From eennadi at gmail.com  Sun Nov  1 17:45:39 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Nov 2020 01:45:39 +0100
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
Message-ID: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>

Hi Carson,
Please I will like to know how to combine the gff results obtained
using  ipr_update_gff
and the gff obtained using maker_functional_gff?
For example the ipr_update_gff adds the following to the gff

scaffold_252    maker   gene    22873   47327   .       -       .
 ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;
      ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -
  .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;


While
maker_functional_gff

scaffold_252    maker   gene    22873   47327   .       -       .
ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .
  -       .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);


Is there a way of making maker reflect the GO and pfam alongside the
functional names?



Also, how can this be reflected in the corresponding protein and transcript
fastas?


Thanks for your support.



Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Wed Nov 11 10:17:50 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:17:50 -0700
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
In-Reply-To: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
References: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
Message-ID: <B63A5683-B905-4648-A027-EE6687247319@gmail.com>

The domain info goes in the the database cross reference field according to GFF3 format. We put any functional info in the Note field as it essentially works as a description according the GFF3 best practices. You can also use iprscan2gff3 to create gff3 features corresponding to the position of domains that can be loaded into a browser.  If you want domain or go info inside of the Note field of the GFF3 or in the fasta header, you would need to make your own scripts for that. Note that browsers like Browse can be configured to link out to appropriate websites for values in the Dbxref attribute.

?Carson


> On Nov 1, 2020, at 5:45 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
> For example the ipr_update_gff adds the following to the gff 
> 
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 
> 
> While 
> maker_functional_gff
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);
> 
> Is there a way of making maker reflect the GO and pfam alongside the functional names?
> 
> 
> Also, how can this be reflected in the corresponding protein and transcript fastas?
> 
> Thanks for your support.
> 
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Wed Nov 11 10:29:21 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:29:21 -0700
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
In-Reply-To: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
References: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
Message-ID: <46C76D52-B7BE-425E-B32E-3E10E815D36D@gmail.com>

Sorry for the slow reply. If you go back further in the STDERR, it may have a little more info describing the failure, also it will contain the command used to run by tblastx that can be run outside of MAKER to further explore the failure.

?Carson




> On Oct 29, 2020, at 10:35 AM, Daren Card <daren.card at gmail.com> wrote:
> 
> Hello,
> 
> I am having an issue running MAKER and am hoping to get some troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am running MAKER with the following command options: "-fix_nucleotides -nodatastore -RM_off". I am providing assembled transcripts from the target species (est) and a close relative (alt-est) and proteins from several species within the same general clade (Squamata). Gene models are being derived from Augustus with est2genome and protein2genome turned off. I have largely successfully run MAKER on a couple of genomes from the same vertebrate genus, but have this lingering problem with a single scaffold from one of the genomes. If it were pretty short, I'd just ignore it, but it is 2 Mb, so I do not want to miss out on annotating it.
> 
> When I ran MAKER on the entire genome, it finished properly except for this problematic scaffold. So I separated that scaffold out and tried running it alone with otherwise the same settings. Each time, it appears I get the same error during the 1st try when MAKER runs.
> ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> ERROR: Failed while doing tblastx of alt-ESTs
> ERROR: Chunk failed at level:4, tier_type:3
> FAILED CONTIG:scaffold_77
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold_77
> Then MAKER keeps retrying and apparently hitting the same problem. I checked the logs the best I can and see the following issue within run.log.child.0 for that scaffold.
> STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
> DIED    RANK    17:4:0:0
> DIED    COUNT   7
> This output file noted there is not present to check, which must stem from whatever issue there is.
> 
> I'm not sure what to do next about this issue and see no obvious information about what the problem is besides failure of tblastx to run. Any help that anyone can provide is greatly appreciated.
> 
> Kind regards,
> Daren Card
> 
> NSF Postdoctoral Fellow
> Harvard University
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Nov 16 20:29:43 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Tue, 17 Nov 2020 03:29:43 +0000
Subject: [maker-devel] Format error detected with maker2eval_gtf
Message-ID: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

I am currently working with an annotation from Maker that has just finished. Unfortunately I think there are some errors in my annotation, as a lot of my reads from a test RNA-seq alignment got discarded from my analysis. The analysis tool suggested my annotation might have overlapping reads.

I am trying to figure out what went wrong with my annotation, and the closest hint I have are error messages that I receive from running maker2eval_gtf on my output merged gff file. It appears every line of my gff is producing the following errors:

Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 244, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 245, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 246, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 35, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 37, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 38, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 39, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 40, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 41, <IN> line 200199481.

Do you know what issue this might indicate for my gff? At this point, I have done no filtering, just merged the files with gff3_merge.

Thank you so much, and please let me know if there is anything else I can provide to inform you more about my issue!

Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From patrick.tranvan at unil.ch  Tue Nov 17 09:22:45 2020
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Tue, 17 Nov 2020 16:22:45 +0000
Subject: [maker-devel] Why my gene is not annotated ?
Message-ID: <f341d9e253e64a388bbb7029d24468d0@unil.ch>

Dear Maker developper,


I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :


###

ctg889_racon_pilon3     tblastx translated_nucleotide_match     153760  157392  137     -       .       ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     tblastx match_part      157186  157392  263     -       .       ID=ctg889_racon_pilon3:hsp:0:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 259 465 -;Gap=M69

ctg889_racon_pilon3     tblastx match_part      157218  157391  284     -       .       ID=ctg889_racon_pilon3:hsp:1:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 291 464 -;Gap=M58

ctg889_racon_pilon3     tblastx match_part      157193  157390  241     -       .       ID=ctg889_racon_pilon3:hsp:2:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 266 463 -;Gap=M66

ctg889_racon_pilon3     tblastx match_part      156985  157056  87      -       .       ID=ctg889_racon_pilon3:hsp:3:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 223 294 -;Gap=M24

ctg889_racon_pilon3     tblastx match_part      156990  157055  96      -       .       ID=ctg889_racon_pilon3:hsp:4:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 228 293 -;Gap=M22

ctg889_racon_pilon3     tblastx match_part      156880  156993  166     -       .       ID=ctg889_racon_pilon3:hsp:5:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 117 230 -;Gap=M38

ctg889_racon_pilon3     tblastx match_part      156879  156986  154     -       .       ID=ctg889_racon_pilon3:hsp:6:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 116 223 -;Gap=M36

ctg889_racon_pilon3     tblastx match_part      156881  156985  141     -       .       ID=ctg889_racon_pilon3:hsp:7:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 118 222 -;Gap=M35

ctg889_racon_pilon3     tblastx match_part      153762  153845  128     -       .       ID=ctg889_racon_pilon3:hsp:8:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 3 86 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153761  153844  134     -       .       ID=ctg889_racon_pilon3:hsp:9:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 2 85 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153760  153843  137     -       .       ID=ctg889_racon_pilon3:hsp:10:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 1 84 -;Gap=M28

ctg889_racon_pilon3     cdna2genome     expressed_sequence_match        153760  157392  2022    +       .       ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     cdna2genome     match_part      153760  153845  2022    +       .       ID=ctg889_racon_pilon3:hsp:11:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 1 86 +;Gap=M86

ctg889_racon_pilon3     cdna2genome     match_part      155744  155774  2022    +       .       ID=ctg889_racon_pilon3:hsp:12:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 87 117 +;Gap=M31

ctg889_racon_pilon3     cdna2genome     match_part      156881  157055  2022    +       .       ID=ctg889_racon_pilon3:hsp:13:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 118 293 +;Gap=M105 I1 M70

ctg889_racon_pilon3     cdna2genome     match_part      157221  157392  2022    +       .       ID=ctg889_racon_pilon3:hsp:14:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 294 465 +;Gap=M172

ctg889_racon_pilon3     blastx  protein_match   153760  157389  133     +       .       ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     blastx  match_part      153760  153846  133     +       .       ID=ctg889_racon_pilon3:hsp:15:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 1 29;Gap=M29

ctg889_racon_pilon3     blastx  match_part      156881  156994  191     +       .       ID=ctg889_racon_pilon3:hsp:16:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 40 77;Gap=M38

ctg889_racon_pilon3     blastx  match_part      156985  157389  314     +       .       ID=ctg889_racon_pilon3:hsp:17:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 75 154;Gap=M19 D35 M4 D20 M57

ctg889_racon_pilon3     protein2genome  protein_match   153760  157389  668     +       .       ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     protein2genome  match_part      153760  153845  668     +       .       ID=ctg889_racon_pilon3:hsp:18:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 1 28;Gap=M28 F2

ctg889_racon_pilon3     protein2genome  match_part      155744  155774  668     +       .       ID=ctg889_racon_pilon3:hsp:19:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 29 39;Gap=R2 M11

ctg889_racon_pilon3     protein2genome  match_part      156881  157055  668     +       .       ID=ctg889_racon_pilon3:hsp:20:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 40 97;Gap=M35 I1 M1 F2 M20 F1 F1

ctg889_racon_pilon3     protein2genome  match_part      157221  157389  668     +       .       ID=ctg889_racon_pilon3:hsp:21:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 98 154;Gap=R2 M57



There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?


Thanks for your help.


Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206
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From dianad.mosa at gmail.com  Tue Nov 24 19:58:37 2020
From: dianad.mosa at gmail.com (=?UTF-8?Q?Diana_Moreno_Santill=C3=A1n?=)
Date: Tue, 24 Nov 2020 20:58:37 -0600
Subject: [maker-devel] Maker failed to annotated whole gene
Message-ID: <CAHqgp1dHhy4gk4GP3OoaFJxkevTY0GBwBOF04NhgESL5TCsPeA@mail.gmail.com>

Hello,
I noticed that some genes on my maker runs were annotated like fragmented
pieces instead of a single gene.

For example,  for a gene composed by 4 exons, I was expecting  to have the
4 exons concatenated in a single protein sequence. I performed annotations
in several species and for some of them I have only one gene annotated, i.e
with the 4 exons merged in a single protein sequence. But for other
species, with the same protein evidence and maker.ctl parameters I got 4
"genes" evidence instead of one. Actually on the blast results is pretty
clear how they are part of the same gene at different positions. This is an
issue because I'm doing gene families expansions and contraction and the
analysis detects as this gene is being expanded, as it has 3 more copies,
but in reality they are part of the same gene.

Have you seen this before? Could you help me to seek for a solution?

Thank you
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From ricardoa at ttu.edu  Tue Nov 24 13:28:13 2020
From: ricardoa at ttu.edu (Chavez Montes, Ricardo Aaron)
Date: Tue, 24 Nov 2020 20:28:13 -0000
Subject: [maker-devel] maker: SQLite database locked warning
Message-ID: <SN6PR06MB63687E54716A41620BF8C462D4FB0@SN6PR06MB6368.namprd06.prod.outlook.com>

Hello,

I've been experiencing a problem when using maker with gff3 input files. maker outputs a "database locked" warning almost always on line 525 of GFFDB.pm, sometimes on line 641. Both are $dbh->selectcol_arrayref(qq{SELECT name FROM sqlite_master WHERE type = 'table'});

I'm using a Dell 7920 standalone workstation (so, no remote or cluster hard drives of any kind; I'm using a ZFS array for data, but I set the tmp directory in maker_opts.ctl to a local, non-ZFS, ssd drive) with two Xeon processors with a total of 96 threads, and I've noticed that the number of warnings is lower and eventually disappears as I use less and less cpus at the mpiexec line. I would think that SQLite can only handle concurrency up to a certain number of processes.


Best,
Ricardo



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From eennadi at gmail.com  Sun Nov  1 17:45:39 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Nov 2020 01:45:39 +0100
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
Message-ID: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>

Hi Carson,
Please I will like to know how to combine the gff results obtained
using  ipr_update_gff
and the gff obtained using maker_functional_gff?
For example the ipr_update_gff adds the following to the gff

scaffold_252    maker   gene    22873   47327   .       -       .
 ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;
      ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -
  .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;


While
maker_functional_gff

scaffold_252    maker   gene    22873   47327   .       -       .
ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .
  -       .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);


Is there a way of making maker reflect the GO and pfam alongside the
functional names?



Also, how can this be reflected in the corresponding protein and transcript
fastas?


Thanks for your support.



Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Wed Nov 11 10:17:50 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:17:50 -0700
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
In-Reply-To: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
References: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
Message-ID: <B63A5683-B905-4648-A027-EE6687247319@gmail.com>

The domain info goes in the the database cross reference field according to GFF3 format. We put any functional info in the Note field as it essentially works as a description according the GFF3 best practices. You can also use iprscan2gff3 to create gff3 features corresponding to the position of domains that can be loaded into a browser.  If you want domain or go info inside of the Note field of the GFF3 or in the fasta header, you would need to make your own scripts for that. Note that browsers like Browse can be configured to link out to appropriate websites for values in the Dbxref attribute.

?Carson


> On Nov 1, 2020, at 5:45 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
> For example the ipr_update_gff adds the following to the gff 
> 
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 
> 
> While 
> maker_functional_gff
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);
> 
> Is there a way of making maker reflect the GO and pfam alongside the functional names?
> 
> 
> Also, how can this be reflected in the corresponding protein and transcript fastas?
> 
> Thanks for your support.
> 
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Wed Nov 11 10:29:21 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:29:21 -0700
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
In-Reply-To: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
References: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
Message-ID: <46C76D52-B7BE-425E-B32E-3E10E815D36D@gmail.com>

Sorry for the slow reply. If you go back further in the STDERR, it may have a little more info describing the failure, also it will contain the command used to run by tblastx that can be run outside of MAKER to further explore the failure.

?Carson




> On Oct 29, 2020, at 10:35 AM, Daren Card <daren.card at gmail.com> wrote:
> 
> Hello,
> 
> I am having an issue running MAKER and am hoping to get some troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am running MAKER with the following command options: "-fix_nucleotides -nodatastore -RM_off". I am providing assembled transcripts from the target species (est) and a close relative (alt-est) and proteins from several species within the same general clade (Squamata). Gene models are being derived from Augustus with est2genome and protein2genome turned off. I have largely successfully run MAKER on a couple of genomes from the same vertebrate genus, but have this lingering problem with a single scaffold from one of the genomes. If it were pretty short, I'd just ignore it, but it is 2 Mb, so I do not want to miss out on annotating it.
> 
> When I ran MAKER on the entire genome, it finished properly except for this problematic scaffold. So I separated that scaffold out and tried running it alone with otherwise the same settings. Each time, it appears I get the same error during the 1st try when MAKER runs.
> ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> ERROR: Failed while doing tblastx of alt-ESTs
> ERROR: Chunk failed at level:4, tier_type:3
> FAILED CONTIG:scaffold_77
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold_77
> Then MAKER keeps retrying and apparently hitting the same problem. I checked the logs the best I can and see the following issue within run.log.child.0 for that scaffold.
> STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
> DIED    RANK    17:4:0:0
> DIED    COUNT   7
> This output file noted there is not present to check, which must stem from whatever issue there is.
> 
> I'm not sure what to do next about this issue and see no obvious information about what the problem is besides failure of tblastx to run. Any help that anyone can provide is greatly appreciated.
> 
> Kind regards,
> Daren Card
> 
> NSF Postdoctoral Fellow
> Harvard University
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Nov 16 20:29:43 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Tue, 17 Nov 2020 03:29:43 +0000
Subject: [maker-devel] Format error detected with maker2eval_gtf
Message-ID: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

I am currently working with an annotation from Maker that has just finished. Unfortunately I think there are some errors in my annotation, as a lot of my reads from a test RNA-seq alignment got discarded from my analysis. The analysis tool suggested my annotation might have overlapping reads.

I am trying to figure out what went wrong with my annotation, and the closest hint I have are error messages that I receive from running maker2eval_gtf on my output merged gff file. It appears every line of my gff is producing the following errors:

Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 244, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 245, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 246, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 35, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 37, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 38, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 39, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 40, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 41, <IN> line 200199481.

Do you know what issue this might indicate for my gff? At this point, I have done no filtering, just merged the files with gff3_merge.

Thank you so much, and please let me know if there is anything else I can provide to inform you more about my issue!

Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From patrick.tranvan at unil.ch  Tue Nov 17 09:22:45 2020
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Tue, 17 Nov 2020 16:22:45 +0000
Subject: [maker-devel] Why my gene is not annotated ?
Message-ID: <f341d9e253e64a388bbb7029d24468d0@unil.ch>

Dear Maker developper,


I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :


###

ctg889_racon_pilon3     tblastx translated_nucleotide_match     153760  157392  137     -       .       ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     tblastx match_part      157186  157392  263     -       .       ID=ctg889_racon_pilon3:hsp:0:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 259 465 -;Gap=M69

ctg889_racon_pilon3     tblastx match_part      157218  157391  284     -       .       ID=ctg889_racon_pilon3:hsp:1:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 291 464 -;Gap=M58

ctg889_racon_pilon3     tblastx match_part      157193  157390  241     -       .       ID=ctg889_racon_pilon3:hsp:2:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 266 463 -;Gap=M66

ctg889_racon_pilon3     tblastx match_part      156985  157056  87      -       .       ID=ctg889_racon_pilon3:hsp:3:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 223 294 -;Gap=M24

ctg889_racon_pilon3     tblastx match_part      156990  157055  96      -       .       ID=ctg889_racon_pilon3:hsp:4:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 228 293 -;Gap=M22

ctg889_racon_pilon3     tblastx match_part      156880  156993  166     -       .       ID=ctg889_racon_pilon3:hsp:5:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 117 230 -;Gap=M38

ctg889_racon_pilon3     tblastx match_part      156879  156986  154     -       .       ID=ctg889_racon_pilon3:hsp:6:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 116 223 -;Gap=M36

ctg889_racon_pilon3     tblastx match_part      156881  156985  141     -       .       ID=ctg889_racon_pilon3:hsp:7:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 118 222 -;Gap=M35

ctg889_racon_pilon3     tblastx match_part      153762  153845  128     -       .       ID=ctg889_racon_pilon3:hsp:8:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 3 86 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153761  153844  134     -       .       ID=ctg889_racon_pilon3:hsp:9:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 2 85 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153760  153843  137     -       .       ID=ctg889_racon_pilon3:hsp:10:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 1 84 -;Gap=M28

ctg889_racon_pilon3     cdna2genome     expressed_sequence_match        153760  157392  2022    +       .       ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     cdna2genome     match_part      153760  153845  2022    +       .       ID=ctg889_racon_pilon3:hsp:11:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 1 86 +;Gap=M86

ctg889_racon_pilon3     cdna2genome     match_part      155744  155774  2022    +       .       ID=ctg889_racon_pilon3:hsp:12:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 87 117 +;Gap=M31

ctg889_racon_pilon3     cdna2genome     match_part      156881  157055  2022    +       .       ID=ctg889_racon_pilon3:hsp:13:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 118 293 +;Gap=M105 I1 M70

ctg889_racon_pilon3     cdna2genome     match_part      157221  157392  2022    +       .       ID=ctg889_racon_pilon3:hsp:14:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 294 465 +;Gap=M172

ctg889_racon_pilon3     blastx  protein_match   153760  157389  133     +       .       ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     blastx  match_part      153760  153846  133     +       .       ID=ctg889_racon_pilon3:hsp:15:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 1 29;Gap=M29

ctg889_racon_pilon3     blastx  match_part      156881  156994  191     +       .       ID=ctg889_racon_pilon3:hsp:16:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 40 77;Gap=M38

ctg889_racon_pilon3     blastx  match_part      156985  157389  314     +       .       ID=ctg889_racon_pilon3:hsp:17:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 75 154;Gap=M19 D35 M4 D20 M57

ctg889_racon_pilon3     protein2genome  protein_match   153760  157389  668     +       .       ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     protein2genome  match_part      153760  153845  668     +       .       ID=ctg889_racon_pilon3:hsp:18:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 1 28;Gap=M28 F2

ctg889_racon_pilon3     protein2genome  match_part      155744  155774  668     +       .       ID=ctg889_racon_pilon3:hsp:19:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 29 39;Gap=R2 M11

ctg889_racon_pilon3     protein2genome  match_part      156881  157055  668     +       .       ID=ctg889_racon_pilon3:hsp:20:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 40 97;Gap=M35 I1 M1 F2 M20 F1 F1

ctg889_racon_pilon3     protein2genome  match_part      157221  157389  668     +       .       ID=ctg889_racon_pilon3:hsp:21:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 98 154;Gap=R2 M57



There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?


Thanks for your help.


Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206
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From dianad.mosa at gmail.com  Tue Nov 24 19:58:37 2020
From: dianad.mosa at gmail.com (=?UTF-8?Q?Diana_Moreno_Santill=C3=A1n?=)
Date: Tue, 24 Nov 2020 20:58:37 -0600
Subject: [maker-devel] Maker failed to annotated whole gene
Message-ID: <CAHqgp1dHhy4gk4GP3OoaFJxkevTY0GBwBOF04NhgESL5TCsPeA@mail.gmail.com>

Hello,
I noticed that some genes on my maker runs were annotated like fragmented
pieces instead of a single gene.

For example,  for a gene composed by 4 exons, I was expecting  to have the
4 exons concatenated in a single protein sequence. I performed annotations
in several species and for some of them I have only one gene annotated, i.e
with the 4 exons merged in a single protein sequence. But for other
species, with the same protein evidence and maker.ctl parameters I got 4
"genes" evidence instead of one. Actually on the blast results is pretty
clear how they are part of the same gene at different positions. This is an
issue because I'm doing gene families expansions and contraction and the
analysis detects as this gene is being expanded, as it has 3 more copies,
but in reality they are part of the same gene.

Have you seen this before? Could you help me to seek for a solution?

Thank you
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From ricardoa at ttu.edu  Tue Nov 24 13:28:13 2020
From: ricardoa at ttu.edu (Chavez Montes, Ricardo Aaron)
Date: Tue, 24 Nov 2020 20:28:13 -0000
Subject: [maker-devel] maker: SQLite database locked warning
Message-ID: <SN6PR06MB63687E54716A41620BF8C462D4FB0@SN6PR06MB6368.namprd06.prod.outlook.com>

Hello,

I've been experiencing a problem when using maker with gff3 input files. maker outputs a "database locked" warning almost always on line 525 of GFFDB.pm, sometimes on line 641. Both are $dbh->selectcol_arrayref(qq{SELECT name FROM sqlite_master WHERE type = 'table'});

I'm using a Dell 7920 standalone workstation (so, no remote or cluster hard drives of any kind; I'm using a ZFS array for data, but I set the tmp directory in maker_opts.ctl to a local, non-ZFS, ssd drive) with two Xeon processors with a total of 96 threads, and I've noticed that the number of warnings is lower and eventually disappears as I use less and less cpus at the mpiexec line. I would think that SQLite can only handle concurrency up to a certain number of processes.


Best,
Ricardo



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From eennadi at gmail.com  Sun Nov  1 17:45:39 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Mon, 2 Nov 2020 01:45:39 +0100
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
Message-ID: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>

Hi Carson,
Please I will like to know how to combine the gff results obtained
using  ipr_update_gff
and the gff obtained using maker_functional_gff?
For example the ipr_update_gff adds the following to the gff

scaffold_252    maker   gene    22873   47327   .       -       .
 ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;
      ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -
  .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;


While
maker_functional_gff

scaffold_252    maker   gene    22873   47327   .       -       .
ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .
  -       .
ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar
to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna
pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);


Is there a way of making maker reflect the GO and pfam alongside the
functional names?



Also, how can this be reflected in the corresponding protein and transcript
fastas?


Thanks for your support.



Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Wed Nov 11 10:17:50 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:17:50 -0700
Subject: [maker-devel] How do I make maker combine interproscan and
 functional_gff results
In-Reply-To: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
References: <CAOXM=CUW8rpKuxq7-wxFerW=z3NTiNOsnX0DDEu9oOZ2BZ7-5w@mail.gmail.com>
Message-ID: <B63A5683-B905-4648-A027-EE6687247319@gmail.com>

The domain info goes in the the database cross reference field according to GFF3 format. We put any functional info in the Note field as it essentially works as a description according the GFF3 best practices. You can also use iprscan2gff3 to create gff3 features corresponding to the position of domains that can be loaded into a browser.  If you want domain or go info inside of the Note field of the GFF3 or in the fasta header, you would need to make your own scripts for that. Note that browsers like Browse can be configured to link out to appropriate websites for values in the Dbxref attribute.

?Carson


> On Nov 1, 2020, at 5:45 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
> For example the ipr_update_gff adds the following to the gff 
> 
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 
> 
> While 
> maker_functional_gff
> scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);
> 
> Is there a way of making maker reflect the GO and pfam alongside the functional names?
> 
> 
> Also, how can this be reflected in the corresponding protein and transcript fastas?
> 
> Thanks for your support.
> 
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Wed Nov 11 10:29:21 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 11 Nov 2020 10:29:21 -0700
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
In-Reply-To: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
References: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>
Message-ID: <46C76D52-B7BE-425E-B32E-3E10E815D36D@gmail.com>

Sorry for the slow reply. If you go back further in the STDERR, it may have a little more info describing the failure, also it will contain the command used to run by tblastx that can be run outside of MAKER to further explore the failure.

?Carson




> On Oct 29, 2020, at 10:35 AM, Daren Card <daren.card at gmail.com> wrote:
> 
> Hello,
> 
> I am having an issue running MAKER and am hoping to get some troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am running MAKER with the following command options: "-fix_nucleotides -nodatastore -RM_off". I am providing assembled transcripts from the target species (est) and a close relative (alt-est) and proteins from several species within the same general clade (Squamata). Gene models are being derived from Augustus with est2genome and protein2genome turned off. I have largely successfully run MAKER on a couple of genomes from the same vertebrate genus, but have this lingering problem with a single scaffold from one of the genomes. If it were pretty short, I'd just ignore it, but it is 2 Mb, so I do not want to miss out on annotating it.
> 
> When I ran MAKER on the entire genome, it finished properly except for this problematic scaffold. So I separated that scaffold out and tried running it alone with otherwise the same settings. Each time, it appears I get the same error during the 1st try when MAKER runs.
> ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> --> rank=23, hostname=holy7c18405.rc.fas.harvard.edu <http://holy7c18405.rc.fas.harvard.edu/>
> ERROR: Failed while doing tblastx of alt-ESTs
> ERROR: Chunk failed at level:4, tier_type:3
> FAILED CONTIG:scaffold_77
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold_77
> Then MAKER keeps retrying and apparently hitting the same problem. I checked the logs the best I can and see the following issue within run.log.child.0 for that scaffold.
> STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
> DIED    RANK    17:4:0:0
> DIED    COUNT   7
> This output file noted there is not present to check, which must stem from whatever issue there is.
> 
> I'm not sure what to do next about this issue and see no obvious information about what the problem is besides failure of tblastx to run. Any help that anyone can provide is greatly appreciated.
> 
> Kind regards,
> Daren Card
> 
> NSF Postdoctoral Fellow
> Harvard University
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Nov 16 20:29:43 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Tue, 17 Nov 2020 03:29:43 +0000
Subject: [maker-devel] Format error detected with maker2eval_gtf
Message-ID: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

I am currently working with an annotation from Maker that has just finished. Unfortunately I think there are some errors in my annotation, as a lot of my reads from a test RNA-seq alignment got discarded from my analysis. The analysis tool suggested my annotation might have overlapping reads.

I am trying to figure out what went wrong with my annotation, and the closest hint I have are error messages that I receive from running maker2eval_gtf on my output merged gff file. It appears every line of my gff is producing the following errors:

Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 244, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 245, <IN> line 200199481.
Use of uninitialized value $att in pattern match (m//) at maker2eval_gtf line 246, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 35, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 37, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 38, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 39, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 40, <IN> line 200199481.
Use of uninitialized value in string eq at maker2eval_gtf line 41, <IN> line 200199481.

Do you know what issue this might indicate for my gff? At this point, I have done no filtering, just merged the files with gff3_merge.

Thank you so much, and please let me know if there is anything else I can provide to inform you more about my issue!

Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From patrick.tranvan at unil.ch  Tue Nov 17 09:22:45 2020
From: patrick.tranvan at unil.ch (Patrick Tran Van)
Date: Tue, 17 Nov 2020 16:22:45 +0000
Subject: [maker-devel] Why my gene is not annotated ?
Message-ID: <f341d9e253e64a388bbb7029d24468d0@unil.ch>

Dear Maker developper,


I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :


###

ctg889_racon_pilon3     tblastx translated_nucleotide_match     153760  157392  137     -       .       ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     tblastx match_part      157186  157392  263     -       .       ID=ctg889_racon_pilon3:hsp:0:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 259 465 -;Gap=M69

ctg889_racon_pilon3     tblastx match_part      157218  157391  284     -       .       ID=ctg889_racon_pilon3:hsp:1:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 291 464 -;Gap=M58

ctg889_racon_pilon3     tblastx match_part      157193  157390  241     -       .       ID=ctg889_racon_pilon3:hsp:2:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 266 463 -;Gap=M66

ctg889_racon_pilon3     tblastx match_part      156985  157056  87      -       .       ID=ctg889_racon_pilon3:hsp:3:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 223 294 -;Gap=M24

ctg889_racon_pilon3     tblastx match_part      156990  157055  96      -       .       ID=ctg889_racon_pilon3:hsp:4:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 228 293 -;Gap=M22

ctg889_racon_pilon3     tblastx match_part      156880  156993  166     -       .       ID=ctg889_racon_pilon3:hsp:5:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 117 230 -;Gap=M38

ctg889_racon_pilon3     tblastx match_part      156879  156986  154     -       .       ID=ctg889_racon_pilon3:hsp:6:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 116 223 -;Gap=M36

ctg889_racon_pilon3     tblastx match_part      156881  156985  141     -       .       ID=ctg889_racon_pilon3:hsp:7:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 118 222 -;Gap=M35

ctg889_racon_pilon3     tblastx match_part      153762  153845  128     -       .       ID=ctg889_racon_pilon3:hsp:8:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 3 86 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153761  153844  134     -       .       ID=ctg889_racon_pilon3:hsp:9:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 2 85 -;Gap=M28

ctg889_racon_pilon3     tblastx match_part      153760  153843  137     -       .       ID=ctg889_racon_pilon3:hsp:10:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 1 84 -;Gap=M28

ctg889_racon_pilon3     cdna2genome     expressed_sequence_match        153760  157392  2022    +       .       ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna

ctg889_racon_pilon3     cdna2genome     match_part      153760  153845  2022    +       .       ID=ctg889_racon_pilon3:hsp:11:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 1 86 +;Gap=M86

ctg889_racon_pilon3     cdna2genome     match_part      155744  155774  2022    +       .       ID=ctg889_racon_pilon3:hsp:12:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 87 117 +;Gap=M31

ctg889_racon_pilon3     cdna2genome     match_part      156881  157055  2022    +       .       ID=ctg889_racon_pilon3:hsp:13:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 118 293 +;Gap=M105 I1 M70

ctg889_racon_pilon3     cdna2genome     match_part      157221  157392  2022    +       .       ID=ctg889_racon_pilon3:hsp:14:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 294 465 +;Gap=M172

ctg889_racon_pilon3     blastx  protein_match   153760  157389  133     +       .       ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     blastx  match_part      153760  153846  133     +       .       ID=ctg889_racon_pilon3:hsp:15:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 1 29;Gap=M29

ctg889_racon_pilon3     blastx  match_part      156881  156994  191     +       .       ID=ctg889_racon_pilon3:hsp:16:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 40 77;Gap=M38

ctg889_racon_pilon3     blastx  match_part      156985  157389  314     +       .       ID=ctg889_racon_pilon3:hsp:17:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 75 154;Gap=M19 D35 M4 D20 M57

ctg889_racon_pilon3     protein2genome  protein_match   153760  157389  668     +       .       ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA

ctg889_racon_pilon3     protein2genome  match_part      153760  153845  668     +       .       ID=ctg889_racon_pilon3:hsp:18:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 1 28;Gap=M28 F2

ctg889_racon_pilon3     protein2genome  match_part      155744  155774  668     +       .       ID=ctg889_racon_pilon3:hsp:19:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 29 39;Gap=R2 M11

ctg889_racon_pilon3     protein2genome  match_part      156881  157055  668     +       .       ID=ctg889_racon_pilon3:hsp:20:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 40 97;Gap=M35 I1 M1 F2 M20 F1 F1

ctg889_racon_pilon3     protein2genome  match_part      157221  157389  668     +       .       ID=ctg889_racon_pilon3:hsp:21:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 98 154;Gap=R2 M57



There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?


Thanks for your help.


Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206
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From dianad.mosa at gmail.com  Tue Nov 24 19:58:37 2020
From: dianad.mosa at gmail.com (=?UTF-8?Q?Diana_Moreno_Santill=C3=A1n?=)
Date: Tue, 24 Nov 2020 20:58:37 -0600
Subject: [maker-devel] Maker failed to annotated whole gene
Message-ID: <CAHqgp1dHhy4gk4GP3OoaFJxkevTY0GBwBOF04NhgESL5TCsPeA@mail.gmail.com>

Hello,
I noticed that some genes on my maker runs were annotated like fragmented
pieces instead of a single gene.

For example,  for a gene composed by 4 exons, I was expecting  to have the
4 exons concatenated in a single protein sequence. I performed annotations
in several species and for some of them I have only one gene annotated, i.e
with the 4 exons merged in a single protein sequence. But for other
species, with the same protein evidence and maker.ctl parameters I got 4
"genes" evidence instead of one. Actually on the blast results is pretty
clear how they are part of the same gene at different positions. This is an
issue because I'm doing gene families expansions and contraction and the
analysis detects as this gene is being expanded, as it has 3 more copies,
but in reality they are part of the same gene.

Have you seen this before? Could you help me to seek for a solution?

Thank you
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From ricardoa at ttu.edu  Tue Nov 24 13:28:13 2020
From: ricardoa at ttu.edu (Chavez Montes, Ricardo Aaron)
Date: Tue, 24 Nov 2020 20:28:13 -0000
Subject: [maker-devel] maker: SQLite database locked warning
Message-ID: <SN6PR06MB63687E54716A41620BF8C462D4FB0@SN6PR06MB6368.namprd06.prod.outlook.com>

Hello,

I've been experiencing a problem when using maker with gff3 input files. maker outputs a "database locked" warning almost always on line 525 of GFFDB.pm, sometimes on line 641. Both are $dbh->selectcol_arrayref(qq{SELECT name FROM sqlite_master WHERE type = 'table'});

I'm using a Dell 7920 standalone workstation (so, no remote or cluster hard drives of any kind; I'm using a ZFS array for data, but I set the tmp directory in maker_opts.ctl to a local, non-ZFS, ssd drive) with two Xeon processors with a total of 96 threads, and I've noticed that the number of warnings is lower and eventually disappears as I use less and less cpus at the mpiexec line. I would think that SQLite can only handle concurrency up to a certain number of processes.


Best,
Ricardo



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