From carsonhh at gmail.com  Fri Dec 11 15:52:57 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:52:57 -0700
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
References: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
Message-ID: <3C8780FE-E998-4BB4-BF49-C1CC31F1E4BB@gmail.com>

Maybe. I?ve never tried it. MAKER just wanders upstream and downstream, then gives up if it doesn?t find anything to add. Perhaps this script does something similar. If it takes GFF3, may be worth a shot.

?Carson


> On Oct 27, 2020, at 9:01 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I always set always_complete=1 yet I still get sequences without start and stop codon. 
> 
> Can https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py <https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py> be used on the final sequence to fix start and stop codon problem?
> 
> 
> 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 charlesgumbi at gmail.com  Tue Dec  8 12:24:28 2020
From: charlesgumbi at gmail.com (Charles Gumbi)
Date: Tue, 8 Dec 2020 14:24:28 -0500
Subject: [maker-devel] Possible precedence issue with control flow operator
 at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805
Message-ID: <CABM+6BJPfRGPRc+yQ6BVasinA5FBq3E4mMh+mH+Zb+5VYTPf2Q@mail.gmail.com>

Dear maker support team
I need your help to troubleshoot this error. I don't know what I'm doing
wrong, this is my first time annotating a genome. I have gone
through almost three  maker tutorials online but it's like the annotation
doesn't generate the datastore folder and I don't know why because I have
provided all the input files.  I am running this analysis on the cluster
platform. Below I have pasted the slurm script and the error message.
Any suggestions and help would be highly appropriated.

Slurm script

#!/bin/bash

#SBATCH --account=austin

#SBATCH --job-name=maker

#SBATCH --mail-type=ALL

#SBATCH --mail-user=charlesgumbi at ufl.edu

#SBATCH --mem=30gb

#SBATCH --ntasks=1

#SBATCH --cpus-per-task2

#SBATCH --time=48:00:00

#SBATCH --output=maker%j.out

#SBATCH --error=maker%j.err

date;hostname;pwd


#loading modules

module purge

module load maker/3.01.03


#runing maker

maker -base natalensis -fix_nucleotides -dsindex maker_bopts.ctl
maker_exe.ctl maker_opts.ctl


#making gff3 files

cd natalensis.maker.output

gff3_merge -d natalensis.maker.output/natalensis_master_datastore_index.log

fasta_merge -d natalensis.maker.output/natalensis_master_datastore_index.log.




Error file

Possible precedence issue with control flow operator at
/apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_datastore


To access files for individual sequences use the datastore index:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_master_datastore_index.log


ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

maker61784163.err (END)


Humble regards

charles
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From carsonhh at gmail.com  Fri Dec 11 15:49:55 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:49:55 -0700
Subject: [maker-devel] Why my gene is not annotated ?
In-Reply-To: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
References: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
Message-ID: <C6CB0E23-5C5E-4F0C-A4A9-C96B24DA5AC6@gmail.com>

Are you running a trained gene predictor? Perhaps the predictor does not like something about the area, so even with hints, it cannot make a sensible model. Non-canonical splice sites, runs of NNN, internal stop codons (indicates assembly issue in the region) can be the cause.

?Carson


> On Nov 17, 2020, at 9:22 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> 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
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Dec 11 16:02:14 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 16:02:14 -0700
Subject: [maker-devel] Format error detected with maker2eval_gtf
In-Reply-To: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <800FEDCE-F74F-44EF-8AB8-09A9DAC7A03C@gmail.com>

Truncated line in the GFF3.  Network mounted file systems can sometimes return true on write operations that actually failed (should have killed the program, but NFS lies, and the program keeps running). Since MAKER does such high IO, this comes up from time to time. If you can identify the contig involved, you can either rerun it or delete just the gff3 files in the folder and let MAEKR rewrite them.

?Carson


> On Nov 16, 2020, at 8:29 PM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> 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 <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From revale at well.ox.ac.uk  Thu Dec 24 09:29:23 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Thu, 24 Dec 2020 16:29:23 +0000
Subject: [maker-devel] processing of simple and complex repeats
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BBC11@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker distinguish between simple and complex repeats from a gff3 file of pre-aligned repeats?

I'm trying to annotate a genome of a non-model Drosophila species and I've already generated a gff3 file with both simple and complex repeats for this species. I would like to use this gff3 file as input for Repeat Masking so Maker won't have to align repeats from any library. My maker_opts.ctl file looks like this:

#-----Repeat Masking
model_org=
rmlib=
repeat_/path/to/te_proteins.fasta
rm_gff=/path/to/Dato_genome.Dato-first.full_mask.out.reformat.gff3
prok_rm=0
softmask=1

By using softmask=1 I understand that Maker will softmask only low complexity repeats (while complex ones will be hardmasked). My question is whether Maker can distinguish between simple and complex repeats from the gff3 file in order to softmask only simple repeats. Also, do you think it would be better to only include complex repeats in the gff3 file and let Maker find simple repeats on its own by using model_org=simple?

Thank you very much in advance.

Best regards,
Santiago

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From nanshangogo at gmail.com  Wed Dec 23 00:03:35 2020
From: nanshangogo at gmail.com (nanshan yang)
Date: Wed, 23 Dec 2020 15:03:35 +0800
Subject: [maker-devel] Qusetion about the ab initio gene predictors result
Message-ID: <CAEoE7cb14w=vzHDAAwgYYPiYwESYb1pn58Sqg2ZfESbnKYONUg@mail.gmail.com>

Hi MAKER community :
I have questions about MAKER output files.I get result from *ab initio* gene
predictors which use snap and augustus by maker,and after fasta_merge
step,there are some fasta files as:
result.maker.augustus_masked.proteins.fasta
result.maker.augustus_masked.transcripts.fasta
result.maker.augustus.proteins.fasta
result.maker.augustus.transcripts.fasta
result.maker.non_overlapping_ab_initio.proteins.fasta
result.maker.non_overlapping_ab_initio.transcripts.fasta
result.maker.snap.proteins.fasta
result.maker.snap_masked..transcripts.fasta
result.maker.snap_masked..proteins.fasta
result.maker.snap.transcripts.fasta
result.maker.proteins.fasta
result.maker.transcripts.fasta
if i continue to analysis the fasta files,which fasta should i choose?
because i choose *ab initio* gene predictors,so the   result
.maker.non_overlapping_ab_initio*fasta can be uesed into the downstream
analysis?or the  result.maker.proteins.fasta
Thanks verymuch for any help or insights
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From revale at well.ox.ac.uk  Tue Dec 29 12:19:11 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Tue, 29 Dec 2020 19:19:11 +0000
Subject: [maker-devel] dispersed_repeat features on rm_gff GFF3 file
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BD476@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker deal with a "dispersed_repeat" one-level features GFF3 file provided to the rm_gff option in the control file?

We're trying to annotate a genome of a non-model Drosophila species using a previously generated GFF3 file with repeats for this species. Some months ago, Carson Holt replied to a post (https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ) saying that "They (repeat models) must be match/match_part two level feature for rm_gff". However, all features on our GFF3 file are 'dispersed_repeat' one-level features.

Here is how our file looks like (extract of the file for a scaffold attached as well, repeats.gff3):

##sequence-region scaffold1062|size32755 1 32755
scaffold1062|size32755  RepeatMasker    dispersed_repeat        1       47      271     -       .       Target=DNAREP1_DM 26 73;ID=2740
scaffold1062|size32755  RepeatMasker    dispersed_repeat        48      83      263     +       .       Target=Dbuz_kz3_5_36225 704 739;ID=2741
scaffold1062|size32755  RepeatMasker    dispersed_repeat        340     386     299     -       .       Target=rnd-1_family-30 19 65;ID=2742
scaffold1062|size32755  RepeatMasker    dispersed_repeat        349     387     247     +       .       Target=rnd-1_family-29 1 71;ID=2743
scaffold1062|size32755  RepeatMasker    dispersed_repeat        388     430     240     +       .       Target=rnd-5_family-3333_TIR_P 3669 3713;ID=2744
scaffold1062|size32755  RepeatMasker    dispersed_repeat        446     555     408     -       .       Target=rnd-1_family-15 16 138;ID=2745


I'm attaching both the log file and the CTL file for what it's worth (Dtest.log / maker_opts.ctl).

I wonder whether Maker handled right our rm_gff file, whether the generated output is reliable. If not, do you think modifying the GFF3 file manually duplicating each row and changing the third column to 'match/match_part' could do the trick?

Thank you very much in advance.

Best regards,
Santiago

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From carsonhh at gmail.com  Fri Dec 11 15:52:57 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:52:57 -0700
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
References: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
Message-ID: <3C8780FE-E998-4BB4-BF49-C1CC31F1E4BB@gmail.com>

Maybe. I?ve never tried it. MAKER just wanders upstream and downstream, then gives up if it doesn?t find anything to add. Perhaps this script does something similar. If it takes GFF3, may be worth a shot.

?Carson


> On Oct 27, 2020, at 9:01 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I always set always_complete=1 yet I still get sequences without start and stop codon. 
> 
> Can https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py <https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py> be used on the final sequence to fix start and stop codon problem?
> 
> 
> 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 charlesgumbi at gmail.com  Tue Dec  8 12:24:28 2020
From: charlesgumbi at gmail.com (Charles Gumbi)
Date: Tue, 8 Dec 2020 14:24:28 -0500
Subject: [maker-devel] Possible precedence issue with control flow operator
 at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805
Message-ID: <CABM+6BJPfRGPRc+yQ6BVasinA5FBq3E4mMh+mH+Zb+5VYTPf2Q@mail.gmail.com>

Dear maker support team
I need your help to troubleshoot this error. I don't know what I'm doing
wrong, this is my first time annotating a genome. I have gone
through almost three  maker tutorials online but it's like the annotation
doesn't generate the datastore folder and I don't know why because I have
provided all the input files.  I am running this analysis on the cluster
platform. Below I have pasted the slurm script and the error message.
Any suggestions and help would be highly appropriated.

Slurm script

#!/bin/bash

#SBATCH --account=austin

#SBATCH --job-name=maker

#SBATCH --mail-type=ALL

#SBATCH --mail-user=charlesgumbi at ufl.edu

#SBATCH --mem=30gb

#SBATCH --ntasks=1

#SBATCH --cpus-per-task2

#SBATCH --time=48:00:00

#SBATCH --output=maker%j.out

#SBATCH --error=maker%j.err

date;hostname;pwd


#loading modules

module purge

module load maker/3.01.03


#runing maker

maker -base natalensis -fix_nucleotides -dsindex maker_bopts.ctl
maker_exe.ctl maker_opts.ctl


#making gff3 files

cd natalensis.maker.output

gff3_merge -d natalensis.maker.output/natalensis_master_datastore_index.log

fasta_merge -d natalensis.maker.output/natalensis_master_datastore_index.log.




Error file

Possible precedence issue with control flow operator at
/apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_datastore


To access files for individual sequences use the datastore index:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_master_datastore_index.log


ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

maker61784163.err (END)


Humble regards

charles
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From carsonhh at gmail.com  Fri Dec 11 15:49:55 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:49:55 -0700
Subject: [maker-devel] Why my gene is not annotated ?
In-Reply-To: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
References: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
Message-ID: <C6CB0E23-5C5E-4F0C-A4A9-C96B24DA5AC6@gmail.com>

Are you running a trained gene predictor? Perhaps the predictor does not like something about the area, so even with hints, it cannot make a sensible model. Non-canonical splice sites, runs of NNN, internal stop codons (indicates assembly issue in the region) can be the cause.

?Carson


> On Nov 17, 2020, at 9:22 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> 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
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Dec 11 16:02:14 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 16:02:14 -0700
Subject: [maker-devel] Format error detected with maker2eval_gtf
In-Reply-To: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <800FEDCE-F74F-44EF-8AB8-09A9DAC7A03C@gmail.com>

Truncated line in the GFF3.  Network mounted file systems can sometimes return true on write operations that actually failed (should have killed the program, but NFS lies, and the program keeps running). Since MAKER does such high IO, this comes up from time to time. If you can identify the contig involved, you can either rerun it or delete just the gff3 files in the folder and let MAEKR rewrite them.

?Carson


> On Nov 16, 2020, at 8:29 PM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> 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 <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From revale at well.ox.ac.uk  Thu Dec 24 09:29:23 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Thu, 24 Dec 2020 16:29:23 +0000
Subject: [maker-devel] processing of simple and complex repeats
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BBC11@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker distinguish between simple and complex repeats from a gff3 file of pre-aligned repeats?

I'm trying to annotate a genome of a non-model Drosophila species and I've already generated a gff3 file with both simple and complex repeats for this species. I would like to use this gff3 file as input for Repeat Masking so Maker won't have to align repeats from any library. My maker_opts.ctl file looks like this:

#-----Repeat Masking
model_org=
rmlib=
repeat_/path/to/te_proteins.fasta
rm_gff=/path/to/Dato_genome.Dato-first.full_mask.out.reformat.gff3
prok_rm=0
softmask=1

By using softmask=1 I understand that Maker will softmask only low complexity repeats (while complex ones will be hardmasked). My question is whether Maker can distinguish between simple and complex repeats from the gff3 file in order to softmask only simple repeats. Also, do you think it would be better to only include complex repeats in the gff3 file and let Maker find simple repeats on its own by using model_org=simple?

Thank you very much in advance.

Best regards,
Santiago

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From nanshangogo at gmail.com  Wed Dec 23 00:03:35 2020
From: nanshangogo at gmail.com (nanshan yang)
Date: Wed, 23 Dec 2020 15:03:35 +0800
Subject: [maker-devel] Qusetion about the ab initio gene predictors result
Message-ID: <CAEoE7cb14w=vzHDAAwgYYPiYwESYb1pn58Sqg2ZfESbnKYONUg@mail.gmail.com>

Hi MAKER community :
I have questions about MAKER output files.I get result from *ab initio* gene
predictors which use snap and augustus by maker,and after fasta_merge
step,there are some fasta files as:
result.maker.augustus_masked.proteins.fasta
result.maker.augustus_masked.transcripts.fasta
result.maker.augustus.proteins.fasta
result.maker.augustus.transcripts.fasta
result.maker.non_overlapping_ab_initio.proteins.fasta
result.maker.non_overlapping_ab_initio.transcripts.fasta
result.maker.snap.proteins.fasta
result.maker.snap_masked..transcripts.fasta
result.maker.snap_masked..proteins.fasta
result.maker.snap.transcripts.fasta
result.maker.proteins.fasta
result.maker.transcripts.fasta
if i continue to analysis the fasta files,which fasta should i choose?
because i choose *ab initio* gene predictors,so the   result
.maker.non_overlapping_ab_initio*fasta can be uesed into the downstream
analysis?or the  result.maker.proteins.fasta
Thanks verymuch for any help or insights
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From revale at well.ox.ac.uk  Tue Dec 29 12:19:11 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Tue, 29 Dec 2020 19:19:11 +0000
Subject: [maker-devel] dispersed_repeat features on rm_gff GFF3 file
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BD476@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker deal with a "dispersed_repeat" one-level features GFF3 file provided to the rm_gff option in the control file?

We're trying to annotate a genome of a non-model Drosophila species using a previously generated GFF3 file with repeats for this species. Some months ago, Carson Holt replied to a post (https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ) saying that "They (repeat models) must be match/match_part two level feature for rm_gff". However, all features on our GFF3 file are 'dispersed_repeat' one-level features.

Here is how our file looks like (extract of the file for a scaffold attached as well, repeats.gff3):

##sequence-region scaffold1062|size32755 1 32755
scaffold1062|size32755  RepeatMasker    dispersed_repeat        1       47      271     -       .       Target=DNAREP1_DM 26 73;ID=2740
scaffold1062|size32755  RepeatMasker    dispersed_repeat        48      83      263     +       .       Target=Dbuz_kz3_5_36225 704 739;ID=2741
scaffold1062|size32755  RepeatMasker    dispersed_repeat        340     386     299     -       .       Target=rnd-1_family-30 19 65;ID=2742
scaffold1062|size32755  RepeatMasker    dispersed_repeat        349     387     247     +       .       Target=rnd-1_family-29 1 71;ID=2743
scaffold1062|size32755  RepeatMasker    dispersed_repeat        388     430     240     +       .       Target=rnd-5_family-3333_TIR_P 3669 3713;ID=2744
scaffold1062|size32755  RepeatMasker    dispersed_repeat        446     555     408     -       .       Target=rnd-1_family-15 16 138;ID=2745


I'm attaching both the log file and the CTL file for what it's worth (Dtest.log / maker_opts.ctl).

I wonder whether Maker handled right our rm_gff file, whether the generated output is reliable. If not, do you think modifying the GFF3 file manually duplicating each row and changing the third column to 'match/match_part' could do the trick?

Thank you very much in advance.

Best regards,
Santiago

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From carsonhh at gmail.com  Fri Dec 11 15:52:57 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:52:57 -0700
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
References: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>
Message-ID: <3C8780FE-E998-4BB4-BF49-C1CC31F1E4BB@gmail.com>

Maybe. I?ve never tried it. MAKER just wanders upstream and downstream, then gives up if it doesn?t find anything to add. Perhaps this script does something similar. If it takes GFF3, may be worth a shot.

?Carson


> On Oct 27, 2020, at 9:01 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson
> I always set always_complete=1 yet I still get sequences without start and stop codon. 
> 
> Can https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py <https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py> be used on the final sequence to fix start and stop codon problem?
> 
> 
> 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 charlesgumbi at gmail.com  Tue Dec  8 12:24:28 2020
From: charlesgumbi at gmail.com (Charles Gumbi)
Date: Tue, 8 Dec 2020 14:24:28 -0500
Subject: [maker-devel] Possible precedence issue with control flow operator
 at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805
Message-ID: <CABM+6BJPfRGPRc+yQ6BVasinA5FBq3E4mMh+mH+Zb+5VYTPf2Q@mail.gmail.com>

Dear maker support team
I need your help to troubleshoot this error. I don't know what I'm doing
wrong, this is my first time annotating a genome. I have gone
through almost three  maker tutorials online but it's like the annotation
doesn't generate the datastore folder and I don't know why because I have
provided all the input files.  I am running this analysis on the cluster
platform. Below I have pasted the slurm script and the error message.
Any suggestions and help would be highly appropriated.

Slurm script

#!/bin/bash

#SBATCH --account=austin

#SBATCH --job-name=maker

#SBATCH --mail-type=ALL

#SBATCH --mail-user=charlesgumbi at ufl.edu

#SBATCH --mem=30gb

#SBATCH --ntasks=1

#SBATCH --cpus-per-task2

#SBATCH --time=48:00:00

#SBATCH --output=maker%j.out

#SBATCH --error=maker%j.err

date;hostname;pwd


#loading modules

module purge

module load maker/3.01.03


#runing maker

maker -base natalensis -fix_nucleotides -dsindex maker_bopts.ctl
maker_exe.ctl maker_opts.ctl


#making gff3 files

cd natalensis.maker.output

gff3_merge -d natalensis.maker.output/natalensis_master_datastore_index.log

fasta_merge -d natalensis.maker.output/natalensis_master_datastore_index.log.




Error file

Possible precedence issue with control flow operator at
/apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_datastore


To access files for individual sequences use the datastore index:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_master_datastore_index.log


ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

maker61784163.err (END)


Humble regards

charles
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From carsonhh at gmail.com  Fri Dec 11 15:49:55 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 15:49:55 -0700
Subject: [maker-devel] Why my gene is not annotated ?
In-Reply-To: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
References: <f341d9e253e64a388bbb7029d24468d0@unil.ch>
Message-ID: <C6CB0E23-5C5E-4F0C-A4A9-C96B24DA5AC6@gmail.com>

Are you running a trained gene predictor? Perhaps the predictor does not like something about the area, so even with hints, it cannot make a sensible model. Non-canonical splice sites, runs of NNN, internal stop codons (indicates assembly issue in the region) can be the cause.

?Carson


> On Nov 17, 2020, at 9:22 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> 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
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Dec 11 16:02:14 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 11 Dec 2020 16:02:14 -0700
Subject: [maker-devel] Format error detected with maker2eval_gtf
In-Reply-To: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839240A39B7CE901358186F9CE20@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <800FEDCE-F74F-44EF-8AB8-09A9DAC7A03C@gmail.com>

Truncated line in the GFF3.  Network mounted file systems can sometimes return true on write operations that actually failed (should have killed the program, but NFS lies, and the program keeps running). Since MAKER does such high IO, this comes up from time to time. If you can identify the contig involved, you can either rerun it or delete just the gff3 files in the folder and let MAEKR rewrite them.

?Carson


> On Nov 16, 2020, at 8:29 PM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> 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 <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From revale at well.ox.ac.uk  Thu Dec 24 09:29:23 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Thu, 24 Dec 2020 16:29:23 +0000
Subject: [maker-devel] processing of simple and complex repeats
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BBC11@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker distinguish between simple and complex repeats from a gff3 file of pre-aligned repeats?

I'm trying to annotate a genome of a non-model Drosophila species and I've already generated a gff3 file with both simple and complex repeats for this species. I would like to use this gff3 file as input for Repeat Masking so Maker won't have to align repeats from any library. My maker_opts.ctl file looks like this:

#-----Repeat Masking
model_org=
rmlib=
repeat_/path/to/te_proteins.fasta
rm_gff=/path/to/Dato_genome.Dato-first.full_mask.out.reformat.gff3
prok_rm=0
softmask=1

By using softmask=1 I understand that Maker will softmask only low complexity repeats (while complex ones will be hardmasked). My question is whether Maker can distinguish between simple and complex repeats from the gff3 file in order to softmask only simple repeats. Also, do you think it would be better to only include complex repeats in the gff3 file and let Maker find simple repeats on its own by using model_org=simple?

Thank you very much in advance.

Best regards,
Santiago

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From nanshangogo at gmail.com  Wed Dec 23 00:03:35 2020
From: nanshangogo at gmail.com (nanshan yang)
Date: Wed, 23 Dec 2020 15:03:35 +0800
Subject: [maker-devel] Qusetion about the ab initio gene predictors result
Message-ID: <CAEoE7cb14w=vzHDAAwgYYPiYwESYb1pn58Sqg2ZfESbnKYONUg@mail.gmail.com>

Hi MAKER community :
I have questions about MAKER output files.I get result from *ab initio* gene
predictors which use snap and augustus by maker,and after fasta_merge
step,there are some fasta files as:
result.maker.augustus_masked.proteins.fasta
result.maker.augustus_masked.transcripts.fasta
result.maker.augustus.proteins.fasta
result.maker.augustus.transcripts.fasta
result.maker.non_overlapping_ab_initio.proteins.fasta
result.maker.non_overlapping_ab_initio.transcripts.fasta
result.maker.snap.proteins.fasta
result.maker.snap_masked..transcripts.fasta
result.maker.snap_masked..proteins.fasta
result.maker.snap.transcripts.fasta
result.maker.proteins.fasta
result.maker.transcripts.fasta
if i continue to analysis the fasta files,which fasta should i choose?
because i choose *ab initio* gene predictors,so the   result
.maker.non_overlapping_ab_initio*fasta can be uesed into the downstream
analysis?or the  result.maker.proteins.fasta
Thanks verymuch for any help or insights
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From revale at well.ox.ac.uk  Tue Dec 29 12:19:11 2020
From: revale at well.ox.ac.uk (Santiago Revale)
Date: Tue, 29 Dec 2020 19:19:11 +0000
Subject: [maker-devel] dispersed_repeat features on rm_gff GFF3 file
Message-ID: <AFFF7CD915879F4384895C341BBB5E876D7BD476@exchange01.well.ox.ac.uk>

Dear Maker developers,

Can Maker deal with a "dispersed_repeat" one-level features GFF3 file provided to the rm_gff option in the control file?

We're trying to annotate a genome of a non-model Drosophila species using a previously generated GFF3 file with repeats for this species. Some months ago, Carson Holt replied to a post (https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ) saying that "They (repeat models) must be match/match_part two level feature for rm_gff". However, all features on our GFF3 file are 'dispersed_repeat' one-level features.

Here is how our file looks like (extract of the file for a scaffold attached as well, repeats.gff3):

##sequence-region scaffold1062|size32755 1 32755
scaffold1062|size32755  RepeatMasker    dispersed_repeat        1       47      271     -       .       Target=DNAREP1_DM 26 73;ID=2740
scaffold1062|size32755  RepeatMasker    dispersed_repeat        48      83      263     +       .       Target=Dbuz_kz3_5_36225 704 739;ID=2741
scaffold1062|size32755  RepeatMasker    dispersed_repeat        340     386     299     -       .       Target=rnd-1_family-30 19 65;ID=2742
scaffold1062|size32755  RepeatMasker    dispersed_repeat        349     387     247     +       .       Target=rnd-1_family-29 1 71;ID=2743
scaffold1062|size32755  RepeatMasker    dispersed_repeat        388     430     240     +       .       Target=rnd-5_family-3333_TIR_P 3669 3713;ID=2744
scaffold1062|size32755  RepeatMasker    dispersed_repeat        446     555     408     -       .       Target=rnd-1_family-15 16 138;ID=2745


I'm attaching both the log file and the CTL file for what it's worth (Dtest.log / maker_opts.ctl).

I wonder whether Maker handled right our rm_gff file, whether the generated output is reliable. If not, do you think modifying the GFF3 file manually duplicating each row and changing the third column to 'match/match_part' could do the trick?

Thank you very much in advance.

Best regards,
Santiago

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