? characters or that an entire transcript sequence is ?NNN??  



> On Oct 25, 2017, at 3:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:42:34 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:42:34 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>

The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.

?Carson




> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:43:37 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:43:37 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
	<96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
Message-ID: <F55EEB1B-9F79-474A-8AE4-5232566D7380@gmail.com>

Also you can check the source of the model by looking a the name. i.e. does it have, augustus, snap, or est2genome in the name?

?Carson

> On Oct 25, 2017, at 9:42 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.
> 
> ?Carson
> 
> 
> 
> 
>> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
>> 
>> Dear guys,
>> 
>> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
>> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
>> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
>> 
>> Thanks!
>> 
>> Wen Yao
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Thu Oct 26 15:34:33 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Thu, 26 Oct 2017 22:34:33 +0100
Subject: [maker-devel] How to remove contigs from GFF file
Message-ID: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>

Hello,

I need to remove sequences from my GFF file can someone help me with
command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in
gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>
 [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ:
gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From bmoore at genetics.utah.edu  Fri Oct 27 07:17:41 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:17:41 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <98FAE3F3-7C52-4EDA-8FBB-5F43DB7D54C9@umail.utah.edu>

Those look suspiciously like the remnants of end-of-line control characters.  Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I?d look at the upstream path of where your files come from and how they?ve been processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server).  One bizarre example we?ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted to MS format.  Good luck?

Barry

On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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maker-devel mailing list
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http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From bmoore at genetics.utah.edu  Fri Oct 27 07:24:44 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:24:44 +0000
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
	<CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
Message-ID: <FB1F1E37-1246-4A10-BD9A-BF0644528F15@umail.utah.edu>

Also, you could probably build these overlap sets on the command line by subsetting the MAKER GFF3 file and then using BedTools intersect for overlap queries.

Barry

On Oct 11, 2017, at 10:19 PM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL

?Carson



On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?

Thanks!!!
Matt Simenc
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From dandence at gmail.com  Fri Oct 27 08:51:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Fri, 27 Oct 2017 10:51:21 -0400
Subject: [maker-devel] How to remove contigs from GFF file
In-Reply-To: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
References: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
Message-ID: <D0CA7ADF-64A3-4B15-ACA3-26FA95B1C5F9@gmail.com>

Hi Emmanuel, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this ?grep -v ?scaffold_name? gff3_file?. 

~Daniel



> On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> 
> I need to remove sequences from my GFF file can someone help me with command line for such removal
> 
> ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
> ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 27 16:00:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Oct 2017 16:00:17 -0600
Subject: [maker-devel] "ALRM" isn't numeric in exit - MAKER warning
 message
In-Reply-To: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
References: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
Message-ID: <399AB5BD-2FC5-45F4-9AC8-1665CCFEA0D1@gmail.com>

Hi Marivi,

The only time MAKER uses the ALRM signal is during exit. Sometimes MPI_Finalize can freeze (it has to do with the fact it is being called from Perl). So we set an alarm just in case. Then if it takes to long we assume it is frozen and let things exit in a less than graceful way rather than let it block forever (it is already finished after all). The complaint you get may be because your system doesn?t support the alarm signal or forks.pm (which tries to intercept signals) is having an issue. Or it may just be ugliness related to parts of the process being killed with other parts still being active (it is an ungraceful exit after all). Or it may be another source of the ALRM all together (but I assume it is the MAKER ALRM given that it happens right after MAKER says it is finished). 

Thanks,
Carson



> On Oct 27, 2017, at 1:03 PM, Marivi Colle <collemar at msu.edu> wrote:
> 
> Hi Carson,
> 
> After running MAKER, I checked my std output and here's the message at the end of the file. I was wondering what this warning message means?
> 
> 
> Start_time: 1508465182
> End_time:   1508950543
> Elapsed:    485361
> 
> 
> Maker is now finished!!!
> 
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184
> 
> 
> Thank you.
> Marivi
> 
> 
> -- 
> Marivi G. Colle
> Research Associate
> Department of Horticulture
> Michigan State University
> 1066 Bogue St., East Lansing
> Michigan 48824-1325, USA

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From patrick.tranvan at unil.ch  Sat Oct 28 08:14:59 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Sat, 28 Oct 2017 14:14:59 +0000
Subject: [maker-devel] Advice on my pipeline
In-Reply-To: <651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
References: <6b029690bace4d3fbae77c0bb1bddce8@prdexch02.ad.unil.ch>
	<A39F4213-70A8-4E07-AB13-00C427E4F244@gmail.com>
	<1498470630221.84642@unil.ch>
	<696C51C6-5606-4ECB-A8B8-9C077182FFFA@gmail.com>
	<1498908228256.16549@unil.ch>
	<58E904BF-9AB8-4AC7-B10B-C902F414E03D@gmail.com>
	<1505986013492.52354@unil.ch>,
	<651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
Message-ID: <1509200133044.96929@unil.ch>

Hi Carson,


If I want to look for alternative splicing variant, can I just add the option


alt_splice=1


only at the last round of maker or do I have to set it since the beggining ? (and perform the 4 rounds with this option).

Cheers,

Patrick


________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: Friday, September 22, 2017 10:08 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Advice on my pipeline

The gff3 passthrough options are there to help users get old data into MAKER when they have lost access to the original files. But for iterative running of the pipeline, it is more effective just to rerun in place so MAKER can access the raw alignment reports. The raw reports from the alignments have more detail than what is stored in the GFF3. Details that are lost when trying to use the GFF3 as input.

?Carson


On Sep 21, 2017, at 3:26 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hi Carson,

I have a doubt for the round 2, so in a previous reply you said:

" Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory). "



Does it means that I don't need to modify the section :

#-----Re-annotation Using MAKER Derived GFF3

?

If I let everything by default such as :


altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no


It will not look again for repeat and protein + transcriptome alignment ?

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, July 3, 2017 10:50 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

maker2zff is just for SNAP training and not for gene filtering (please do not use it for filtering, it does not do what you think).

So the final annotation set after maker with correct_est_fusion is 16,850. To decide which set is better, look at them in a browser (gene counts are not useful for guaging result). A well annotated genome will have evidence clusters that closely match the final models. A poorly annoted genome will have evidence clusters that are split or merged by the models.

The corrected_est_fusion does two things. It trims long overlapping UTR fragments, and it stops evidence clusters from being merged on BLASTP evidence alone (so gene predictors will get unmerged hint regions if clusters are split).

You may also find that using jaccard_clip with Trinity has reduced sensitivity for the transcript data (you may lose things that were there before, but now have better specificity, i.e. fewer false positives). Make sure you provided protein data from at least two related species to help maintain sensitivity lost form the transcript data. You can also add rejected genes models back in after the fact by using iprscan to identify unsupported models with identifiable protein domains ?> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/

Thanks,
Carson




On Jul 1, 2017, at 5:21 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

So I have assembled my transcriptome with Trinity using the jaccard clip option and I have run maker with and without corrected_est_fusion.

I have then use SNAP to train/filter it with:

maker2zff  specie.all.gff

Here are my results:

Number of gene after maker -> Number of gene after maker2zff

- Without corrected_est_fusion: 21621 -> 13875
- With corrected_est_fusion: 16850 -> 9098

1 )If I understand well how works corrected_est_fusion, because it prevents gene merging, shouldn't be the invert ?
Normally I should find more genes with corrected_est_fusion right ?

2) I think I should find something like 13000-14000 genes for my specie. SHould I go with the "Without corrected_est_fusion" for the 2nd iteration of maker ?

 Thanks for your help



Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 26, 2017 11:38 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Sorry the option is ?> correct_est_fusion

It is in the maker_opts.ctl file.

I would use both SNAP and Augustus on a few large contigs then review the results manually. If one of them is not behaving well, then drop it. If both behave well (i.e. correlate well with evidence alignemnts) then keep them both.

?Carson



On Jun 26, 2017, at 3:48 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Thanks for your answer.

1) Do you think that adding a Augustus training in addition to SNAP at the step 3 and 5 will add more confidence (instead of adding Augustus only for the final round) ?
Because I am using autoAug for this and it tooks a while to compute ..

2) I don't see this option : 'avoid_est_fusion=1' . I have tried to add it but I got this error:

WARNING: Invalid option 'avoid_est_fusion' in control file maker_opts.ctl

(I am using v 2.31.8 )


Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 5, 2017 8:29 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Your plan sounds good. A couple of related notes.

Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.

Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory).

?Carson


On Jun 2, 2017, at 3:56 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hello,

This is my first time running Maker for an insect genome annotation.

I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:


What I have:
- RNA evidence: transcriptome
- Proteine evidence: swissprot/uniprot + busco protein set of insect
- Cegma and busco results of my genome


1) Train SNAP with CEGMA

2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).

3) Create SNAP model from run A.

4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

5) Create SNAP model from run B.

6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

7)  Create SNAP model from run C AND Create Augustus gene model from run C

8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1). + Use keep_preds=1



Does it seems coherent ?

Cheers,

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org







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From dandence at gmail.com  Mon Oct  2 07:17:57 2017
From: dandence at gmail.com (Daniel Ence)
Date: Mon, 2 Oct 2017 09:17:57 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
Message-ID: <F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>

Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink
The fasta headers in this file are different from the fasta header that the file you used has: 
>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1

Let us know if that helps, 
Daniel

> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> I intend to rename genes for Genebank submission
> 
> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
> 
> the output of BLAST RESULT looks like this
> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
> 
> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
> 
> I got the following result
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
> 
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
> 
> What can I do?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
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From michael.s.campbell1 at gmail.com  Mon Oct  2 07:30:43 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 09:30:43 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
Message-ID: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 

Thanks,
Mike


> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hello-
> 
> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
> 
> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
> 
> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
> 
> Thanks for your help,
> 
> Best,
> 
> Chris Willett
> 
>   
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: 2252 Genome Science Building
> phone:
> 919-843-8663
> fax:
> 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:19:51 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:19:51 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
Message-ID: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
> On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi Mike-
> 
> I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?
> 
> Thanks for your help,
> 
> Best,
> 
> Chris
> 
> 
> 
>> On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com <mailto:michael.s.campbell1 at gmail.com>> wrote:
>> 
>> Hi Chris,
>> 
>> This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1. 
>> 
>> Thanks,
>> Mike
>> 
>> 
>>> On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu <mailto:willett4 at email.unc.edu>> wrote:
>>> 
>>> Hello-
>>> 
>>> We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this? 
>>> 
>>> Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?  
>>> 
>>> The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.
>>> 
>>> Thanks for your help,
>>> 
>>> Best,
>>> 
>>> Chris Willett
>>> 
>>>   
>>> 
>>> 
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Research Associate Professor
>>> Department of Biology
>>> CB#3280 Coker Hall
>>> University of North Carolina, Chapel Hill
>>> Chapel Hill, NC, 27599-3280 
>>> 
>>> Office: 2252 Genome Science Building
>>> phone:
>>> 919-843-8663
>>> fax:
>>> 919-962-1625
>>> 
>>> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
> 

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From michael.s.campbell1 at gmail.com  Mon Oct  2 13:35:55 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Mon, 2 Oct 2017 15:35:55 -0400
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
	<FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>
Message-ID: <4C4E3DE7-CE28-4DF7-B234-E88701CAD172@gmail.com>

Hi Chris,

It?s this line here:
model_gff=/proj/willetlb/users/cwillett/MAKER_analyses/dovetail_ann/SDv1.0_est-forward-SDv2.1.gff

Anything passed to model_gff is treated as sacred by MAKER and will be kept regardless of AED. If you pass it in as pred_gff= then it will be subject to the AED filters.

I hope this helps,
Mike
> On Oct 2, 2017, at 3:28 PM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> <maker_opts.ctl_full8>




From daren.card at gmail.com  Wed Oct  4 09:53:42 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 4 Oct 2017 10:53:42 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
Message-ID: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>

Hi all,

I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?

I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).

Any help would be greatly appreciated.
Daren Card

University of Texas Arlington

###################################################
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=3, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

deleted:0 hits
deleted:0 hits
###################################################




From carsonhh at gmail.com  Wed Oct  4 10:03:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 10:03:52 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
Message-ID: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>

The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.

?Carson


> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi all,
> 
> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
> 
> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
> 
> Any help would be greatly appreciated.
> Daren Card
> 
> University of Texas Arlington
> 
> ###################################################
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
> #-------------------------------#
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=3, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> doing blastx repeats
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
> #-------------------------------#
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> deleted:0 hits
> deleted:0 hits
> ###################################################
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From qwzhang0601 at gmail.com  Wed Oct  4 16:31:09 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 18:31:09 -0400
Subject: [maker-devel] About eAED
Message-ID: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>

Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I
found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be
the reason of the great difference between AED and eAED. For this gene it
has a very low AED score, is it still a reliable gene model if its eAED
equals 1?

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei
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From xvazquezc at gmail.com  Wed Oct  4 16:35:41 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 5 Oct 2017 09:35:41 +1100
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>

Carson commented on this here
https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:

> Hello:
>
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
> I found there are several hundred genes with eAED 1.
>
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
> be the reason of the great difference between AED and eAED. For this gene
> it has a very low AED score, is it still a reliable gene model if its eAED
> equals 1?
>
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
> QI:75|0|0|1|0|0|2|111|35
>
> Thanks
>
> Best
> Quanwei
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From carsonhh at gmail.com  Wed Oct  4 16:38:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:38:00 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
Message-ID: <77155DA5-6454-4B25-BCF6-DE6B077BA548@gmail.com>

eAED is an extended AED calculation that does some inference about the evidence (i.e. checks reading frame and not just overlap, and may infer support for an exon if by splice sites are confirmed etc.). If eAED is 1 that means that while there is evidence supporting the model, the evidence is more likely to be spurious, so it may be a false model.

?Carson

 
> On Oct 4, 2017, at 4:31 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct  4 16:39:52 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 16:39:52 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
Message-ID: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>

This one is an even better explanation than the answer I just gave. Thank you.

?Carson

> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> Hello:
> 
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
> 
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
> 
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
> 
> Thanks
> 
> Best
> Quanwei
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 
> 
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From eennadi at gmail.com  Sun Oct  1 23:03:01 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Oct 2017 06:03:01 +0100
Subject: [maker-devel] Error with Maker_functional_gff
Message-ID: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>

Hello,
I intend to rename genes for Genebank submission

I downloaded swissprot.fa from NCBI and used blast MAKER generated file to
swissprot.

the output of BLAST RESULT looks like this

snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1
49.315  73      37      0       43      115     874     946     2.61e-14
    71.6


I attempted to run maker_funtional_gff using the swissprot.fa downloaded
and the blastp result


I got the following result

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 2897906.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 2897906.

Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin;
AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP;
AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName:
Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1;
Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor



Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139,
<$IN> line 1608599.

Use of uninitialized value $id in hash element at
/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141,
<$IN> line 1608599.

Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X
methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase


What can I do?



Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From willett4 at email.unc.edu  Mon Oct  2 09:04:38 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 15:04:38 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
Message-ID: <DBEB554A-5809-4EB8-AC78-8B410E73B0C4@ad.unc.edu>

Hi Mike-

Thanks for getting back to me. I was using the grep -cP '\tgene\t? syntax to count the numbers and it seems to be giving me the same numbers I got before when I was counting either the transcripts or the genes in the fasta output files from our original run. I will have to look at the files a bit more to see if I can find some examples of genes that fit what you are suggesting.

Best,

Chris


On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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From willett4 at email.unc.edu  Mon Oct  2 13:28:19 2017
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 2 Oct 2017 19:28:19 +0000
Subject: [maker-devel] question on gene numbers with quality_filter.pl
In-Reply-To: <0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
References: <16C1890A-2042-4BE1-93CE-8A8DC0C18151@ad.unc.edu>
	<30C718DD-D3E5-4659-B83D-B9520DD20E34@gmail.com>
	<4C24415C-8A2A-499F-A55A-0026F7D1329F@ad.unc.edu>
	<0A5A51F2-C551-493B-943B-7F5F81C294BF@gmail.com>
Message-ID: <FDBB7F63-B1B8-4702-A0F5-6903F1E71FEF@ad.unc.edu>

Hi Mike-

Here is the control file for the last run of MAKER with keep_preds=0 and here is an example of one mRNA retained from the gff file:

Chromosome_6    maker   mRNA    556000  557215  .       +       .       ID=maker-Chromosome_6-exonerate_est2genome-gene-5.3-mRNA-1;Parent=maker-Chromosome_6-exonerate_est2genome-gene-5.3;Name=TCALIF_02833-PA;_AED=1.00;_eAED=1.00;_QI=15|0|0|0|1|1|2|75|338;score=100;Alias=TCALIF_02833-PA

Thanks,

Chris






On Oct 2, 2017, at 3:19 PM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

Yeah By default MAKER shouldn?t keep any annotation with an AED of 1. I?ve ccd the dev list on this to see if anyone else has any idea why you might get AED 1 genes with keep_preds=0. Could you send me the maker_opts.ctl file for the run. There may be something informative in there.

Thanks,
Mike
On Oct 2, 2017, at 2:32 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hi Mike-

I was looking at the lists of mRNAs and I think what is happening is that there are still genes retained in our initial output from MAKER that have an AED=1 that are then getting trimmed out of the filtered file. If I am setting the AED threshold equal to 1 in the control file for the MAKER run is that less than one or less than or equal to one for retention? Should these AED=1 genes be making it into the gene and mRNA pools if we have the keep predictions parameter set to 0?

Thanks for your help,

Best,

Chris



On Oct 2, 2017, at 9:30 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Chris,

This is interesting. -d in quality_filter.pl should only filter out genes based on AED. Is there a chance that you counted transcripts instead of genes? If there is a transcript with an AED of 1 then quality filter should remove it but leave the gene and the transcripts with AEDs less than 1. I can have a look at it if you send me one of the genes (in GFF3 format)  that was filtered out by quality_filter.pl even though it had an AED less than 1.

Thanks,
Mike


On Sep 29, 2017, at 1:20 PM, Willett, Christopher S <willett4 at email.unc.edu<mailto:willett4 at email.unc.edu>> wrote:

Hello-

We are getting to the final stages (hopefully) of a reannotation of a new assembly of a copepod genome using MAKER and we had some questions about which set of genes to use.  Our latest runs were using Pfam domains to define default vs standard set using the quality_filter.pl script and I had a question about stringency of the filters for this script. It appears that the default is more stringent than the output that we get from MAKER without using this script (all with AED max set to 1). Are there additional filters in this script beyond AED that would cause this?

Here is what we are seeing if more details would be helpful. With a run with or without the keep_pred turned our final MAKER run gives ~21500 predicted genes with or 15200 without the keep predictions turned on. What I was wondering about was why this 15200 is higher than the default set  (which gives ~14500 genes) after we filter the gff using the -d setting in quality_filter.pl. For completeness the standard set (-s setting) is retaining ~14800 genes and if I filter the 15200 gff file with the default parameters that yields ~14100 genes. So I was curious what else was going on in the filter script beyond AED that would trim out genes?

The genes sets look pretty good overall and seem like reasonable numbers so we were debating which set to use as our final set. I am also trying a few other analyses in InterProScan to see if that identifies additional genes beyond Pfam for retention but that seems a bit independent from the question above.

Thanks for your help,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: 2252 Genome Science Building
phone: 919-843-8663
fax: 919-962-1625


http://labs.bio.unc.edu/Willett/

_______________________________________________
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From qwzhang0601 at gmail.com  Wed Oct  4 20:35:55 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 22:35:55 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
Message-ID: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>

Thank you all.  Most time, the AED is equal to or lower than eAED, but
there are some genes whose eAED is smaller than AED. I feel the eAED is
more stringent than AED. Would you give me an example, under what condition
eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do
you think eAED is a better choice to filter gene models than AED?

Best
Quanwei



2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> This one is an even better explanation than the answer I just gave. Thank
> you.
>
> ?Carson
>
> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Carson commented on this here
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
>> Hello:
>>
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But
>> I found there are several hundred genes with eAED 1.
>>
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>> be the reason of the great difference between AED and eAED. For this gene
>> it has a very low AED score, is it still a reliable gene model if its eAED
>> equals 1?
>>
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>> QI:75|0|0|1|0|0|2|111|35
>>
>> Thanks
>>
>> Best
>> Quanwei
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From carsonhh at gmail.com  Wed Oct  4 20:38:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:38:25 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
Message-ID: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>

The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

?Carson


> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
> 
> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
> 
> Best
> Quanwei
> 
>  
> 
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> This one is an even better explanation than the answer I just gave. Thank you.
> 
> ?Carson
> 
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>> 
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>> 
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> Hello:
>> 
>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>> 
>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>> 
>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>> 
>> Thanks
>> 
>> Best
>> Quanwei
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
>> 
>> 
>> -- 
>> Xabier V?zquez-Campos, PhD
>> Research Associate
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From carsonhh at gmail.com  Wed Oct  4 20:43:28 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 4 Oct 2017 20:43:28 -0600
Subject: [maker-devel] About eAED
In-Reply-To: <5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
Message-ID: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>

eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn?t exist, it just means you should spend a little more time deciding if you really believe it or not.

?Carson


> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The previous linked comment explains in detail ?> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
> 
> Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>> 
>> Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?
>> 
>> The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED? 
>> 
>> Best
>> Quanwei
>> 
>>  
>> 
>> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
>> This one is an even better explanation than the answer I just gave. Thank you.
>> 
>> ?Carson
>> 
>>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>>> 
>>> Carson commented on this here
>>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ <https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ>
>>> 
>>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
>>> Hello:
>>> 
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1. 
>>> 
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>>> 
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>>> 
>>> Thanks
>>> 
>>> Best
>>> Quanwei
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Xabier V?zquez-Campos, PhD
>>> Research Associate
>>> NSW Systems Biology Initiative
>>> School of Biotechnology and Biomolecular Sciences
>>> The University of New South Wales
>>> Sydney NSW 2052 AUSTRALIA
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
> 

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From qwzhang0601 at gmail.com  Wed Oct  4 21:25:24 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Wed, 4 Oct 2017 23:25:24 -0400
Subject: [maker-devel] About eAED
In-Reply-To: <C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
References: <CAOW6FSL1AkT-KQOVstHqdiVo100c9uLDtbwQ8L0ha22qwCMYQg@mail.gmail.com>
	<CAL0hg4EtPpgvM0JxSR0DL3HqXxWkbGjDeCs2ohdQoOOpd1LYJg@mail.gmail.com>
	<606958D2-D9BB-477D-ACE8-E096A9AD9666@gmail.com>
	<CAOW6FS+g-Rm9VteeX5hKPOiTBoSioeC_xNi+EaiOAUJUbv4mzA@mail.gmail.com>
	<5DEAC021-9925-4B41-9332-AB48685D7304@gmail.com>
	<C2AFCAB3-ABEA-4E09-AF9D-01C2318E893E@gmail.com>
Message-ID: <CAOW6FSKZzHUVFm=b+3V82whb+gWNdAgERfO=e5f1k1HSRGz=kw@mail.gmail.com>

Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> eAED can be better for edge cases, but neither is perfect. Low AED
> generally correlates with better models. But a high AED does not mean the
> model doesn?t exist, it just means you should spend a little more time
> deciding if you really believe it or not.
>
> ?Carson
>
>
>
> On Oct 4, 2017, at 8:38 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> The previous linked comment explains in detail ?>
> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ
>
> Basically the middle support of exon is inferred from edge support even
> though no overlap exists (so eAED infers support and AED does not).
>
> ?Carson
>
>
> On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Thank you all.  Most time, the AED is equal to or lower than eAED, but
> there are some genes whose eAED is smaller than AED. I feel the eAED is
> more stringent than AED. Would you give me an example, under what condition
> eAED can be smaller than AED?
>
> The default maker2 gene set includes all genes with AED less than 1.  Do
> you think eAED is a better choice to filter gene models than AED?
>
> Best
> Quanwei
>
>
>
> 2017-10-04 18:39 GMT-04:00 Carson Holt <carsonhh at gmail.com>:
>
>> This one is an even better explanation than the answer I just gave. Thank
>> you.
>>
>> ?Carson
>>
>> On Oct 4, 2017, at 4:35 PM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
>> wrote:
>>
>> Carson commented on this here
>> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-
>> ko/iC4KTuIitGEJ
>>
>> On 5 October 2017 at 09:31, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>>> Hello:
>>>
>>> I ran the maker2 pipeline and got the default gene sets (with AED<1).
>>> But I found there are several hundred genes with eAED 1.
>>>
>>> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can
>>> be the reason of the great difference between AED and eAED. For this gene
>>> it has a very low AED score, is it still a reliable gene model if its eAED
>>> equals 1?
>>>
>>> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00
>>> QI:75|0|0|1|0|0|2|111|35
>>>
>>> Thanks
>>>
>>> Best
>>> Quanwei
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>> --
>> Xabier V?zquez-Campos, *PhD*
>> *Research Associate*
>> NSW Systems Biology Initiative
>> School of Biotechnology and Biomolecular Sciences
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
>
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From dandence at gmail.com  Thu Oct  5 08:00:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Thu, 5 Oct 2017 10:00:21 -0400
Subject: [maker-devel] Error with Maker_functional_gff
In-Reply-To: <CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
References: <CAOXM=CVWm90ry-EMSSSfBc6O8DHAmLF64sd=gq_qaiKdKz9LBQ@mail.gmail.com>
	<F24AEEE8-C671-4DDD-90A6-0D7ADD7FD14C@gmail.com>
	<CAOXM=CV_dy3yzoMTmO04Jy5vWiQN9bc2XwY8meXJS4+xo8HaBQ@mail.gmail.com>
Message-ID: <ECCCAE79-FEDA-4C6E-B7E4-A8FC0C3AD1C2@gmail.com>

Hi Emmanuel, 

I can?t tell whether it?s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you?ll run after all the blasts are complete. 

Assembly isn?t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. 

How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I?d recommend starting with a  review like this one: http://www.sciencedirect.com/science/article/pii/S1672022912000095 <http://www.sciencedirect.com/science/article/pii/S1672022912000095>

~Daniel

> On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Daniel,
> 
> Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now
> 
> it looks like this
> 
> MUCPR_041061-RA	sp|P10978|POLX_TOBAC	49.315	73	37	0	43	115	874	946	2.95e-14	71.6
> MUCPR_026643-RA	sp|Q00451|PRF1_SOLLC	86.207	87	11	1	243	328	257	343	3.65e-32	126
> 
> Is it ok?
> 
> I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?
> 
> I wish to assemble my sequence into scaffold can you advice on the best software to use?
> 
> I attempted using SSPACE: a new stand-alone scaffolding tool for small and large genomes
> but am having problem with the library. Funny enough the software does not have support to solve problems
> 
> Thanks
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> Hi Emmanuel, I think this script is expecting the file ?uniprot_sprot.fasta? downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink <http://www.uniprot.org/downloads#uniprotkblink>
> The fasta headers in this file are different from the fasta header that the file you used has: 
> >sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1
> 
> Let us know if that helps, 
> Daniel
> 
>> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Hello,
>> I intend to rename genes for Genebank submission
>> 
>> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
>> 
>> the output of BLAST RESULT looks like this
>> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
>> 
>> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
>> 
>> I got the following result
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
>> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
>> 
>> 
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
>> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
>> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
>> 
>> What can I do?
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
> 

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From daren.card at gmail.com  Fri Oct  6 06:23:36 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Fri, 6 Oct 2017 07:23:36 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
Message-ID: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>

Dear Carson,

Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.

Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.

Thank you,
Daren Card


################################################
doing repeat masking
re reading repeat masker report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
doing blastx repeats
re reading blast report.
/home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
deleted:2 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=NA, hostname=moonunit0
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold-1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold-1

examining contents of the fasta file and run log
################################################



> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
> 
> ?Carson
> 
> 
>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>> 
>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>> 
>> Any help would be greatly appreciated.
>> Daren Card
>> 
>> University of Texas Arlington
>> 
>> ###################################################
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=3, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> doing blastx repeats
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>> #-------------------------------#
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> deleted:0 hits
>> deleted:0 hits
>> ###################################################
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Sat Oct  7 15:34:46 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sat, 7 Oct 2017 22:34:46 +0100
Subject: [maker-devel] jbrowse not working
Message-ID: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse.

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Sun Oct  8 18:37:12 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 8 Oct 2017 18:37:12 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
Message-ID: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>

MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).

The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/ <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/>

?Carson





> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Dear Carson,
> 
> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
> 
> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
> 
> Thank you,
> Daren Card
> 
> 
> ################################################
> doing repeat masking
> re reading repeat masker report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
> doing blastx repeats
> re reading blast report.
> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
> deleted:2 hits
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> doing blastx repeats
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=NA, hostname=moonunit0
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:scaffold-1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:scaffold-1
> 
> examining contents of the fasta file and run log
> ################################################
> 
> 
> 
>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>> 
>> ?Carson
>> 
>> 
>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Hi all,
>>> 
>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>> 
>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>> 
>>> Any help would be greatly appreciated.
>>> Daren Card
>>> 
>>> University of Texas Arlington
>>> 
>>> ###################################################
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>> #-------------------------------#
>>> deleted:0 hits
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=3, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> doing blastx repeats
>>> running  blast search.
>>> #--------- command -------------#
>>> Widget::blastx:
>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>> #-------------------------------#
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> deleted:0 hits
>>> deleted:0 hits
>>> ###################################################
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 

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From carsonhh at gmail.com  Mon Oct  9 18:35:49 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 9 Oct 2017 18:35:49 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
Message-ID: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>

Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Please,
> I ran the command line
> 
> maker2jbrowse muc1_genome_snap2.all.gff
> 
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
> 
> Please what does it mean? How can I view it in jbrowse. 
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From eennadi at gmail.com  Mon Oct  9 22:42:35 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 10 Oct 2017 05:42:35 +0100
Subject: [maker-devel] jbrowse not working
In-Reply-To: <83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
Message-ID: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge ?d
dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse
/Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse
-d
/Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log
\-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the
jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31
contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of
> the file? That can happen if you use the -n option with gff3_merge.
> Alternatively it?s possible one of the individual contig gff3 used to build
> the merged gff3 is truncated. If that is the case then gff3_merge should
> have thrown some sort of error or warning when you run it.
>
> Thanks,
> Carson
>
>
>
>
> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Please,
> I ran the command line
>
> maker2jbrowse muc1_genome_snap2.all.gff
>
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
>
> Please what does it mean? How can I view it in jbrowse.
>
> Thanks
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
>
>
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From jacques.dainat at nbis.se  Tue Oct 10 03:24:34 2017
From: jacques.dainat at nbis.se (Jacques Dainat)
Date: Tue, 10 Oct 2017 11:24:34 +0200
Subject: [maker-devel] MAKER annotation submission (EMBLmyGFF3)
Message-ID: <967873FE-D61F-4233-A004-C877A60A2AC1@nbis.se>

Hi MAKER users,

I take advantage to this mailing list to share a tool that I hope will be useful for MAKER's users. One of the steps once we are happy of our wonderful annotation is to submit it to the public archives through one of the three INSDC databases (EMBL-EBI / NCBI / DDBJ).
We developed EMBLmyGFF3, allowing to easily convert any kind of GFF3 annotation to the EMBL flat file format in order to submit to the European Nucleotide Archive (ENA) Database that is part of EMBL-EBI.
It works well, amongst others, with the MAKER annotation output. We hope the tool will ease the submission process of your annotations.

You will find it here:
https://github.com/NBISweden/EMBLmyGFF3

A typical usage case will look like that (where ERSXXXXXX and PRJXXXXXX are the accession number and the project ID provided by EMBL-EBI prior to any submission):
./EMBLmyGFF3.py maker.gff3 maker.fa --data_class STD --topology linear --molecule_type 'genomic DNA' --table 1 --species 'Drosophila melanogaster (fly)' --taxonomy INV --accession ERSXXXXXXX --project_id PRJXXXXXXX --rg MYGROUP -o result.embl

Best regards,

Jacques Dainat, PhD
---------------------------------------
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
---------------------------------------
Uppsala University, Biomedicinska Centrum
Department of Medical Biochemistry Microbiology, Genomics


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From mcsimenc at gmail.com  Wed Oct 11 08:53:36 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 07:53:36 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons with
 EST only?
Message-ID: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence
supporting gene models in my MAKER annotation where the left side shows
number of genes with EST support only, the right side shows number of genes
with protein support only, and the intersection shows number of genes with
EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be
fraction of exons that overlap an EST alignment and possibly also a protein
alignment. If that is the case then we can't calculate the number of genes
that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to
get this?

Thanks!!!
Matt Simenc
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From michael.s.campbell1 at gmail.com  Wed Oct 11 09:18:54 2017
From: michael.s.campbell1 at gmail.com (Michael Campbell)
Date: Wed, 11 Oct 2017 11:18:54 -0400
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
Message-ID: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
> 
> Hey MAKER people,
> 
> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
> 
> QI summary has:
> 
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
> 
> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
> 
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
> 
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 11 09:22:54 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Oct 2017 09:22:54 -0600
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
Message-ID: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>

Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL <https://github.com/The-Sequence-Ontology/GAL>

?Carson


 
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Matt,
> 
> I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.
> 
> To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.
> 
> Hope this helps,
> Mike
> 
>> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>> 
>> Hey MAKER people,
>> 
>> I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.
>> 
>> QI summary has:
>> 
>> Fraction of exons that overlap an EST alignment
>> Fraction of exons that overlap EST or Protein alignments
>> 
>> Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.
>> 
>> Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?
>> 
>> Thanks!!!
>> Matt Simenc
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From mcsimenc at gmail.com  Wed Oct 11 22:19:04 2017
From: mcsimenc at gmail.com (Matt Simenc)
Date: Wed, 11 Oct 2017 21:19:04 -0700
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
Message-ID: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Also look at GAL for building GFF3 feature queries ?>
> https://github.com/The-Sequence-Ontology/GAL
>
> ?Carson
>
>
>
>
> On Oct 11, 2017, at 9:18 AM, Michael Campbell <
> michael.s.campbell1 at gmail.com> wrote:
>
> Hi Matt,
>
> I have a hacky way that I?ve done it. It requires running MAKER two more
> times but they are quicker runs.
>
> To identify the genes that have protein support I pass all of the
> annotation back to MAKER using the model_gff option in the maker_opts.ctl
> file. Then I pull out all of the protein2genome features from the big MAKER
> GFF3 file and pass them in using the protein_gff option. I turn off all
> repeat masking and run MAKER. It runs fast because it doesn?t have to run
> any gene finders, align evidence, or repeatmask. In the output any gene
> with an AED less than 1 has protein support. Then I do the same thing with
> est2genome lines from the big GFF3 file and put them in as est_gff. The
> output of that one gives you genes with EST support. Then the genes with an
> AED of less than one in both sets have support from protein and EST.
>
> Hope this helps,
> Mike
>
> On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com> wrote:
>
> Hey MAKER people,
>
> I would like to make a Venn diagram showing the kinds of evidence
> supporting gene models in my MAKER annotation where the left side shows
> number of genes with EST support only, the right side shows number of genes
> with protein support only, and the intersection shows number of genes with
> EST and protein support.
>
> QI summary has:
>
> Fraction of exons that overlap an EST alignment
> Fraction of exons that overlap EST or Protein alignments
>
> Please correct me if I'm wrong, because I am interpreting the first to be
> fraction of exons that overlap an EST alignment and possibly also a protein
> alignment. If that is the case then we can't calculate the number of genes
> that overlap only EST or (EST and protein) from the QI information.
>
> Anyone have a way to do this or have a script to parse the MAKER GFF3 to
> get this?
>
> Thanks!!!
> Matt Simenc
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From scott at scottcain.net  Thu Oct 12 17:33:05 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:33:05 -0400
Subject: [maker-devel] GMOD hackathon before PAG San Diego in January
Message-ID: <CA+JTaoytocv6efRcY6LqKXRjPZXeqa9JFFStCPxE0VunjmB-Nw@mail.gmail.com>

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From daren.card at gmail.com  Thu Oct 12 20:22:54 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Thu, 12 Oct 2017 21:22:54 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
Message-ID: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>

Hi Carson,

Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.

Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.

I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.

What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.

Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.

Thanks,
Daren


> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
> 
> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
> 
> ?Carson
> 
> 
> 
> 
> 
>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Dear Carson,
>> 
>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>> 
>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>> 
>> Thank you,
>> Daren Card
>> 
>> 
>> ################################################
>> doing repeat masking
>> re reading repeat masker report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>> doing blastx repeats
>> re reading blast report.
>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>> deleted:2 hits
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> doing blastx repeats
>> collecting blastx repeatmasking
>> processing all repeats
>> in cluster::shadow_cluster...
>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>> --> rank=NA, hostname=moonunit0
>> ERROR: Failed while processing all repeats
>> ERROR: Chunk failed at level:3, tier_type:1
>> FAILED CONTIG:scaffold-1
>> 
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:scaffold-1
>> 
>> examining contents of the fasta file and run log
>> ################################################
>> 
>> 
>> 
>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>> 
>>> ?Carson
>>> 
>>> 
>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>> 
>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>> 
>>>> Any help would be greatly appreciated.
>>>> Daren Card
>>>> 
>>>> University of Texas Arlington
>>>> 
>>>> ###################################################
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>> #-------------------------------#
>>>> deleted:0 hits
>>>> collecting blastx repeatmasking
>>>> processing all repeats
>>>> in cluster::shadow_cluster...
>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>> --> rank=3, hostname=moonunit0
>>>> ERROR: Failed while processing all repeats
>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> doing blastx repeats
>>>> running  blast search.
>>>> #--------- command -------------#
>>>> Widget::blastx:
>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>> #-------------------------------#
>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>> FAILED CONTIG:scaffold-1
>>>> 
>>>> deleted:0 hits
>>>> deleted:0 hits
>>>> ###################################################
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>> 
> 




From robert.zimmermann at univie.ac.at  Wed Oct 11 13:42:14 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Wed, 11 Oct 2017 21:42:14 +0200
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
Message-ID: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>

Hello,

I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 

My gene prediction section of the maker_opts.ctl file looks like this:
...
augustus_species=all_combined #Augustus gene prediction species model
...
pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
?

It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.

Thanks for your help!

Bob


From xvazquezc at gmail.com  Thu Oct 12 00:09:32 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Thu, 12 Oct 2017 17:09:32 +1100
Subject: [maker-devel] choosing the right gene model
Message-ID: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>

Hi there,

I was visualising the annotations and I realised that in some cases, what
it seems to be a gene is splitted according to one of the gene models,
despite that the other 2, est2genome and prot2genome suggest that it isn't
the case.



Although the opposite also happens.


?
For some reason, the "out of place" model is always (or almost) the one
from Genemark.

How much weight does carry the RNAseq and protein data on this decision (if
any)?
How exactly is the final gene selected?

Cheers,
Xabi

-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From jan.nagel at fabi.up.ac.za  Thu Oct 12 01:37:07 2017
From: jan.nagel at fabi.up.ac.za (Jan FABI)
Date: Thu, 12 Oct 2017 09:37:07 +0200
Subject: [maker-devel] Maker problem
Message-ID: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution
to it online.

I am running maker on a new genome, using BRAKER trained models for
Augustus and GeneMark. This was successful and performed as expected,
except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with
intron models. I have made sure that the input fasta does not contain
characters other than ATCGN or contains "windows"/non-UNIX carriage
returns.

I include the relevant portion of the log below. Could you help me
determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus
--species=Np_2017_braker --UTR=off
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 >
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

-- 
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : jan.nagel at fabi.up.ac.za

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

-- 
This message and attachments are subject to a disclaimer.
Please refer to 
http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf for full 
details.
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From scott at scottcain.net  Thu Oct 12 17:40:33 2017
From: scott at scottcain.net (Scott Cain)
Date: Thu, 12 Oct 2017 19:40:33 -0400
Subject: [maker-devel] Call for presentations at GMOD workshop at PAG
Message-ID: <CA+JTaoyZEYHX0RyKMW7+3d+wic+PyshCUUfhzCzeroXnmyVECw@mail.gmail.com>

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From carsonhh at gmail.com  Fri Oct 13 09:37:25 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:37:25 -0600
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
Message-ID: <C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>

So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.

Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi <http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi>

?Carson



> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
> 
> Hi Carson,
> 
> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
> 
> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
> 
> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
> 
> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
> 
> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
> 
> Thanks,
> Daren
> 
> 
>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>> 
>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>> 
>> ?Carson
>> 
>> 
>> 
>> 
>> 
>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>> 
>>> Dear Carson,
>>> 
>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>> 
>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>> 
>>> Thank you,
>>> Daren Card
>>> 
>>> 
>>> ################################################
>>> doing repeat masking
>>> re reading repeat masker report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>> doing blastx repeats
>>> re reading blast report.
>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>> deleted:2 hits
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> doing blastx repeats
>>> collecting blastx repeatmasking
>>> processing all repeats
>>> in cluster::shadow_cluster...
>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>> --> rank=NA, hostname=moonunit0
>>> ERROR: Failed while processing all repeats
>>> ERROR: Chunk failed at level:3, tier_type:1
>>> FAILED CONTIG:scaffold-1
>>> 
>>> ERROR: Chunk failed at level:2, tier_type:0
>>> FAILED CONTIG:scaffold-1
>>> 
>>> examining contents of the fasta file and run log
>>> ################################################
>>> 
>>> 
>>> 
>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>> 
>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>> 
>>>> ?Carson
>>>> 
>>>> 
>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>> 
>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>> 
>>>>> Any help would be greatly appreciated.
>>>>> Daren Card
>>>>> 
>>>>> University of Texas Arlington
>>>>> 
>>>>> ###################################################
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>> #-------------------------------#
>>>>> deleted:0 hits
>>>>> collecting blastx repeatmasking
>>>>> processing all repeats
>>>>> in cluster::shadow_cluster...
>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>> --> rank=3, hostname=moonunit0
>>>>> ERROR: Failed while processing all repeats
>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> doing blastx repeats
>>>>> running  blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>> #-------------------------------#
>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>> FAILED CONTIG:scaffold-1
>>>>> 
>>>>> deleted:0 hits
>>>>> deleted:0 hits
>>>>> ###################################################
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> 
>>> 
>> 
> 

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From carsonhh at gmail.com  Fri Oct 13 09:42:41 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:42:41 -0600
Subject: [maker-devel] custom "ab initio" predictions with automatic
 hint-based predictions
In-Reply-To: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
References: <BB1193B3-F5CF-4E56-933D-77F08E9EF0F5@univie.ac.at>
Message-ID: <947BFB2F-A893-417B-A043-07CE71F6F97E@gmail.com>

Hi Bob,

pred_gff is a way to get models MAKER cannot run into the analysis. Input to pred_gff will not get hints since MAKER is not running the program. Setting augustus_species allows MAKER to run Augustus with and without hints and then those models compete against each other. You cannot just run with hints as the raw model is also used as a filter to help reduce false positive gene models that result from bad hints. If the gff3 you are providing is the same as the MAKER run of Augustus, I would recommend not providing it. If it is different in some way, then you can leave it in.  If you run under MPI (it?s ok to run MPI on a single machine), then MAKER will parallelize the Augustus run by running multiple configs and contig chunks at the same time.

Thanks,
Carson





> On Oct 11, 2017, at 1:42 PM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hello,
> 
> I would like to run maker with a custom set of ab initio predictions (based on hints given to augustus from RNAseq data), but allowing it to incorporate EST and protein data to make an additional run of augustus using hints derived from those alignments. 
> 
> My gene prediction section of the maker_opts.ctl file looks like this:
> ...
> augustus_species=all_combined #Augustus gene prediction species model
> ...
> pred_gff=../ab_initio_predictions/all_combined.augustus_masked.gff3 #ab-initio predictions from an external GFF3 file
> model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
> est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
> protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
> ?
> 
> It seems as though even if pred_gff is set, augustus will still be run for ab initio predictions with no hints if an augustus_species setting is present. I was curious if there was any way around this, partly because custom ab initios could improve my annotation and also because the ab initio step can take long.
> 
> Thanks for your help!
> 
> Bob
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Fri Oct 13 09:50:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:50:26 -0600
Subject: [maker-devel] Maker problem
In-Reply-To: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
References: <CAFrHSsXhtPQ+2LEO+qH=oBzfy6XNr9wT=UmRcOGgTTv41-cd6Q@mail.gmail.com>
Message-ID: <FE4BF464-D049-415D-9AC2-D013B0FB727B@gmail.com>

If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.

Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER

Example ?> 
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta

If it still fails, you now have a test file and command you can send to Mario Stanke (mario.stanke at uni-greifswald.de <mailto:mario.stanke at uni-greifswald.de>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.

?Carson


> On Oct 12, 2017, at 1:37 AM, Jan FABI <jan.nagel at fabi.up.ac.za> wrote:
> 
> Dear Maker team
> 
> I am experiencing a problem while running maker and cannot find a solution to it online. 
> 
> I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. 
> 
> This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. 
> 
> I include the relevant portion of the log below. Could you help me determine the cause of this error.
> 
> 
> 
> setting up GFF3 output and fasta chunks
> preparing ab-inits
> running  augustus.
> #--------- command -------------#
> Widget::augustus:
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=26570
> 
> /home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
>     Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx-VirtualBox
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:0, tier_type:2
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 
> 
> -- 
> Regards 
> Jan Nagel
> ----------------------------------------------------------------------
> PhD Genetics student
> Department of Genetics
> Forestry and Agricultural Biotechnology Institute (FABI) 
> FABI 1, Room 1-55
> University of Pretoria
> 74 Lunnon Rd. Hillcrest
> 0002
> Gauteng Province
> South Africa
> 
> Email : jan.nagel at fabi.up.ac.za <mailto:jan.nagel at fabi.up.ac.za>
> 
> Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961 <http://www.fabinet.up.ac.za/index.php/people-profile?profile=961>
> This message and attachments are subject to a disclaimer.
> Please refer to http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf <http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf> for full details.
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 09:56:43 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 09:56:43 -0600
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
Message-ID: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>

Both transcript and protein evidence will go into the AED calculation for overlap support. So in both cases the chosen model had better overlap (protein evidence will not count toward the eAED overlap calculation if it is out of frame with the model it is supposed to be supporting). The larger merged model generates a clutering affect on it?s evidence, so it?s evidence set for AED calculation is slightly different than the SNAP and Augustus model would generate. In both cases, I think GeneMark is hurting more than it is helping. You may want to just drop it from the analysis (unless it?s a fungi, I often find GeneMark can have that affect).

?Carson


> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi there,
> 
> I was visualising the annotations and I realised that in some cases, what it seems to be a gene is splitted according to one of the gene models, despite that the other 2, est2genome and prot2genome suggest that it isn't the case.
> 
> <split-gene.png>
> 
> Although the opposite also happens.
> 
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one from Genemark.
> 
> How much weight does carry the RNAseq and protein data on this decision (if any)?
> How exactly is the final gene selected?
> 
> Cheers,
> Xabi
> 
> -- 
> Xabier V?zquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 13 10:56:30 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Oct 2017 10:56:30 -0600
Subject: [maker-devel] jbrowse not working
In-Reply-To: <CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
References: <CAOXM=CV8iwX_SV4t3TiA5FmpgzitvGwmUSGxN1KyzbrNCO9X2w@mail.gmail.com>
	<83AFE420-D54D-4CE8-833F-DE6CCC34A229@gmail.com>
	<CAOXM=CVQYHph4Dt+KZd62sTx9ceCEQYxPoWQCr-ZZGJh+SJ=eA@mail.gmail.com>
Message-ID: <2D6E11BC-6853-458D-AEB1-12EF74D041A3@gmail.com>

The master_datastore_index.log file has a list of failed and finished contigs.  You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.

Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it?s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).

You will need to see if you can identify which contig file is truncated and rerun it.

?Carson






> On Oct 9, 2017, at 10:42 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> Thanks for the reply
> 
> I generated the off with this command gff3_merge ?d dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
> I had to rerun browse with the following command
> 
> maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb
> 
> Although its showing
> 
> WARNING: No matching features found for mRNA I don't know what it means
> 
> I don't understand what it means
> 
> 
> Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host
> 
> 
> The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?
> 
> 
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it?s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.
> 
> Thanks,
> Carson
> 
> 
> 
> 
>> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com <mailto:eennadi at gmail.com>> wrote:
>> 
>> Please,
>> I ran the command line
>> 
>> maker2jbrowse muc1_genome_snap2.all.gff
>> 
>> The command created some folders. However, at the end it read
>> No reference sequences defined in configuration, nothing to do.
>> 
>> Please what does it mean? How can I view it in jbrowse. 
>> 
>> Thanks
>> 
>> 
>> Nnadi Nnaemeka Emmanuel
>> Department of Microbiology,
>> Faculty of Natural and Applied Science,
>> Plateau State University, Bokkos, Plateau State, Nigeria.
>> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> 

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From xvazquezc at gmail.com  Fri Oct 13 14:26:40 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Sat, 14 Oct 2017 07:26:40 +1100
Subject: [maker-devel] choosing the right gene model
In-Reply-To: <821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
References: <CAL0hg4GkjJf1hacE7pTQyg1sNyWMFb5pMaMZ_zVN-8TqM8TTBw@mail.gmail.com>
	<821CB4FC-5571-41B1-AB2F-5FDD691C49D9@gmail.com>
Message-ID: <CAL0hg4Hxgrfhbah+7euuQV0YSCjYkV+WqxVu4_QYyf38pYts3Q@mail.gmail.com>

Actually, it's a fungal genome. Although not very typical, almost half of
it are repeats. Worth mention that Genemark generates a lot of predictions
that overlap LTRs and other complex repeats, something that neither SNAP or
Augustus do. Have you seen this before?

On 14 Oct. 2017 02:56, "Carson Holt" <carsonhh at gmail.com> wrote:

> Both transcript and protein evidence will go into the AED calculation for
> overlap support. So in both cases the chosen model had better overlap
> (protein evidence will not count toward the eAED overlap calculation if it
> is out of frame with the model it is supposed to be supporting). The larger
> merged model generates a clutering affect on it?s evidence, so it?s
> evidence set for AED calculation is slightly different than the SNAP and
> Augustus model would generate. In both cases, I think GeneMark is hurting
> more than it is helping. You may want to just drop it from the analysis
> (unless it?s a fungi, I often find GeneMark can have that affect).
>
> ?Carson
>
>
> On Oct 12, 2017, at 12:09 AM, Xabier V?zquez-Campos <xvazquezc at gmail.com>
> wrote:
>
> Hi there,
>
> I was visualising the annotations and I realised that in some cases, what
> it seems to be a gene is splitted according to one of the gene models,
> despite that the other 2, est2genome and prot2genome suggest that it isn't
> the case.
>
> <split-gene.png>
>
> Although the opposite also happens.
>
> <merged-gene.png>
> ?
> For some reason, the "out of place" model is always (or almost) the one
> from Genemark.
>
> How much weight does carry the RNAseq and protein data on this decision
> (if any)?
> How exactly is the final gene selected?
>
> Cheers,
> Xabi
>
> --
> Xabier V?zquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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From z2.stewart at qut.edu.au  Sat Oct 14 23:02:08 2017
From: z2.stewart at qut.edu.au (ZACHARY STEWART)
Date: Sun, 15 Oct 2017 05:02:08 +0000
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
Message-ID: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>

Hello MAKER team,


I am hoping I could have a bit of your time if that isn't a problem. I am currently performing the advanced repeat library construction as described on the MAKER wiki, and everything appears to work as expected until I reach "2.1.5 Building examplars". At this point I encounter a problem previously documented in the Google group (title: advanced repeat masking library constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta" and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify what you meant by simplifying the sequence names. The genomic contig names are in a format such as ">001676F" and I modified the MITE library to have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]" which I have not tried changing since I suspect the name is important for later reassociation. If you could point me in the right direction that would be very appreciated.


Regards,

Zac.
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From eennadi at gmail.com  Sun Oct 15 15:32:10 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Sun, 15 Oct 2017 22:32:10 +0100
Subject: [maker-devel] Backlash running through my sequence
Message-ID: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>

Hi all,
I am trying to running annotation on some of my sequences but noticed that
i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From xvazquezc at gmail.com  Mon Oct 16 01:26:56 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Mon, 16 Oct 2017 18:26:56 +1100
Subject: [maker-devel] Advanced repeat library construction - CRL step 4
 assistance
In-Reply-To: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
References: <SYXPR01MB0880CB6E6121CDD444B74505FE4E0@SYXPR01MB0880.ausprd01.prod.outlook.com>
Message-ID: <CAL0hg4Gz=vfaDkQEb3J-JPDw0TiRsmH2Fae2YsKX5AtZe0YYjA@mail.gmail.com>

Hi Zac,
The contig names you indicate shouldn't give any problems. And if you
changed the names of MITE.lib right after creation and before using it
downstream, it shouldn't be an issue.

Have you confirmed if the prior blastx output has any results?

Also, be sure you use the same version of makeblastdb and blastx/blastn. I
remember reading before running the protocol for first time that in some
cases, switching versions could give problems.
And be careful if you copy/paste from the wiki page, there are a few typos
and dashes instead of minus characters in the command line option flags,
all of which will result in errors

Xabi

On 15 October 2017 at 16:02, ZACHARY STEWART <z2.stewart at qut.edu.au> wrote:

> Hello MAKER team,
>
>
> I am hoping I could have a bit of your time if that isn't a problem. I am
> currently performing the advanced repeat library construction as described
> on the MAKER wiki, and everything appears to work as expected until I reach
> "2.1.5 Building examplars". At this point I encounter a problem previously
> documented in the Google group (title: advanced repeat masking library
> constructions & rna-seq assembly choices) where the "Inner_Seq_For_BLAST.fasta"
> and "lLTRs_Seq_For_BLAST.fasta" are empty. I was hoping you could clarify
> what you meant by simplifying the sequence names. The genomic contig names
> are in a format such as ">001676F" and I modified the MITE library to
> have names like ">mite1, >mite2" etc. The passed_outinner_sequence.fasta
> has sequence names such as ">000021F_(dbseq-nr_766)_[918983,922225]"
> which I have not tried changing since I suspect the name is important for
> later reassociation. If you could point me in the right direction that
> would be very appreciated.
>
>
> Regards,
>
> Zac.
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From yuejiaxing at gmail.com  Mon Oct 16 02:54:42 2017
From: yuejiaxing at gmail.com (Jia-Xing Yue)
Date: Mon, 16 Oct 2017 10:54:42 +0200
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>

Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning
message about uninitialized value (see the warning message below) although
still finished the installation.

[jxyue at paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/bu
ild/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm
line 3082.
Use of uninitialized value $line in substitution (s///) at
/home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/
cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors
about cannot find my specified snaphmm model for the annotation, despite
that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the
"maker_opts.ctl" file and this configuration information has been
successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap
/home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm
/tmp/maker_m8TVEQ/chrI.abinit_masked.0 >
/tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap
S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta >
/tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening
file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot
about the path to  my specified hmm file and instead looks for this file in
its default installation location)

It is worth noting that the parallel installation and run with
maker-3.00.0-beta finish smoothly without any problem. So I suspect both
the installation warning and the executing error are caused by the changes
during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check
about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker
(e.g. 3.00.0-beta in this particular case) when the user finish the
registration in the maker download page? This will help users to roll back
to older version when needed.  Also this helps for the version control when
other developers develop annotation pipelines that use maker as a
dependency package. Thanks for the consideration!


Best,
Jia-Xing

-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Facult? de M?decine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/
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From carsonhh at gmail.com  Mon Oct 16 10:20:32 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 16 Oct 2017 10:20:32 -0600
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
Message-ID: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



> On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi all,
> I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
>  I attached the sequence
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications><sample_1.fasta>

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From cjfields at illinois.edu  Tue Oct 17 13:11:39 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 17 Oct 2017 19:11:39 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
Message-ID: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson Holt <carsonhh at gmail.com>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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From carsonhh at gmail.com  Tue Oct 17 13:33:26 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Oct 2017 13:33:26 -0600
Subject: [maker-devel] maker-devel Digest, Vol 113, Issue 13
In-Reply-To: <CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
References: <mailman.4.1508103335.987018.maker-devel_yandell-lab.org@box290.bluehost.com>
	<CAETgyPQw_2-dYiLHz3_ZSFA2ZhdM52O7vS480PXPZNPaZa75uw@mail.gmail.com>
Message-ID: <30F2FDFE-3B4E-4951-89D8-63C2FC772B63@gmail.com>

Thanks. The map_fasta_ids script was empty in the bin directory for some reason, so the installer through an error because it could not find the #!/usr/bin/perl line. I have put it back in the bin directory where it was supposed to be and the issue goes away for the install.

For the second issue, I think I found it and have updated a new tar ball to the website.

Also here is a link to download the old 3.00-beta, although I would not recommend making it part of a pipeline because version 3 is still beta and still has bugs (you should use 2.31.9 instead for piplines).  ?> http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz <http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz>

?Carson


 
> On Oct 16, 2017, at 2:54 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
> 
> Dear maker developers,
> 
> I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation. 
> 
> [jxyue at paralog src]$ ./Build install
> Building MAKER
> Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
> Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
> Installing MAKER...
> Building MAKER
> ...
> 
> Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
> #-------------------------------#
> 
> # (my comment: up to now everything looks fine)
> ....
> 
> running  snap.
> #--------- command -------------#
> Widget::snap:
> /home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
> /maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
> #-------------------------------#
> ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
> ZOE library version 2017-03-01
> ERROR: Snap failed
> --> rank=NA, hostname=paralog.itc.unipi.it <http://paralog.itc.unipi.it/>
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chrI
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chrI
> 
> examining contents of the fasta file and run log
> 
> # (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)
> 
> It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!
> 
> Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!
> 
> 
> Best,
> Jia-Xing
> 
> -- 
> Jia-Xing Yue 
> 
> Population Genomics and Complex Traits Group
> Tour Pasteur 8eme etage
> Facult? de M?decine
> Institute for Research on Cancer and Aging, Nice (IRCAN)
> CNRS UMR 7284 - INSERM U 1081 - Universit? C?te d?Azur (UCA)
> 28 Avenue de Valombrose
> 06107 NICE Cedex 2
> France
> 
> Personal website: http://www.iamphioxus.org/ <http://www.iamphioxus.org/>
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From patrick.tranvan at unil.ch  Wed Oct 18 05:47:35 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Wed, 18 Oct 2017 11:47:35 +0000
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>,
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <1508327278733.19140@unil.ch>

Hi Carson,


1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?


2) I am trying to annotate a 1GB specie but it's superslow.

I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ?

Cheers,

Patrick Tran Van


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From carsonhh at gmail.com  Wed Oct 18 09:09:10 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 18 Oct 2017 09:09:10 -0600
Subject: [maker-devel] MPI vs multiple instance for speed
In-Reply-To: <1508327278733.19140@unil.ch>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
	<1508327278733.19140@unil.ch>
Message-ID: <486FE3D5-0902-4B05-A3E1-96642C68E422@gmail.com>

MAKER can coordinate parallelization under MPI in a way it can?t even with multiple simultaneous runs. Because processes can comunicate among themselves under MPI, MAKER can break larger contigs into chunks or even pull off individual steps and pass them onto another processor, then receive the results back from that processor. So multiple BLAST, RepeatMasker, Exonerate, and prediction processes can all run at the same time for the same contig. Then they all pass their result back to the parent process so it can produce output for that contig. MPI was chosen as the parallelization framework rather than threads because it works both within a single machine as well as across multiple machines, so you can scale up to hundreds of processes if needed.

?Carson


> On Oct 18, 2017, at 5:47 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi Carson, 
> 
> 1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?
> 
> 2) I am trying to annotate a 1GB specie but it's superslow.
> I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ? 
> 
> Cheers,
> 
> Patrick Tran Van
> 
> 

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From jhumann at wsu.edu  Wed Oct 18 14:38:41 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Wed, 18 Oct 2017 20:38:41 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
Message-ID: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>

Hello,

I was wondering if there was any way to enable the '-fix_nucleotides' option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu


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From robert.zimmermann at univie.ac.at  Thu Oct 19 09:25:08 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:25:08 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
Message-ID: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>

Hi Maker Developers,

I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.

Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?

Thanks for your help!

Best,
Bob

?

Department of Molecular Evolution and Development
Universit?t Wien
Althanstra?e 14 (UZA I), Zimmer 2.019 
1090 Vienna
Austria

+43 1 427757002




From robert.zimmermann at univie.ac.at  Thu Oct 19 09:28:17 2017
From: robert.zimmermann at univie.ac.at (Bob Zimmermann)
Date: Thu, 19 Oct 2017 17:28:17 +0200
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
Message-ID: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>

Correction to the above numbers, the median lengths are 1414 and 1256.

> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Hi Maker Developers,
> 
> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
> 
> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
> 
> Thanks for your help!
> 
> Best,
> Bob
> 
> ?
> 
> Department of Molecular Evolution and Development
> Universit?t Wien
> Althanstra?e 14 (UZA I), Zimmer 2.019 
> 1090 Vienna
> Austria
> 
> +43 1 427757002
> 




From carsonhh at gmail.com  Thu Oct 19 09:44:07 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 09:44:07 -0600
Subject: [maker-devel] Fewer gene models output with a superset of EST
 evidence
In-Reply-To: <CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
References: <B9BD41C0-8C50-44BE-8139-1C8BD1B32FF6@univie.ac.at>
	<CD12BD68-2C83-44DA-B8F7-ACEAE83B776B@univie.ac.at>
Message-ID: <62F04A76-F3F1-4044-B4AD-129B15A9EEB2@gmail.com>

You should look at both in a browser to get a better idea of what?s going on. What MAKER does is take the evidence given, clusters it (strand specific clustering) then uses the transcript evidence as intron hints to the predictors and protein alignments as exon hints (will also use polished protein hints to generate intron hints in the absence of transcript intron hints). Finally it uses overlapping transcript evidence to generate UTR. So look at it in a browser. See if the apparent overlap clusters are different in extent, also look for mRNA-seq evidence being merged. If the cluster is falsely merging between two loci because the mRNA-seq is merged, one of two things will happen you will get multiple models since the predictor can?t make a single model work within the cluster using the hints, or you will get a model with a really long UTR that is blocking other models from existing in the region. Also as depending on the mRNA-seq evidence coming in, you may be generating false models because of noise in the data. Essentially everything is transcribed at a basal level, so as you get more and more mRNA-seq, you generate more and more spurious alignments. So more evidence might gernate fewer long alignments for true loci or by falsely merging genes while simultaneously adding a number of very short spurious results.

?Carson



> On Oct 19, 2017, at 9:28 AM, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
> 
> Correction to the above numbers, the median lengths are 1414 and 1256.
> 
>> On 19 Oct 2017, at 17:25, Bob Zimmermann <robert.zimmermann at univie.ac.at> wrote:
>> 
>> Hi Maker Developers,
>> 
>> I have been playing around with several data sets as input to annotate our newly reassembled genome. We have 3 RNA seq datasets which have been assembled into de novo transcripts using Trinity. These are input into the maker pipeline along with protein evidence. What is strange is that when I run maker with the de novo transcripts from a single set, I optain more maker transcripts than when I run with a combined set (1619 vs 1450 on one chromosome) and they are longer (median transcript length 1619 vs 1450, IQR 872-2160 vs 667-2026). It might make sense if they were more and shorter if the additional evidence was joining transcripts, but this would indicate that it is not the case.
>> 
>> Therefore I?m trying to understand the algorithm. From what I understand if it finds evidence for an ab initio prediction for which the internal splice junctions agree, then it is considered for improvement. Why, then, if my combined set is a strict superset of the single set, do i get more transcripts with the single set?
>> 
>> Thanks for your help!
>> 
>> Best,
>> Bob
>> 
>> ?
>> 
>> Department of Molecular Evolution and Development
>> Universit?t Wien
>> Althanstra?e 14 (UZA I), Zimmer 2.019 
>> 1090 Vienna
>> Austria
>> 
>> +43 1 427757002
>> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Thu Oct 19 11:32:44 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 11:32:44 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Thu Oct 19 12:46:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 19 Oct 2017 12:46:17 -0600
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
	<SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>
Message-ID: <052F801C-3B37-4B0F-B40A-A905F5F2B1CE@gmail.com>

Yes. That is the current version.

?Carson

> On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?
>  
> Jodi
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Thursday, October 19, 2017 10:33 AM
> To: Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] fix nucleotides option on MWAS
>  
> Hi Jodi,
>  
> I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).
>  
> Somewhere inside the script there will be a line like this ?>
>  $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
>  
> You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.
>  
> Thanks,
> Carson
>  
>  
> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>> wrote:
>  
> Hello,
>  
> I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
>  
> ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
>  
> The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>
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From jhumann at wsu.edu  Thu Oct 19 12:45:43 2017
From: jhumann at wsu.edu (Humann, Jodi Lynn)
Date: Thu, 19 Oct 2017 18:45:43 +0000
Subject: [maker-devel] fix nucleotides option on MWAS
In-Reply-To: <F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
References: <SN2PR01MB2014720139574F690F0A7741AA4D0@SN2PR01MB2014.prod.exchangelabs.com>
	<F51EB371-989D-4F6D-BAA3-41BD06DD342D@gmail.com>
Message-ID: <SN2PR01MB201492C64FA59A9CE9069EFAAA420@SN2PR01MB2014.prod.exchangelabs.com>

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?

Jodi

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <jhumann at wsu.edu>
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] fix nucleotides option on MWAS

Hi Jodi,

I didn?t even know anyone else even had an MWAS server running (I?ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (?/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this ?>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It?s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N?s.

Thanks,
Carson


On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu<mailto:jhumann at wsu.edu>> wrote:

Hello,

I was wondering if there was any way to enable the ??fix_nucleotides? option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

Thanks,
Jodi

Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
jhumann at wsu.edu<mailto:jhumann at wsu.edu>


_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=sjiBWge-tc_aDILjhkHIpQ&m=7nOgiwSuJW7wKtU5_OZ2RZDzFskBA7Yk8WLfake--xA&s=lcaUdUqhNL9Ec9r5vegW06NCls9G3OQ_LnGwBcmY87U&e=>

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From eennadi at gmail.com  Mon Oct 23 07:30:07 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 23 Oct 2017 14:30:07 +0100
Subject: [maker-devel] Contamination report from NCBI
Message-ID: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>

Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this
contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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SUBID     	BioProject	BioSample	Organism
--------------------------------------------------------
SUB3124577	PRJNA414658	SAMN07821433	Mucuna pruriens

[] We ran your sequences through our Contamination Screen. The screen found 
contigs that need to be trimmed and/or excluded. Please adjust the 
sequences appropriately and then resubmit your sequences. After you remove the 
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

Note that hits in eukaryotic genomes to mitochondrial sequences can be ignored 
when specific criteria are met. Those criteria are explained below.

Note that mismatches between the name of the adaptor/primer identified in the screen 
and the sequencing technology used to generate the sequencing data should not be used 
to discount the validity of the screen results as the adaptors/primers of many 
different sequencing platforms share sequence similarity.



[] Some of the sequences hit primers or adaptors used in Illumina or 
454 or other sequencing strategies or platforms.  Primers at the 
end of a sequence should be removed. However, if primers are 
present within sequences then you should strongly consider 
splitting the sequences at the primers because the primer sequence 
could have been the region of overlap, causing a misassembly.


Screened 26,016 sequences, 396,641,426 bp.
Note: 5,610 sequences with runs of Ns 10 bp or longer (or those longer that 20 MB) were split before screening.
428 sequences with locations to mask/trim
(31 split spans to exclude, 397 split spans with locations to mask/trim)

Trim:
Sequence name, length, span(s), apparent source
contig_10109	13138	13078..13138	adaptor:NGB00847.1
contig_10200	20270	1..76	adaptor:NGB00847.1
contig_10202	22517	1..44	adaptor:NGB00360.1
contig_10218	55661	55592..55661	adaptor:NGB00847.1
contig_10283	11575	1..79	adaptor:NGB00847.1
contig_1038	91134	91073..91134	adaptor:NGB00360.1
contig_104	10061	10005..10061	adaptor:NGB00360.1
contig_10405	24076	1..43	adaptor:NGB00847.1
contig_10425	16694	16639..16694	adaptor:NGB00360.1
contig_10447	37445	37233..37445	adaptor:NGB00360.1
contig_10466	19368	1..52	adaptor:NGB00847.1
contig_10576	12053	12003..12053	adaptor:NGB00360.1
contig_1059	34516	34457..34516	adaptor:NGB00847.1
contig_106	49997	1..45	adaptor:NGB00360.1
contig_10695	27664	1..38	adaptor:NGB01029.1
contig_10753	12481	12413..12481	adaptor:NGB00847.1
contig_10822	33522	33441..33522	adaptor:NGB00847.1
contig_1083	10637	1..23	adaptor:NGB01096.1
contig_10851	36752	36682..36752	adaptor:NGB00360.1
contig_10878	27925	27848..27925	adaptor:NGB00360.1
contig_10965	23597	1..57	adaptor:NGB00360.1
contig_10968	7413	1..40	adaptor:NGB00847.1
contig_1099	35847	1..70	adaptor:NGB00360.1
contig_11034	10224	10166..10224	adaptor:NGB00360.1
contig_11058	32994	1..23	adaptor:NGB01088.1
contig_11138	17426	1..73	adaptor:NGB00847.1
contig_11166	6306	6266..6306	adaptor:NGB00360.1
contig_11182	26558	1..30	adaptor:NGB01096.1
contig_11216	15160	1..59	adaptor:NGB00847.1
contig_11269	14732	14655..14732	adaptor:NGB00847.1
contig_11306	28246	28199..28246	adaptor:NGB00360.1
contig_1136	28186	1..73	adaptor:NGB00847.1
contig_1141	58119	58028..58119	adaptor:NGB00847.1
contig_11416	8561	8539..8561	adaptor:NGB01088.1
contig_11504	8890	8840..8890	adaptor:NGB00360.1
contig_1158	17422	17398..17422	adaptor:NGB01088.1
contig_11647	7021	1..69	adaptor:NGB00847.1
contig_11684	17442	17418..17442	adaptor:NGB01096.1
contig_11752	38337	38314..38337	adaptor:NGB01088.1
contig_11767	6366	6324..6366	adaptor:NGB00847.1
contig_11791	22415	1..43	adaptor:NGB00847.1
contig_11792	58260	1..29	adaptor:NGB01096.1
contig_1187	39501	39462..39501	adaptor:NGB01029.1
contig_12059	10094	1..72	adaptor:NGB00360.1
contig_12130	13210	13164..13210	adaptor:NGB00360.1
contig_12164	17561	17539..17561	adaptor:NGB01096.1
contig_12169	14178	139..196	adaptor:NGB00360.1
contig_12183	15822	61..112	adaptor:NGB00360.1
contig_12266	11704	11640..11704	adaptor:NGB00360.1
contig_12300	9550	9360..9550	adaptor:NGB01088.1
contig_12324	49997	49891..49997	adaptor:NGB00847.1
contig_12423	45971	45860..45918	adaptor:NGB00360.1
contig_12441	15141	1..42	adaptor:NGB00847.1
contig_12514	14655	1..69	adaptor:NGB00847.1
contig_12515	5355	5326..5355	adaptor:NGB01088.1
contig_12535	22496	22458..22496	adaptor:NGB01029.1
contig_12544	19615	19559..19615	adaptor:NGB00360.1
contig_12558	20026	20007..20026	adaptor:NGB01088.1
contig_12613	6880	6793..6880	adaptor:NGB00847.1
contig_12701	18439	18330..18382	adaptor:NGB00360.1
contig_12713	13341	13274..13341	adaptor:NGB00360.1
contig_12723	17913	1..38	adaptor:NGB01088.1
contig_12730	55277	55249..55277	adaptor:NGB01096.1
contig_12739	6792	1..48	adaptor:NGB00360.1
contig_12787	30950	1..19	adaptor:NGB01096.1
contig_1279	18699	18670..18699	adaptor:NGB01088.1
contig_12815	5168	5091..5168	adaptor:NGB00847.1
contig_12846	20753	1..70	adaptor:NGB00360.1
contig_1288	34784	1..31	adaptor:NGB01096.1
contig_12888	12204	1..23	adaptor:NGB01096.1
contig_12919	10315	1..71	adaptor:NGB00360.1
contig_13031	8972	8938..8972	adaptor:NGB01093.1
contig_13088	6275	1..22	adaptor:NGB01088.1
contig_13140	36197	1..48	adaptor:NGB00360.1
contig_13233	16414	16355..16414	adaptor:NGB00847.1
contig_1330	33261	1..44	adaptor:NGB00847.1
contig_13319	19747	1..20	adaptor:NGB01096.1
contig_13367	36004	35868..35931	adaptor:NGB00847.1
contig_13395	5338	1..79	adaptor:NGB00360.1
contig_1341	30756	30734..30756	adaptor:NGB01088.1
contig_13481	9637	9600..9637	adaptor:NGB00360.1
contig_13506	5704	5662..5704	adaptor:NGB00360.1
contig_13548	5814	79..121	adaptor:NGB00360.1
contig_13567	21576	1..47	adaptor:NGB00847.1
contig_13669	8336	1..24	adaptor:NGB01088.1
contig_13718	23500	1..25	adaptor:NGB01096.1
contig_13783	18720	1..41	adaptor:NGB00847.1
contig_13830	32395	32367..32395	adaptor:NGB01096.1
contig_13845	15572	15493..15572	adaptor:NGB00360.1
contig_13854	10932	1..48	adaptor:NGB00360.1
contig_13943	37701	37674..37701	adaptor:NGB01096.1
contig_13957	7159	1..30	adaptor:NGB01096.1
contig_14014	29735	29672..29735	adaptor:NGB00360.1
contig_14027	21418	21340..21418	adaptor:NGB00360.1
contig_14032	47642	1..53	adaptor:NGB00847.1
contig_14047	26936	1..28	adaptor:NGB01088.1
contig_14048	45832	1..22	adaptor:NGB01088.1
contig_14061	11471	1..179	adaptor:NGB01096.1
contig_14113	17661	1..67	adaptor:NGB00360.1
contig_14173	17601	1..41	adaptor:NGB00847.1
contig_1418	31840	1..248	adaptor:NGB00847.1
contig_14194	7456	7294..7456	adaptor:NGB01096.1
contig_14210	8814	1971..2025	adaptor:NGB00360.1
contig_14223	12513	12489..12513	adaptor:NGB01096.1
contig_14317	21472	21410..21472	adaptor:NGB00360.1
contig_14424	6040	5973..6040	adaptor:NGB00360.1
contig_14425	6404	6379..6404	adaptor:NGB01096.1
contig_14426	31457	31398..31457	adaptor:NGB00847.1
contig_14458	6814	6623..6814	adaptor:NGB01088.1
contig_14524	9488	9431..9488	adaptor:NGB00847.1
contig_14584	20433	1..96	adaptor:NGB00847.1
contig_1459	32979	1..32	adaptor:NGB01096.1
contig_14601	19077	1..28	adaptor:NGB01096.1
contig_14641	21747	1..45	adaptor:NGB00847.1
contig_14664	48155	48118..48155	adaptor:NGB00360.1
contig_14711	11854	11827..11854	adaptor:NGB01096.1
contig_14736	21360	1..37	adaptor:NGB01029.1
contig_14749	12830	1..33	adaptor:NGB01093.1
contig_14966	9962	9891..9962	adaptor:NGB00360.1
contig_14999	5248	1..41	adaptor:NGB00360.1
contig_15010	17976	1..43	adaptor:NGB00360.1
contig_15011	26484	26462..26484	adaptor:NGB01096.1
contig_15017	9331	9291..9331	adaptor:NGB00360.1
contig_1503	63533	1..33	adaptor:NGB01096.1
contig_15032	32240	32157..32240	adaptor:NGB00847.1
contig_15060	15050	15010..15050	adaptor:NGB00847.1
contig_15065	13062	12996..13062	adaptor:NGB00360.1
contig_15070	29943	1..29	adaptor:NGB01096.1
contig_15132	20431	1..71	adaptor:NGB00847.1
contig_15169	7086	7051..7086	adaptor:NGB00846.1
contig_15174	19921	1..23	adaptor:NGB01096.1
contig_15194	16100	16039..16100	adaptor:NGB00847.1
contig_15212	9272	1..50	adaptor:NGB00847.1
contig_15215	15591	1..58	adaptor:NGB00360.1
contig_15271	37699	37647..37699	adaptor:NGB00847.1
contig_15276	11087	11031..11087	adaptor:NGB00847.1
contig_15309	10118	1..42	adaptor:NGB00847.1
contig_15320	7963	7901..7963	adaptor:NGB00847.1
contig_15334	5683	1..36	adaptor:NGB00846.1
contig_15364	17306	76..139	adaptor:NGB00847.1
contig_15374	28301	28263..28301	adaptor:NGB00360.1
contig_15377	10470	10428..10470	adaptor:NGB00360.1
contig_15398	24069	23999..24069	adaptor:NGB00847.1
contig_15500	9289	9271..9289	adaptor:NGB01096.1
contig_15507	25565	1..22	adaptor:NGB01088.1
contig_15523	5782	5762..5782	adaptor:NGB01088.1
contig_15529	10225	10143..10225	adaptor:NGB00360.1
contig_15569	9645	9612..9645	adaptor:NGB01090.1
contig_15596	7163	1..42	adaptor:NGB00360.1
contig_15605	18521	1..31	adaptor:NGB01096.1
contig_15672	8446	1..213	adaptor:NGB01088.1
contig_15686	22141	58..90	adaptor:NGB00847.1
contig_15708	18098	17996..18098	adaptor:NGB00847.1
contig_15736	18284	18252..18284	adaptor:NGB01096.1
contig_15777	17192	1..45	adaptor:NGB00360.1
contig_15812	8602	1..77	adaptor:NGB00360.1
contig_15959	10936	10913..10936	adaptor:NGB01096.1
contig_15972	11324	1..71	adaptor:NGB00360.1
contig_15974	24312	24243..24312	adaptor:NGB00847.1
contig_16057	8838	8775..8838	adaptor:NGB00847.1
contig_16088	7608	1..71	adaptor:NGB00360.1
contig_16142	10392	1..53	adaptor:NGB00847.1
contig_1617	14870	255..310	adaptor:NGB00360.1
contig_16183	9226	9205..9226	adaptor:NGB01088.1
contig_16188	62666	62586..62666	adaptor:NGB00847.1
contig_16370	7868	1..42	adaptor:NGB00847.1
contig_16416	19512	1..21	adaptor:NGB01088.1
contig_1645	25016	24951..25016	adaptor:NGB00360.1
contig_16510	31845	31776..31845	adaptor:NGB00847.1
contig_16529	17342	1..45	adaptor:NGB00360.1
contig_16558	9338	9097..9338	adaptor:NGB00360.1
contig_16573	6590	6521..6590	adaptor:NGB00847.1
contig_16608	7397	7324..7397	adaptor:NGB00847.1
contig_16631	11055	1..50	adaptor:NGB00360.1
contig_16641	5482	1..190	adaptor:NGB01088.1
contig_1667	35244	35200..35244	adaptor:NGB01029.1
contig_16682	14500	1..71	adaptor:NGB00847.1
contig_16699	6216	6148..6216	adaptor:NGB00360.1
contig_16734	12674	12625..12674	adaptor:NGB00360.1
contig_16790	6341	1..51	adaptor:NGB00360.1
contig_16807	7512	1..36	adaptor:NGB01096.1
contig_16817	20743	1..155	adaptor:NGB01088.1
contig_16839	6969	1..69	adaptor:multiple
contig_16870	10948	1..49	adaptor:NGB00847.1
contig_16880	5622	5549..5622	adaptor:NGB00360.1
contig_16889	9182	1..40	adaptor:NGB00360.1
contig_16911	6691	1..28	adaptor:NGB01088.1
contig_16921	9432	9358..9432	adaptor:NGB00360.1
contig_16951	14285	14262..14285	adaptor:NGB01088.1
contig_17021	12242	1..75	adaptor:NGB00360.1
contig_17092	22712	1..64	adaptor:NGB00360.1
contig_17147	7706	7685..7706	adaptor:NGB01096.1
contig_17195	15668	15643..15668	adaptor:NGB01096.1
contig_17214	7881	7819..7881	adaptor:NGB00847.1
contig_17299	7861	7830..7861	adaptor:NGB01088.1
contig_17344	8915	8765..8823	adaptor:NGB00360.1
contig_17361	8425	1..26	adaptor:NGB01096.1
contig_17422	11017	10964..11017	adaptor:NGB00360.1
contig_17471	5988	5964..5988	adaptor:NGB01096.1
contig_17505	10208	1..74	adaptor:NGB00360.1
contig_17506	6091	1..61	adaptor:NGB00360.1
contig_17520	6084	6028..6084	adaptor:NGB00360.1
contig_17538	5796	5766..5796	adaptor:NGB01096.1
contig_17558	7066	6837..7066	adaptor:NGB01080.1
contig_17561	15165	1..206	adaptor:NGB01083.1
contig_17594	6976	1..26	adaptor:NGB01088.1
contig_17655	14371	14177..14371	adaptor:NGB01088.1
contig_17671	17801	1..50	adaptor:NGB00847.1
contig_17680	5752	5693..5752	adaptor:NGB00847.1
contig_17738	6456	1..44	adaptor:NGB00360.1
contig_17741	10917	10889..10917	adaptor:NGB01096.1
contig_17775	5928	1..79	adaptor:NGB00847.1
contig_17804	11597	11562..11597	adaptor:NGB00846.1
contig_17872	11319	11278..11319	adaptor:NGB00847.1
contig_17876	5647	5613..5647	adaptor:NGB01083.1
contig_17925	9923	1..22	adaptor:NGB01088.1
contig_17938	5246	1..23	adaptor:NGB01088.1
contig_18016	8044	1..29	adaptor:NGB01096.1
contig_18017	6668	6647..6668	adaptor:NGB01096.1
contig_18044	11330	11299..11330	adaptor:NGB01096.1
contig_18049	10560	1..88	adaptor:NGB00847.1
contig_18173	12243	1..159	adaptor:NGB01096.1
contig_18175	8788	8765..8788	adaptor:NGB01096.1
contig_18177	11418	11340..11418	adaptor:multiple
contig_18182	11901	11832..11901	adaptor:NGB00847.1
contig_18201	6059	6038..6059	adaptor:NGB01096.1
contig_18222	11216	11136..11216	adaptor:NGB00847.1
contig_18228	8386	8361..8386	adaptor:NGB01088.1
contig_18321	5922	5897..5922	adaptor:NGB01096.1
contig_18370	5400	5085..5116	adaptor:NGB00747.1
contig_18453	5849	1..38	adaptor:NGB00360.1
contig_1846	23210	1..64	adaptor:NGB00360.1
contig_18479	5209	1..44	adaptor:NGB00360.1
contig_18486	5749	5726..5749	adaptor:NGB01088.1
contig_18488	5217	1..19	adaptor:NGB01088.1
contig_1969	65776	1..60	adaptor:NGB00360.1
contig_197	9215	1..83	adaptor:NGB00847.1
contig_1977	13765	1..35	adaptor:NGB01093.1
contig_1999	53427	53398..53427	adaptor:NGB01096.1
contig_2125	11803	11769..11803	adaptor:NGB01083.1
contig_2151	9544	1..37	adaptor:NGB01029.1
contig_2179	38972	1..67	adaptor:NGB00360.1
contig_2186	31110	30935..31110	adaptor:NGB01096.1
contig_2203	60314	60124..60187	adaptor:NGB00847.1
contig_2278	33271	1..36	adaptor:NGB01090.1
contig_2305	17957	1..58	adaptor:NGB00360.1
contig_2361	48816	48764..48816	adaptor:NGB00847.1
contig_242	49604	49535..49604	adaptor:NGB00360.1
contig_2429	76318	76242..76318	adaptor:NGB00847.1
contig_2430	70439	70373..70439	adaptor:NGB00847.1
contig_2459	63920	1..96	adaptor:NGB00847.1
contig_2485	31300	31260..31300	adaptor:NGB00360.1
contig_2508	25152	25095..25152	adaptor:NGB00847.1
contig_2650	36583	1..58	adaptor:NGB00847.1
contig_2668	22089	22052..22089	adaptor:NGB01029.1
contig_2735	13614	1..19	adaptor:NGB01088.1
contig_2781	50403	1..70	adaptor:NGB00847.1
contig_2800	30768	22802..22846	adaptor:NGB00360.1
contig_2824	44109	1..38	adaptor:NGB00847.1
contig_2888	19121	1..89	adaptor:NGB00360.1
contig_2900	36871	1..32	adaptor:NGB01088.1
contig_2949	25959	25916..25959	adaptor:NGB00360.1
contig_2970	20833	1..46	adaptor:NGB00360.1
contig_2986	16429	1..43	adaptor:NGB00360.1
contig_3069	38956	38904..38956	adaptor:NGB00847.1
contig_3106	9135	1..87	adaptor:NGB00847.1
contig_3124	70101	70072..70101	adaptor:NGB01088.1
contig_3129	30402	30379..30402	adaptor:NGB01088.1
contig_3147	10611	10586..10611	adaptor:NGB01096.1
contig_3190	117726	117687..117726	adaptor:NGB01029.1
contig_3243	44291	44273..44291	adaptor:NGB01096.1
contig_3276	57911	1..42	adaptor:NGB00360.1
contig_341	67008	1..22	adaptor:NGB01096.1
contig_3542	16855	1..60	adaptor:NGB00847.1
contig_3595	29288	1..79	adaptor:NGB00847.1
contig_3712	73078	1..78	adaptor:NGB00847.1
contig_3840	40472	40414..40472	adaptor:NGB00360.1
contig_3868	33875	33819..33875	adaptor:NGB00360.1
contig_3903	40080	40010..40080	adaptor:NGB00847.1
contig_3996	44010	43970..44010	adaptor:NGB00360.1
contig_4001	26085	1..73	adaptor:NGB00847.1
contig_4014	30676	30590..30676	adaptor:NGB00360.1
contig_4019	49543	1..76	adaptor:NGB00360.1
contig_4036	58848	58696..58848	adaptor:NGB00846.1
contig_4084	41308	41210..41308	adaptor:NGB00360.1
contig_4095	24801	1..70	adaptor:NGB00847.1
contig_4098	27393	1..189	adaptor:NGB01096.1
contig_410	57740	57678..57740	adaptor:NGB00360.1
contig_4172	20870	9717..9749	adaptor:NGB01096.1
contig_4318	55870	55805..55870	adaptor:NGB00360.1
contig_432	58593	58569..58593	adaptor:NGB01088.1
contig_4323	87370	87304..87370	adaptor:NGB00847.1
contig_4365	27401	27350..27401	adaptor:NGB00847.1
contig_4516	14480	1..98	adaptor:NGB00847.1
contig_452	34031	1..23	adaptor:NGB01096.1
contig_4530	63069	63006..63069	adaptor:NGB00360.1
contig_4651	67570	67518..67570	adaptor:NGB00847.1
contig_4679	20970	1..38	adaptor:NGB00360.1
contig_4686	7411	1..24	adaptor:NGB01096.1
contig_4743	37926	1..79	adaptor:NGB00360.1
contig_4765	11248	11167..11248	adaptor:NGB00360.1
contig_4801	91339	1..50	adaptor:NGB00360.1
contig_4812	37300	37121..37300	adaptor:NGB01093.1
contig_4820	80899	80862..80899	adaptor:NGB00360.1
contig_4904	9220	1..52	adaptor:NGB00847.1
contig_4916	29759	29718..29759	adaptor:NGB00847.1
contig_4924	19015	1..49	adaptor:NGB00847.1
contig_4939	23620	23574..23620	adaptor:NGB01029.1
contig_4956	40890	1..24	adaptor:NGB01088.1
contig_4994	71509	71447..71509	adaptor:NGB00847.1
contig_501	34157	34116..34157	adaptor:NGB00847.1
contig_5036	13162	1..77	adaptor:NGB00360.1
contig_5052	64212	1..170	adaptor:NGB01096.1
contig_5063	35265	35243..35265	adaptor:NGB01096.1
contig_5090	27510	27441..27510	adaptor:NGB00847.1
contig_5157	5988	5805..5988	adaptor:NGB00847.1
contig_5168	6086	6051..6086	adaptor:NGB00846.1
contig_5176	9131	1..41	adaptor:NGB00360.1
contig_5243	44178	1..88	adaptor:NGB00847.1
contig_5270	39229	39177..39229	adaptor:NGB00847.1
contig_5452	30446	1..36	adaptor:NGB00846.1
contig_5576	58918	1..34	adaptor:NGB01096.1
contig_5582	108611	1..87	adaptor:NGB00847.1
contig_5590	55235	55210..55235	adaptor:NGB01088.1
contig_5700	8246	1..82	adaptor:NGB00847.1
contig_5815	99837	1..63	adaptor:NGB00847.1
contig_5820	11616	1..202	adaptor:NGB00847.1
contig_5878	55755	1..26	adaptor:NGB01096.1
contig_59	12390	1..24	adaptor:NGB01096.1
contig_5959	11737	11532..11737	adaptor:NGB01096.1
contig_6065	11492	1..32	adaptor:NGB01088.1
contig_6067	19311	1..39	adaptor:NGB01029.1
contig_6092	14700	1..37	adaptor:NGB01029.1
contig_6194	32760	1..19	adaptor:NGB01088.1
contig_620	10761	1..206	adaptor:NGB01029.1
contig_6259	83001	1..50	adaptor:NGB00360.1
contig_6321	29279	29260..29279	adaptor:NGB01096.1
contig_6408	14690	1..74	adaptor:NGB00360.1
contig_6455	68530	68497..68530	adaptor:NGB01090.1
contig_6513	12061	11986..12061	adaptor:NGB00847.1
contig_6542	45321	1..41	adaptor:NGB00360.1
contig_6569	19579	19500..19579	adaptor:NGB00847.1
contig_6628	13125	13107..13125	adaptor:NGB01096.1
contig_6673	6733	6699..6733	adaptor:NGB01088.1
contig_6676	13298	13265..13298	adaptor:NGB01088.1
contig_6692	17411	1..43	adaptor:NGB00847.1
contig_6703	57771	1..63	adaptor:NGB00360.1
contig_6785	8258	8237..8258	adaptor:NGB01088.1
contig_6908	53004	52732..52792	adaptor:NGB00847.1
contig_6940	18777	18580..18777	adaptor:NGB00360.1
contig_6941	42032	41980..42032	adaptor:NGB00847.1
contig_6945	53258	1..71	adaptor:NGB00360.1
contig_6986	49101	1..21	adaptor:NGB01088.1
contig_701	57358	1..28	adaptor:NGB01096.1
contig_7017	41786	1..88	adaptor:NGB00360.1
contig_7035	53503	53477..53503	adaptor:NGB01096.1
contig_7046	12860	12812..12860	adaptor:NGB00360.1
contig_7081	27746	1..78	adaptor:NGB00847.1
contig_7082	26783	1..73	adaptor:NGB00847.1
contig_7083	44465	1..70	adaptor:NGB00847.1
contig_7117	33739	33661..33739	adaptor:NGB00360.1
contig_7197	5439	5361..5439	adaptor:NGB00360.1
contig_720	34826	34755..34826	adaptor:NGB00360.1
contig_7210	16719	1..30	adaptor:NGB01096.1
contig_7225	51589	51483..51519	adaptor:NGB01090.1
contig_7228	37410	1..64	adaptor:NGB00360.1
contig_7296	6652	1..80	adaptor:NGB00847.1
contig_7317	11682	1..30	adaptor:NGB01088.1
contig_7323	47612	47560..47612	adaptor:NGB00847.1
contig_7353	50534	50506..50534	adaptor:NGB01096.1
contig_7478	44000	43977..44000	adaptor:NGB01088.1
contig_7510	11029	1..22	adaptor:NGB01096.1
contig_7540	12614	12566..12614	adaptor:NGB00360.1
contig_7587	74260	74065..74260	adaptor:NGB00847.1
contig_7607	14652	1..31	adaptor:NGB01088.1
contig_7612	27455	27299..27354	adaptor:NGB00360.1
contig_7705	39772	1..49	adaptor:NGB00360.1
contig_7729	22305	1..172	adaptor:NGB00360.1
contig_7747	11568	11502..11568	adaptor:NGB00847.1
contig_7750	52785	52748..52785	adaptor:NGB01029.1
contig_7800	20628	20588..20628	adaptor:NGB00360.1
contig_7851	53514	53439..53514	adaptor:NGB00360.1
contig_7989	51399	1..97	adaptor:NGB00847.1
contig_7992	9120	9035..9120	adaptor:NGB00360.1
contig_7995	103073	103034..103073	adaptor:NGB00360.1
contig_8000	16924	1..85	adaptor:NGB00847.1
contig_8071	73728	73657..73728	adaptor:NGB00360.1
contig_809	20474	20399..20474	adaptor:NGB00360.1
contig_8139	33627	1..25	adaptor:NGB01088.1
contig_8165	17003	16958..17003	adaptor:NGB00847.1
contig_8207	30300	30275..30300	adaptor:NGB01096.1
contig_821	111683	111656..111683	adaptor:NGB01096.1
contig_8236	30705	1..70	adaptor:NGB00360.1
contig_8261	49091	1..181	adaptor:NGB00847.1
contig_8265	28139	27940..28139	adaptor:NGB00360.1
contig_8307	32654	32591..32654	adaptor:NGB00360.1
contig_8340	12953	12925..12953	adaptor:NGB01096.1
contig_8389	19738	1..75	adaptor:NGB00847.1
contig_8399	35159	1..147	adaptor:NGB01096.1
contig_8569	19455	1..38	adaptor:multiple
contig_8735	42362	42335..42362	adaptor:NGB01088.1
contig_8737	22308	1..70	adaptor:NGB00360.1
contig_8790	14216	14198..14216	adaptor:NGB01096.1
contig_8797	6889	1..95	adaptor:NGB00847.1
contig_8815	39194	1..80	adaptor:NGB00360.1
contig_886	10028	1..76	adaptor:NGB00360.1
contig_8861	12192	12145..12192	adaptor:NGB00360.1
contig_8909	11109	11042..11109	adaptor:NGB00360.1
contig_8932	8331	8281..8331	adaptor:NGB00847.1
contig_8975	8730	8671..8730	adaptor:NGB00847.1
contig_8992	12682	12661..12682	adaptor:NGB01088.1
contig_8994	7982	7950..7982	adaptor:NGB01096.1
contig_9017	8069	7896..8069	adaptor:NGB00360.1
contig_9045	35343	535..598	adaptor:NGB00847.1
contig_9082	10766	1..28	adaptor:NGB01096.1
contig_9271	17773	17750..17773	adaptor:NGB01096.1
contig_9273	12180	1..180	adaptor:NGB01096.1
contig_9287	6067	1..77	adaptor:NGB00847.1
contig_9474	33382	33060..33111	adaptor:NGB00360.1
contig_9495	19348	19274..19348	adaptor:NGB00847.1
contig_9540	30855	30836..30855	adaptor:NGB01088.1
contig_9591	10604	1..41	adaptor:NGB00847.1
contig_9628	15083	1..34	adaptor:NGB01096.1
contig_9677	5510	5486..5510	adaptor:NGB01088.1
contig_9693	9823	1..84	adaptor:NGB00847.1
contig_9825	54363	54309..54363	adaptor:NGB00847.1
contig_9863	14033	14013..14033	adaptor:NGB01088.1
contig_9993	35388	1..26	adaptor:NGB01096.1



From xvazquezc at gmail.com  Mon Oct 23 16:02:47 2017
From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=)
Date: Tue, 24 Oct 2017 09:02:47 +1100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's
actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the
contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the
"Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a
different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com> wrote:

> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this
> contamination report.
>
> Please how do I use maker to effect the correction
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier V?zquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From cjfields at illinois.edu  Mon Oct 23 17:21:06 2017
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 23 Oct 2017 23:21:06 +0000
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<CAL0hg4FTpTi04oWXv0G4tM2Px9G3O5YxQrBUUhtFXmriAkQJrw@mail.gmail.com>
Message-ID: <8B4331B5-9D10-478A-91A5-80AF702CD9CD@illinois.edu>

It looks like the adapter is primarily at the ends, which is easy to remove.  However, I agree, removing these and redoing the assembly may improve the assembly quality.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Xabier V?zquez-Campos <xvazquezc at gmail.com>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>, "Ence, daniel" <d.ence at ufl.edu>
Subject: Re: [maker-devel] Contamination report from NCBI

Hi there,
Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations
Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
Xabier V?zquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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From mmokrejs at gmail.com  Tue Oct 24 04:23:38 2017
From: mmokrejs at gmail.com (=?UTF-8?Q?Martin_MOKREJ=c5=a0?=)
Date: Tue, 24 Oct 2017 12:23:38 +0200
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
Message-ID: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>

Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
> 
> Good day.
> 
> Please I submitted my sequence to NCBI and they sent back this contamination report.
> 
> Please how do I use maker to effect the correction

-- 
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/



From eennadi at gmail.com  Tue Oct 24 04:44:20 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Tue, 24 Oct 2017 11:44:20 +0100
Subject: [maker-devel] Contamination report from NCBI
In-Reply-To: <a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
References: <CAOXM=CU2VsNA1jpJrM93CZV8jq3zeAtYVenLMKdGO16MAYm-6Q@mail.gmail.com>
	<a9f32b89-e9d5-6390-e736-b1da0e2e5cd0@gmail.com>
Message-ID: <CAOXM=CX=AiSo-u8gQ7de1KrgZLUbBZ2GXPbdU6kG3hjrUBjE1A@mail.gmail.com>

Thanks!
Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications



On Oct 24, 2017 11:23 AM, "Martin MOKREJ?" <mmokrejs at gmail.com> wrote:

> Hi Emmanuel,
>   use trimmomatic or cutadapt to remove the adapters and check the output
> file for unremoved cases. Once they are all removed redo the assembly.
> Martin
>
> Emmanuel Nnadi wrote:
> > Hello
> >
> > Good day.
> >
> > Please I submitted my sequence to NCBI and they sent back this
> contamination report.
> >
> > Please how do I use maker to effect the correction
>
> --
> Martin Mokrejs, Ph.D.
> Adapter/artefact removal from datasets based on the following technologies:
>   454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
> http://www.bioinformatics.cz/software/supported-protocols/
>
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From qwzhang0601 at gmail.com  Tue Oct 24 10:54:13 2017
From: qwzhang0601 at gmail.com (Quanwei Zhang)
Date: Tue, 24 Oct 2017 12:54:13 -0400
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
Message-ID: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>

Dear Carson:

Thank you again for your suggestions. I just get the new genome assembly of
NMR and start to do gene annotation. I understand you ideas about this. But
can I simply use the old genome transcripts as transcript evidence, and
just following the standard Maker2 pipeline? I set est2genome=1 and provide
the mRNA sequences in the fasta format for the first round training of SNAP.

For transcripts I have the following choices. I think the first choice is
more reliable and better, right?
(1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded
those sequences in fasta format.
(2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by
trinity for each sample and then get the transcripts. But I think most of
the RNA-seq should have been submitted to NCBI.

BTW, if we use the RefSeq data from NCBI, we can download the mRNA
sequences, coding sequences or protein sequences. I wonder which type of
data are the best to train the SNAP? For Augustus, we will use BUSCO to
train it.

Many thanks.

Best
Quanwei




2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> You can try using the est2genome=1 option to map the old models forward
> onto the new assembly as if they were ESTs (add a line that says
> est_forward=1 to the control file to maintain old naming and set est=1 to
> the old model transcript file). Then provide the final models as a pred_gff
> for a subsuquent run (i.e. a traditional MAKER run where you are annotating
> the new assembly with transcript and protein evidence and ab initio
> predictors). Don?t supply the old models to est= on that run.
>
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will
> change. So by doing it this way, you will at least be able to move many
> models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are
> just letting old models compete against new annotations. They will be
> rejected if they have no evidence support, or can be kept if they score
> better than alternate models from SNAP/Augustus. That way you have the
> chance to integrate old models while at the same time rejecting some old
> models that have no evidence overlap.
>
> ?Carson
>
>
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been
> assembled and annotated a few years ago. We can download the gene
> annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder
> how can I fully make use of existing annotations. On the other hand, since
> the previous genome is not very well assemblies, some genes annotation
> maybe false positives. I hope those false positive genes in previous
> annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Tue Oct 24 16:26:00 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 24 Oct 2017 16:26:00 -0600
Subject: [maker-devel] gene annotation for a better genome
In-Reply-To: <CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
References: <CAOW6FSKn__0Gcco+7V+rtv9of4hbTp=LE4J+V51LPFZ1gnm7OQ@mail.gmail.com>
	<5AFEDD05-DF02-463F-A6EE-1619A9BB968D@gmail.com>
	<CAOW6FSJRmZureS-eeidVcDgkJdTWh4DmS4xcuq2qOS19wEwtaw@mail.gmail.com>
Message-ID: <C02680FC-A5ED-4CD9-8517-3018CA1A0D69@gmail.com>

Yes. If you use est2genome it will just align the model, and then find the longest ORF. So it is a quick way to jsut align old models to the new assembly. Alternatively you can just do de novo annotation.

?Carson



> On Oct 24, 2017, at 10:54 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Dear Carson:
> 
> Thank you again for your suggestions. I just get the new genome assembly of NMR and start to do gene annotation. I understand you ideas about this. But can I simply use the old genome transcripts as transcript evidence, and just following the standard Maker2 pipeline? I set est2genome=1 and provide the mRNA sequences in the fasta format for the first round training of SNAP.
> 
> For transcripts I have the following choices. I think the first choice is more reliable and better, right?
> (1) There are about 60,000 RefSeq transcripts from NCBI. So I downloaded those sequences in fasta format.
> (2) We have the raw data of RNA-seq from 11 tissues, we can do assembly by trinity for each sample and then get the transcripts. But I think most of the RNA-seq should have been submitted to NCBI. 
> 
> BTW, if we use the RefSeq data from NCBI, we can download the mRNA sequences, coding sequences or protein sequences. I wonder which type of data are the best to train the SNAP? For Augustus, we will use BUSCO to train it. 
> 
> Many thanks. 
> 
> Best
> Quanwei
> 
> 
> 
> 
> 2017-09-29 12:36 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> You can try using the est2genome=1 option to map the old models forward onto the new assembly as if they were ESTs (add a line that says est_forward=1 to the control file to maintain old naming and set est=1 to the old model transcript file). Then provide the final models as a pred_gff for a subsuquent run (i.e. a traditional MAKER run where you are annotating the new assembly with transcript and protein evidence and ab initio predictors). Don?t supply the old models to est= on that run.
> 
> The idea behind doing it this way is:
> 1. You need to get old models onto the new assembly so coordinates will change. So by doing it this way, you will at least be able to move many models forward based on homology.
> 2. By providing the models to pred_gff on a subsequent MAKER run, you are just letting old models compete against new annotations. They will be rejected if they have no evidence support, or can be kept if they score better than alternate models from SNAP/Augustus. That way you have the chance to integrate old models while at the same time rejecting some old models that have no evidence overlap.
> 
> ?Carson
> 
> 
> > On Sep 28, 2017, at 6:05 AM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> >
> > Hello:
> >
> > Recently, we got a new version of NMR genome, whose genome had been assembled and annotated a few years ago. We can download the gene annotation from NCBI.
> >
> > Now we want to annotate the new genome using Maker2 pipeline. I wonder how can I fully make use of existing annotations. On the other hand, since the previous genome is not very well assemblies, some genes annotation maybe false positives. I hope those false positive genes in previous annotation won't mislead Maker2 for current gene annotation.
> >
> > Do you have any suggestions. Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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From daren.card at gmail.com  Wed Oct 25 06:17:13 2017
From: daren.card at gmail.com (Daren C. Card)
Date: Wed, 25 Oct 2017 07:17:13 -0500
Subject: [maker-devel] MAKER RepeatRunner error on long scaffolds only
In-Reply-To: <49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
References: <DE6FAAF4-DA54-4407-8E23-3D3CD151EB0C@gmail.com>
	<2460BB61-C918-40B5-ABF2-03193BF13CCC@gmail.com>
	<52A27F91-063E-45C5-BEE0-BED0BF4E861E@gmail.com>
	<228ECD18-7B0E-47EB-9F58-FA3C31421A52@gmail.com>
	<90B18E05-63DB-4458-BC9B-807972BE1414@gmail.com>
	<C4C70AF4-DAB8-4903-A42A-420431B12B37@gmail.com>
	<97656D7C-3613-4B0B-9D99-0441AC28ABCC@gmail.com>
	<49A07052-11CE-4D20-A8E1-2E036F04C45C@gmail.com>
Message-ID: <0406D4C3-9C43-4198-B2EA-241C6C504425@gmail.com>

Hi Carson (and CCed MAKER list for the record),

Thanks for troubleshooting my issue further. Good to hear that the run should ultimately work, but strange it isn?t for me. I?ll keep playing with it and will hopefully get it sorted out by running through the list you suggested. 

Thanks again for the help,
Daren


> On Oct 24, 2017, at 11:27 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> I cannot seem to replicate this. I ran with MAKER 2.31.8 and 2.31.9, both with and without the GFF3 file (total of 4 runs). It succeeded without issues in every case.
> 
> The only things I can think to try are.
> 1. Reinstall BLAST+. Even though you have 2.6.0, just try it anyways. Also Install rmblast 2.6.0 for use wth RepeatMasker (requires that you install from source).
> 2. Maker sure you run ./configure inside RepeatMasker to let it know about the new rmblast installation.
> 3. Change the location of blast and related scripts in maker_exe.ctl otherwise MAKER won?t know to use your new installation.
> 4. delete the mpi_blastdb directory under MAKER?s output directory tp force it to rebuild all BLAST indexes.
> 5. delete any fle with a ?.db? extension in the maker output directory to force it to rebuld all GFF3 indexes.
> 6. Update BioPerl to the current CPAN version.
> 
> Also here is a link to the results I got for your contig (version 2.31.8 using the repeat masking GFF3 file) ?> http://weatherby.genetics.utah.edu/data/scaffold-1.tgz
> 
> ?Carson
> 
> 
> 
>> On Oct 17, 2017, at 6:46 AM, Daren C. Card <daren.card at gmail.com> wrote:
>> 
>> Hi Carson,
>> 
>> Thanks for offering to take a further look at this. I?ve uploaded all the files that I think you?d need to run MAKER on your systems, but let me know if you need anything else. My username is ?guest_5038?. 
>> 
>> Repeat annotations GFF is from RepeatModeler, with simple repeats filtered away. Transcript evidence was from Trinity assembly of several RNAseq libraries. Several sets of protein evidence from related species. Also have augustus HMM trained based on the genome assembly using BUSCO with retraining turned on. 
>> 
>> The command I?ve used is below, and here are the software versions I?m working with: 
>> 
>> Maker - 2.31.8
>> BLAST - 2.6.0
>> Augustus - 3.2.3
>> RepeatMasker - 4.0.6
>> 
>> mpiexec -n 12 maker -base CroVir_rnd1_chr1 round1_maker_opts.chr1.ctl maker_bopts.ctl maker_exe.ctl
>> 
>> Thanks again!
>> Daren
>> 
>> 
>>> On Oct 13, 2017, at 10:37 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> 
>>> So you have an input GFF3 file? Could you send it to me along with the problem contig. If you want you can upload the maker control files and evidence sets, and I can just recreate the run for the contig.
>>> 
>>> Upload here ?> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>>> 
>>> ?Carson
>>> 
>>> 
>>> 
>>>> On Oct 12, 2017, at 8:22 PM, Daren C. Card <daren.card at gmail.com> wrote:
>>>> 
>>>> Hi Carson,
>>>> 
>>>> Thanks for the help. Issue is still lingering. I?ve tried my full ?ideal? run using both the BLAST legacy 2.2.26 and also 2.6 and get the same error, so doesn?t seem to be a BLAST issue. Or is one that won?t be easy to overcome.
>>>> 
>>>> Using BLAST v. 2.6, I tried some more runs turning off RepeatRunner or excluding the complex repeat GFF I?m trying to supply. Seems to be running fine without my GFF, which indicates to me that the issue is this file and not BLAST. Disclaimer: I didn?t run the entire scaffold since it is quite large, but it went well past the point at which it was otherwise failing which leads me to believe it would finish okay.
>>>> 
>>>> I validated the GFF at http://genometools.org/cgi-bin/gff3validator.cgi. I had previously had <10 negative start coordinates for the repeat coordinates in the attributes field of the GFF, which I just set to 1 to give a clean GFF. This was what I used for the runs I described above, so whatever issue there is with this GFF is a mystery to me.
>>>> 
>>>> What advice do you have for further troubleshooting to try to determine what part of the GFF is causing the issue? I don?t see any obvious way info about how the sequence or the GFF is partitioned up for the annotation among the output files produced, so any help you can provide would be great.
>>>> 
>>>> Hoping I can resolve this as maybe this is useful to others. Weird that I?m getting this error, as I?ve annotated several other genomes in a similar manner and never had this issue. They were less contiguous, but can?t imagine that really mattering.
>>>> 
>>>> Thanks,
>>>> Daren
>>>> 
>>>> 
>>>>> On Oct 8, 2017, at 7:37 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>> 
>>>>> MAKER will use whatever blast is indicated in maker_exe.ctl, so make sure the new installation is the one indicated there. RepeatRunner is not part of RepeatMasker, and is a separate step that is essentially just a modified BLASTX against a protein database. So the standard NCBI blast+ installation is what gets used for that (not RMBLAST).
>>>>> 
>>>>> The error you get is because the BLAST report is truncated. At the top of a BLAST report there is a summary of results, and then below there are details about each result. What is happening is that there are results in the top summary that are not being found in the bottom detail section. If Updating to BLAST+ 2.6 does not fix it for you, you may need to drop to legacy NCBI BLAST (i.e. the one that is not the BLAST+ rewrite). Here ?> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/
>>>>> 
>>>>> ?Carson
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 6, 2017, at 6:23 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>> 
>>>>>> Dear Carson,
>>>>>> 
>>>>>> Thanks so much for the quick reply. I updated BLAST to v2.6 and reran the configure script for RepeatMasker. Looks like MAKER should natively work with the BLAST that is available in the $PATH.
>>>>>> 
>>>>>> Unfortunately, I?m still getting the same error what appears to be at roughly the same spot (~child 226). I?ve copied the stderr below. I checked my GFF file and I don?t see any issues with coordinates. I?m going to try running without a GFF of repeat annotations to see what that does, but in the meantime I wanted to send an update and see if there is anything else I should look into.
>>>>>> 
>>>>>> Thank you,
>>>>>> Daren Card
>>>>>> 
>>>>>> 
>>>>>> ################################################
>>>>>> doing repeat masking
>>>>>> re reading repeat masker report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.simple.rb.out
>>>>>> doing blastx repeats
>>>>>> re reading blast report.
>>>>>> /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/68/scaffold-1.227.te_proteins%2Efasta.repeatrunner
>>>>>> deleted:2 hits
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> doing blastx repeats
>>>>>> collecting blastx repeatmasking
>>>>>> processing all repeats
>>>>>> in cluster::shadow_cluster...
>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>> --> rank=NA, hostname=moonunit0
>>>>>> ERROR: Failed while processing all repeats
>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>> FAILED CONTIG:scaffold-1
>>>>>> 
>>>>>> examining contents of the fasta file and run log
>>>>>> ################################################
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Oct 4, 2017, at 11:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>>>>>> 
>>>>>>> The point where it dies is because there is no start/end coordinate for one of the alignments. The issue can either be with the GFF3 you gave it or is a truncated BLAST report. Recently there have been a number of weird BLAST+ issues related to truncated reports. Updating to 2.6+ seems to solve it for most people. There is also a 2.6 update for rmblast inside RepeatMasker. I submitted a bug report and example set to BLAST a few months ago.
>>>>>>> 
>>>>>>> ?Carson
>>>>>>> 
>>>>>>> 
>>>>>>>> On Oct 4, 2017, at 9:53 AM, Daren C. Card <daren.card at gmail.com> wrote:
>>>>>>>> 
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> I?ve been having an issue with MAKER (v. 2.31.8) that I haven?t been able to overcome, and no former questions have really addressed or helped fix the problem. I?ve run MAKER on a vertebrate genome and it runs fine and finishes all but the 8 longest scaffolds. These are all above 65Mb (others are below 5Mb) and most are around 20% Ns (one is 35%). The 9th longest sequence, which is just above 60Mb and 27% Ns finished fine too, which is strange because it is the only really long scaffold to run to completion. The fact that MAKER works fine on all but a few scaffolds indicates to me that the issue is those scaffolds and not MAKER/my settings, but the only difference is the length of the sequences. Is there an upper limit on scaffold size?
>>>>>>>> 
>>>>>>>> I originally ran whole genome as MPI, but have since tried to rerun individual scaffolds using a single core and still get issues. The error I get is below, but I can?t find any additional info in the program-specific logs to help figure this out. MAKER actually runs a little bit longer after this error before stalling and trying again. Seems to have something to do with RepeatRunner. For repeats I?m providing a GFF of complex repeats obtained from custom RepeatMasker annotations (using rm_gff option) and letting MAKER handle simple repeats (model_org=simple) and protein-based annotation with RepeatRunner (with default library).
>>>>>>>> 
>>>>>>>> Any help would be greatly appreciated.
>>>>>>>> Daren Card
>>>>>>>> 
>>>>>>>> University of Texas Arlington
>>>>>>>> 
>>>>>>>> ###################################################
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_xiChvf/1/scaffold-1.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> deleted:0 hits
>>>>>>>> collecting blastx repeatmasking
>>>>>>>> processing all repeats
>>>>>>>> in cluster::shadow_cluster...
>>>>>>>> Died at /opt/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
>>>>>>>> --> rank=3, hostname=moonunit0
>>>>>>>> ERROR: Failed while processing all repeats
>>>>>>>> ERROR: Chunk failed at level:3, tier_type:1
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> doing blastx repeats
>>>>>>>> running  blast search.
>>>>>>>> #--------- command -------------#
>>>>>>>> Widget::blastx:
>>>>>>>> /usr/bin/blastx -db /tmp/maker_xiChvf/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_xiChvf/3/scaffold-1.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/castoelab/Desktop/daren/cvv_annotation/chr1-8/CroVir_rnd1_chr1.maker.output/CroVir_rnd1_chr1_datastore/51/66/scaffold-1//theVoid.scaffold-1/67/scaffold-1.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
>>>>>>>> #-------------------------------#
>>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>>> FAILED CONTIG:scaffold-1
>>>>>>>> 
>>>>>>>> deleted:0 hits
>>>>>>>> deleted:0 hits
>>>>>>>> ###################################################
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 




From venyao at qq.com  Wed Oct 25 01:25:25 2017
From: venyao at qq.com (=?ISO-8859-1?B?V2VuIFlhbw==?=)
Date: Wed, 25 Oct 2017 15:25:25 +0800
Subject: [maker-devel] NNN in maker output transcript
Message-ID: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>

Dear guys,


Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.


Thanks!


Wen Yao
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From dandence at gmail.com  Wed Oct 25 09:42:04 2017
From: dandence at gmail.com (Daniel Ence)
Date: Wed, 25 Oct 2017 11:42:04 -0400
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <4913D7BA-CD9B-4B7F-83EF-B8072B4950A6@gmail.com>

Hi Wen Yao, 

Do you mean that some of the transcript sequences contain ?N? characters or that an entire transcript sequence is ?NNN??  



> On Oct 25, 2017, at 3:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:42:34 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:42:34 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
Message-ID: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>

The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.

?Carson




> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear guys,
> 
> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
> 
> Thanks!
> 
> Wen Yao
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From carsonhh at gmail.com  Wed Oct 25 09:43:37 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Oct 2017 09:43:37 -0600
Subject: [maker-devel] NNN in maker output transcript
In-Reply-To: <96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
References: <tencent_14ABFF76509501E4D181F06A4DDD7ACC860A@qq.com>
	<96D45DF3-83D0-4EF3-AE29-1B929A369B81@gmail.com>
Message-ID: <F55EEB1B-9F79-474A-8AE4-5232566D7380@gmail.com>

Also you can check the source of the model by looking a the name. i.e. does it have, augustus, snap, or est2genome in the name?

?Carson

> On Oct 25, 2017, at 9:42 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The gene predictor generates the model. I don?t think snap will generate a model that contain an N. Augustus might be able to across a single codon (I?m not sure there). The N means that the nucleotide is unknown (i.e. it can be A, T, C or G). An NNN codon produces the amino acid X (which is the unknown amino acid code). So it is possible that for something as short as one or two codon?s that the predictor thinks it?s ok to assume that it will produce a valid codon and uses it to complete the reading frame. Alternatively if you are using est2genome=1 or est_gff then what you are seeing is just the result of an alignment which can align to a couple of N's. You should not use est2genome=1 for anything but training. Also est_gff or pred_gff will not be filtered if you supplied an feature location that includes an N.
> 
> ?Carson
> 
> 
> 
> 
>> On Oct 25, 2017, at 1:25 AM, Wen Yao <venyao at qq.com> wrote:
>> 
>> Dear guys,
>> 
>> Recently, I run maker to annotate a genome. I found that the transcript fasta file output by Maker contains "NNN". Is this normal?
>> If not, what's going on? Is this a bug of maker or my configuration of maker is not correct? 
>> I told maker to use snap and augustus for de novo prediction and use exonerate to align ESTs and proteins.
>> 
>> Thanks!
>> 
>> Wen Yao
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 




From eennadi at gmail.com  Thu Oct 26 15:34:33 2017
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Thu, 26 Oct 2017 22:34:33 +0100
Subject: [maker-devel] How to remove contigs from GFF file
Message-ID: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>

Hello,

I need to remove sequences from my GFF file can someone help me with
command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in
gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>
 [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ:
gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From bmoore at genetics.utah.edu  Fri Oct 27 07:17:41 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:17:41 +0000
Subject: [maker-devel] Backlash running through my sequence
In-Reply-To: <8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
References: <CAOXM=CXM4Zz-Sani4BRL112Lb56t3ozjNpEhfg70x4ABhcaGkg@mail.gmail.com>
	<09603A3A-9DC0-40DC-A111-9DC1FCDF80BB@gmail.com>
	<8FD23F25-92D4-4A9C-873B-BB559B2CCBF4@illinois.edu>
Message-ID: <98FAE3F3-7C52-4EDA-8FBB-5F43DB7D54C9@umail.utah.edu>

Those look suspiciously like the remnants of end-of-line control characters.  Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I?d look at the upstream path of where your files come from and how they?ve been processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server).  One bizarre example we?ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted to MS format.  Good luck?

Barry

On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
?

I?m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Backlash running through my sequence

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

?Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From bmoore at genetics.utah.edu  Fri Oct 27 07:24:44 2017
From: bmoore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 27 Oct 2017 13:24:44 +0000
Subject: [maker-devel] QI codes insufficient - how to get frac exons
 with EST only?
In-Reply-To: <CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
References: <CAH2F1py7U-PQsGsELEvdkSjdPq5itLrBXfhMUJd0X7QQDB95ng@mail.gmail.com>
	<93934B45-909D-48FD-A840-B4F59F15AB53@gmail.com>
	<6A3091A3-5F0E-470D-89F3-4B6C16E50F4B@gmail.com>
	<CAH2F1pwpCagS-byQC9u_PYhfaGEe+4QoOgh-YiJ5JTHnq3ZETQ@mail.gmail.com>
Message-ID: <FB1F1E37-1246-4A10-BD9A-BF0644528F15@umail.utah.edu>

Also, you could probably build these overlap sets on the command line by subsetting the MAKER GFF3 file and then using BedTools intersect for overlap queries.

Barry

On Oct 11, 2017, at 10:19 PM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Very good, thank you!

Matt

On Wed, Oct 11, 2017 at 8:22 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
Also look at GAL for building GFF3 feature queries ?> https://github.com/The-Sequence-Ontology/GAL

?Carson



On Oct 11, 2017, at 9:18 AM, Michael Campbell <michael.s.campbell1 at gmail.com<mailto:michael.s.campbell1 at gmail.com>> wrote:

Hi Matt,

I have a hacky way that I?ve done it. It requires running MAKER two more times but they are quicker runs.

To identify the genes that have protein support I pass all of the annotation back to MAKER using the model_gff option in the maker_opts.ctl file. Then I pull out all of the protein2genome features from the big MAKER GFF3 file and pass them in using the protein_gff option. I turn off all repeat masking and run MAKER. It runs fast because it doesn?t have to run any gene finders, align evidence, or repeatmask. In the output any gene with an AED less than 1 has protein support. Then I do the same thing with est2genome lines from the big GFF3 file and put them in as est_gff. The output of that one gives you genes with EST support. Then the genes with an AED of less than one in both sets have support from protein and EST.

Hope this helps,
Mike

On Oct 11, 2017, at 10:53 AM, Matt Simenc <mcsimenc at gmail.com<mailto:mcsimenc at gmail.com>> wrote:

Hey MAKER people,

I would like to make a Venn diagram showing the kinds of evidence supporting gene models in my MAKER annotation where the left side shows number of genes with EST support only, the right side shows number of genes with protein support only, and the intersection shows number of genes with EST and protein support.

QI summary has:

Fraction of exons that overlap an EST alignment
Fraction of exons that overlap EST or Protein alignments

Please correct me if I'm wrong, because I am interpreting the first to be fraction of exons that overlap an EST alignment and possibly also a protein alignment. If that is the case then we can't calculate the number of genes that overlap only EST or (EST and protein) from the QI information.

Anyone have a way to do this or have a script to parse the MAKER GFF3 to get this?

Thanks!!!
Matt Simenc
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From dandence at gmail.com  Fri Oct 27 08:51:21 2017
From: dandence at gmail.com (Daniel Ence)
Date: Fri, 27 Oct 2017 10:51:21 -0400
Subject: [maker-devel] How to remove contigs from GFF file
In-Reply-To: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
References: <CAOXM=CWkHiGpVfC+cvPkVH=ufSv8CQtgLjKDSf6nhUGB+8y6fg@mail.gmail.com>
Message-ID: <D0CA7ADF-64A3-4B15-ACA3-26FA95B1C5F9@gmail.com>

Hi Emmanuel, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this ?grep -v ?scaffold_name? gff3_file?. 

~Daniel



> On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> 
> I need to remove sequences from my GFF file can someone help me with command line for such removal
> 
> ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
> ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Fri Oct 27 16:00:17 2017
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Oct 2017 16:00:17 -0600
Subject: [maker-devel] "ALRM" isn't numeric in exit - MAKER warning
 message
In-Reply-To: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
References: <CANCoJeT8eUwu+P-nERrp7L7ow+=_zJFmxPNXaNgJJVGexwL3dQ@mail.gmail.com>
Message-ID: <399AB5BD-2FC5-45F4-9AC8-1665CCFEA0D1@gmail.com>

Hi Marivi,

The only time MAKER uses the ALRM signal is during exit. Sometimes MPI_Finalize can freeze (it has to do with the fact it is being called from Perl). So we set an alarm just in case. Then if it takes to long we assume it is frozen and let things exit in a less than graceful way rather than let it block forever (it is already finished after all). The complaint you get may be because your system doesn?t support the alarm signal or forks.pm (which tries to intercept signals) is having an issue. Or it may just be ugliness related to parts of the process being killed with other parts still being active (it is an ungraceful exit after all). Or it may be another source of the ALRM all together (but I assume it is the MAKER ALRM given that it happens right after MAKER says it is finished). 

Thanks,
Carson



> On Oct 27, 2017, at 1:03 PM, Marivi Colle <collemar at msu.edu> wrote:
> 
> Hi Carson,
> 
> After running MAKER, I checked my std output and here's the message at the end of the file. I was wondering what this warning message means?
> 
> 
> Start_time: 1508465182
> End_time:   1508950543
> Elapsed:    485361
> 
> 
> Maker is now finished!!!
> 
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184.
> Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm <http://forks.pm/> line 2184
> 
> 
> Thank you.
> Marivi
> 
> 
> -- 
> Marivi G. Colle
> Research Associate
> Department of Horticulture
> Michigan State University
> 1066 Bogue St., East Lansing
> Michigan 48824-1325, USA

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From patrick.tranvan at unil.ch  Sat Oct 28 08:14:59 2017
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Sat, 28 Oct 2017 14:14:59 +0000
Subject: [maker-devel] Advice on my pipeline
In-Reply-To: <651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
References: <6b029690bace4d3fbae77c0bb1bddce8@prdexch02.ad.unil.ch>
	<A39F4213-70A8-4E07-AB13-00C427E4F244@gmail.com>
	<1498470630221.84642@unil.ch>
	<696C51C6-5606-4ECB-A8B8-9C077182FFFA@gmail.com>
	<1498908228256.16549@unil.ch>
	<58E904BF-9AB8-4AC7-B10B-C902F414E03D@gmail.com>
	<1505986013492.52354@unil.ch>,
	<651D4267-0FD7-4A92-B778-8976B47353BB@gmail.com>
Message-ID: <1509200133044.96929@unil.ch>

Hi Carson,


If I want to look for alternative splicing variant, can I just add the option


alt_splice=1


only at the last round of maker or do I have to set it since the beggining ? (and perform the 4 rounds with this option).

Cheers,

Patrick


________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: Friday, September 22, 2017 10:08 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Advice on my pipeline

The gff3 passthrough options are there to help users get old data into MAKER when they have lost access to the original files. But for iterative running of the pipeline, it is more effective just to rerun in place so MAKER can access the raw alignment reports. The raw reports from the alignments have more detail than what is stored in the GFF3. Details that are lost when trying to use the GFF3 as input.

?Carson


On Sep 21, 2017, at 3:26 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hi Carson,

I have a doubt for the round 2, so in a previous reply you said:

" Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory). "



Does it means that I don't need to modify the section :

#-----Re-annotation Using MAKER Derived GFF3

?

If I let everything by default such as :


altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no


It will not look again for repeat and protein + transcriptome alignment ?

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, July 3, 2017 10:50 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

maker2zff is just for SNAP training and not for gene filtering (please do not use it for filtering, it does not do what you think).

So the final annotation set after maker with correct_est_fusion is 16,850. To decide which set is better, look at them in a browser (gene counts are not useful for guaging result). A well annotated genome will have evidence clusters that closely match the final models. A poorly annoted genome will have evidence clusters that are split or merged by the models.

The corrected_est_fusion does two things. It trims long overlapping UTR fragments, and it stops evidence clusters from being merged on BLASTP evidence alone (so gene predictors will get unmerged hint regions if clusters are split).

You may also find that using jaccard_clip with Trinity has reduced sensitivity for the transcript data (you may lose things that were there before, but now have better specificity, i.e. fewer false positives). Make sure you provided protein data from at least two related species to help maintain sensitivity lost form the transcript data. You can also add rejected genes models back in after the fact by using iprscan to identify unsupported models with identifiable protein domains ?> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/

Thanks,
Carson




On Jul 1, 2017, at 5:21 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

So I have assembled my transcriptome with Trinity using the jaccard clip option and I have run maker with and without corrected_est_fusion.

I have then use SNAP to train/filter it with:

maker2zff  specie.all.gff

Here are my results:

Number of gene after maker -> Number of gene after maker2zff

- Without corrected_est_fusion: 21621 -> 13875
- With corrected_est_fusion: 16850 -> 9098

1 )If I understand well how works corrected_est_fusion, because it prevents gene merging, shouldn't be the invert ?
Normally I should find more genes with corrected_est_fusion right ?

2) I think I should find something like 13000-14000 genes for my specie. SHould I go with the "Without corrected_est_fusion" for the 2nd iteration of maker ?

 Thanks for your help



Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 26, 2017 11:38 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Sorry the option is ?> correct_est_fusion

It is in the maker_opts.ctl file.

I would use both SNAP and Augustus on a few large contigs then review the results manually. If one of them is not behaving well, then drop it. If both behave well (i.e. correlate well with evidence alignemnts) then keep them both.

?Carson



On Jun 26, 2017, at 3:48 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Thanks for your answer.

1) Do you think that adding a Augustus training in addition to SNAP at the step 3 and 5 will add more confidence (instead of adding Augustus only for the final round) ?
Because I am using autoAug for this and it tooks a while to compute ..

2) I don't see this option : 'avoid_est_fusion=1' . I have tried to add it but I got this error:

WARNING: Invalid option 'avoid_est_fusion' in control file maker_opts.ctl

(I am using v 2.31.8 )


Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

________________________________
From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Sent: Monday, June 5, 2017 8:29 PM
To: Patrick Tran Van
Cc: maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Advice on my pipeline

Your plan sounds good. A couple of related notes.

Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.

Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more for getting data into the run from jobs performed a long time ago (so they can?t be run in the same directory).

?Carson


On Jun 2, 2017, at 3:56 AM, Patrick Tran Van <Patrick.TranVan at unil.ch<mailto:Patrick.TranVan at unil.ch>> wrote:

Hello,

This is my first time running Maker for an insect genome annotation.

I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:


What I have:
- RNA evidence: transcriptome
- Proteine evidence: swissprot/uniprot + busco protein set of insect
- Cegma and busco results of my genome


1) Train SNAP with CEGMA

2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).

3) Create SNAP model from run A.

4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

5) Create SNAP model from run B.

6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).

7)  Create SNAP model from run C AND Create Augustus gene model from run C

8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1). + Use keep_preds=1



Does it seems coherent ?

Cheers,

Patrick Tran Van

Groups Chapuisat, Robinson-Rechavi & Schwander
Department of Ecology and Evolution
University of Lausanne
Le Biophore
CH-1015 Lausanne
Switzerland
Office 3206

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