From Fungi at uwyo.edu  Tue Oct  5 14:48:13 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Tue, 5 Oct 2021 20:48:13 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
Message-ID: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!


Sincerely,
Steve Miller
Botany
University of Wyoming
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211005/1a05caf5/attachment.html>

From jason.stajich at gmail.com  Wed Oct  6 10:33:50 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 09:33:50 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
Message-ID: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To
gain better help you might specify the problems you are having in running
or installing?

I'll also point out a parallel genome annotation tool we have built called
funannotate which does the prediction training automatically from BUSCO or
RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda
https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Sorry to say probably not a new issue.  I saw that MAKER is an
> easy-to-use genome annotation pipeline designed to be usable by small
> research groups with little bioinformatics experience.  That statement
> describes me to a t.  I am new to Whole Genome Sequencing and associated
> analysis, and have a limited skill set with computers.  I have a a 1.52
> GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I
> would like to predict functional genes.  I have tried to follow the
> tutorial that you have posted for Winter School 2018 to see if I can
> duplicate your installation and implementation for my HPC.  I doubt that
> you will be impressed, but I recently received a ?certificate? for
> completing our HPC Linux course path the University of Wyoming. .  I
> realize now how much I don?t know and how much work it will take to
> complete an annotation, but I am needing to generate at least some
> preliminary data to include in an upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/6e71c865/attachment.html>

From myandell at genetics.utah.edu  Wed Oct  6 11:11:47 2021
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Wed, 6 Oct 2021 17:11:47 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
Message-ID: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Jason Stajich <jason.stajich at gmail.com>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming
_______________________________________________
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/a0ebc1b3/attachment-0001.html>

From jason.stajich at gmail.com  Wed Oct  6 18:53:42 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 17:53:42 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <CALf8LpzFGsrV7DFAP19WaUNBx80XeDuCzmGZKEkPrvbgAeDdAQ@mail.gmail.com>

It?s just a genome assembly as input. Nothing more.

On Wed, Oct 6, 2021 at 1:28 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach
> and as you predicted my dataset is too large to run an annotation locally
> on my laptop - about 157 x too large by my calculations.  I would be happy
> to try your funannotate tool, but my dataset is in Fasta, and I would have
> to run BUSCO to get my Fasta data into a different format?  Because of the
> size of my WGS, that would likely have to be done on the HPC?
>
> Although I do not have all the experience necessary to pull this off
> quickly, I am thinking about my experimental design and the steps that I
> will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this
> plant functions differently from its fully photosynthetic cousin and if all
> related non-photosynthetic plants function in the same way.  There are two
> annotated genomes of closely related plants in NCBI: 1.  another fairly
> closely related non-photosynthetic plant and 2. a fairly closely related
> fully photosynthetic plant.  I do not have a clue as to how good either
> these annotations are.
>
> For the annotation portion of my WGS, I can understand using the fairly
> closely related fully photosynthetic plant to train my annotation gene
> prediction, assuming that all functional genes required for photosynthesis
> and metabolism are present in this plant.  Once my WGS is annotated, I can
> then move on to compare the functional genes in both non-photosynthetic
> plants.
>
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version
> 2.31.10 is installed on my HPC, but I don?t know if all the associated
> tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I
> would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI
> (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again
> in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER
> (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from
> InterProScan and a BLAST report of homology and script maker_map_ids to
> make pretty graphics
>
> Thanks again for any help you can provide.  I wish there was an upcoming
> workshop I could attend to get into this process in a hurry!
>
>
>
> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu>
> wrote:
>
> ? This message was sent from a non-UWYO address. Please exercise caution
> when clicking links or opening attachments from external sources.
>
>
> Thanks, Jason!
>
> *From: *maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of
> Jason Stajich <jason.stajich at gmail.com>
> *Date: *Wednesday, October 6, 2021 at 10:35 AM
> *To: *"Steven L. Miller" <Fungi at uwyo.edu>
> *Cc: *"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> *Subject: *Re: [maker-devel] Adapting MAKER pipeline for my HPC
>
> Steven -
>
> You might start with the galaxy install and tutorial or the cyverse one.
>
> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
>
> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
> http://gmod.org/wiki/MAKER_Tutorial
> Not sure if the space needed will be too much for your large genome.  To
> gain better help you might specify the problems you are having in running
> or installing?
>
> I'll also point out a parallel genome annotation tool we have built called
> funannotate which does the prediction training automatically from BUSCO or
> RNASeq datasets.
> https://funannotate.readthedocs.io/en/latest/ -
>
> installation with conda
> https://funannotate.readthedocs.io/en/latest/install.html
>  also docker image.
> https://hub.docker.com/r/nextgenusfs/funannotate
> https://github.com/reslp/funannotate-docker
>
> Jason Stajich
>
>
> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:
>
> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use
> genome annotation pipeline designed to be usable by small research groups
> with little bioinformatics experience.  That statement describes me to a t.
>   I am new to Whole Genome Sequencing and associated analysis, and have a
> limited skill set with computers.  I have a a 1.52 GB, 75k unitigs,
> non-photosynthetic vascular plant assembly for which I would like to
> predict functional genes.  I have tried to follow the tutorial that you
> have posted for Winter School 2018 to see if I can duplicate your
> installation and implementation for my HPC.  I doubt that you will be
> impressed, but I recently received a ?certificate? for completing our HPC
> Linux course path the University of Wyoming. .  I realize now how much I
> don?t know and how much work it will take to complete an annotation, but I
> am needing to generate at least some preliminary data to include in an
> upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> --
Jason Stajich
jason.stajich at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/426fb22f/attachment.html>

From Fungi at uwyo.edu  Wed Oct  6 14:28:16 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Wed, 6 Oct 2021 20:28:16 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
Message-ID: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>

Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?

Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
My experimental design is this:
I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.

For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.

So, these are the steps I must figure out to run this analysis on my HPC:
1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics

Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!



On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).


 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming

_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/2396e851/attachment-0001.html>

From Fungi at uwyo.edu  Thu Oct 14 14:22:33 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Thu, 14 Oct 2021 20:22:33 +0000
Subject: [maker-devel] failed to run MAKER tutorial test data
Message-ID: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>

As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module?
Thanks,
Steve Miller
University of Wyoming

[fungi at tlog2 testdata]$ maker
Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
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:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: contig-dpp-500-500
Length: 32156
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased


Maker is now finished!!!



Start_time: 1634230718
End_time:   1634230724
Elapsed:    6
[fungi at tlog2 testdata]$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211014/de5af1c9/attachment-0001.html>

From carsonhh at gmail.com  Tue Oct 19 21:33:05 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 21:33:05 -0600
Subject: [maker-devel] failed to run MAKER tutorial test data
In-Reply-To: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
References: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
Message-ID: <EA18D7B7-BE1C-4354-A03A-889D24EAE8C6@gmail.com>

RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER install it for you.

*Delete the MAKER installed copy ?> /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker
*Then download and install it yourself following the instructions here ?> https://www.repeatmasker.org/RepeatMasker/
*Then change the location of RepeatMasker= in the maker_exe.ctl file to point to the new installation

At the very least you will be able to see any failure messages during the RepeatMasker install that will indicate what is happening on your local system.

?Carson


> On Oct 14, 2021, at 2:22 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module? 
> Thanks,
> Steve Miller
> University of Wyoming
> 
> [fungi at tlog2 testdata]$ maker
> 
> Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
> 
> 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:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore
> 
>  
> To access files for individual sequences use the datastore index:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
>  
> STATUS: Now running MAKER...
> 
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> #---------------------------------------------------------------------
> 
> Now starting the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
> #---------------------------------------------------------------------
> 
> Now retrying the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> Tries: 2!!
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
>  
>  
> Maker is now finished!!!
> 
>  
>  
>  
> Start_time: 1634230718
> 
> End_time:   1634230724
> 
> Elapsed:    6
> 
> [fungi at tlog2 testdata]$
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0001.p7s>

From carsonhh at gmail.com  Tue Oct 19 23:40:56 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 23:40:56 -0600
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <A34FA21F-F20B-4EE1-95C7-513D2586F09F@gmail.com>

Funnanotate takes FASTA as input. But if you still choose the MAKER route, BUSCO can train Augustus for you (BUSCO also runs much faster than MAKER). Once you have trained Augustus, you could use MAKER to annotate just a few contigs (not the whole genome). That might give you something to work with, since you are only looking for some preliminary data.

?Carson


> On Oct 6, 2021, at 2:28 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?
> 
> Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.
> 
> For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.
> 
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics
> 
> Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!
> 
> 
> 
>> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>> wrote:
>> 
>> ? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.
>> 
>> Thanks, Jason!
>>  
>> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>>
>> Date: Wednesday, October 6, 2021 at 10:35 AM
>> To: "Steven L. Miller" <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>>
>> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC
>>  
>> Steven - 
>>  
>> You might start with the galaxy install and tutorial or the cyverse one.
>> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html <https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html>
>> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html <https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html>
>> http://gmod.org/wiki/MAKER_Tutorial <http://gmod.org/wiki/MAKER_Tutorial>
>> Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?
>>  
>> I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets. 
>> https://funannotate.readthedocs.io/en/latest/ <https://funannotate.readthedocs.io/en/latest/> - 
>>  
>> installation with conda https://funannotate.readthedocs.io/en/latest/install.html <https://funannotate.readthedocs.io/en/latest/install.html> 
>>  also docker image.
>> https://hub.docker.com/r/nextgenusfs/funannotate <https://hub.docker.com/r/nextgenusfs/funannotate>
>> https://github.com/reslp/funannotate-docker <https://github.com/reslp/funannotate-docker>
>>  
>> Jason Stajich
>>  
>>  
>> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>> wrote:
>>> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).  
>>>  
>>>  I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.
>>>  
>>> I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!
>>>  
>>> Sincerely,
>>> Steve Miller
>>> Botany
>>> University of Wyoming
>>> _______________________________________________
>>> 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>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0001.p7s>

From carsonhh at gmail.com  Wed Oct 20 00:07:19 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 20 Oct 2021 00:07:19 -0600
Subject: [maker-devel] How do I extract matrix from annotation
In-Reply-To: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
References: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
Message-ID: <3A1F8537-5566-4F98-B507-2EDAC41EAC89@gmail.com>

This is an older email that looks like never got an answer. Briefly you need to use Linux command line tools to evaluate the GFF3 file.

Examples:

#count protein coding transcripts
cat annotations.gff | grep -c -P ?\tmRNA\t"

#count tRNA transcripts
cat annotations.gff | grep -c -P ?\ttRNA\t"

#count snoRNA transcripts
cat annotations.gff | grep -c -P ?\tsnoRNA\t"


You can also pull out the Parent feature and count uniq entries to look at genes instead of transcripts. Example:

#count protein coding genes
cat annotations.gff | grep -c -P ?\tmRNA\t? | perl -ane ?/Parent=([^\;\n]+)/; print "$1\n?? | sort | uniq | grep -c ?"


You can also try tools like SOBA from the Sequence Ontology that give statistics on GFF3 features ?> http://www.sequenceontology.org/cgi-bin/soba.cgi

?Carson



> On Jul 27, 2021, at 9:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Carson, Greetings from Nigeria.
> Please how can I extract these matrix from my annotations?
> 
> Number of  protein-coding genes in the assembled tea plant genome  Those with known proteins and/or domains . Annotation of noncoding RNA genes  ribosomal RNA genes Number of  transfer RNA genes, Number  transcription factor genes and  simple sequence 
> 
> Thanks
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
> 
> https://orcid.org/0000-0002-8424-4859 <https://orcid.org/0000-0002-8424-4859>
> 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment.p7s>

From barry.moore at genetics.utah.edu  Fri Oct 29 00:24:36 2021
From: barry.moore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 29 Oct 2021 06:24:36 +0000
Subject: [maker-devel] Support on maker
In-Reply-To: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
Message-ID: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>

Hi Gez,

I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:

http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

Cheers,

Barry

From: Gezahegn Girma <ggirmate at purdue.edu>
Date: Thursday, October 28, 2021 at 12:19 PM
To: Marvin B Moore <barry.moore at genetics.utah.edu>
Subject: Support on maker
Hi Barry,

I am using maker for genome annotation of sorghum genotype.

Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.

=========================================================
STATUS: Now running MAKER...
WARNING: Cannot find >0, trying to re-index the fasta.
stop here: 0
ERROR: Fasta index error
 at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
        Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
10-nompi/bin/../lib/Process/MpiTiers.pm line 73
          Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
         eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
          Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
iers.pm line 79
        Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
Process/MpiTiers.pm line 56
         Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
1.10-nompi/bin/maker line 669
--> rank=NA, hostname=bell-a105.rcac.purdue.edu<http://bell-a105.rcac.purdue.edu>
ERROR: Failed in tier preparation
examining contents of the fasta file and run log
.
.
.
Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its
translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
================================================================================
Regards,
Gez


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/05ba96d9/attachment-0001.html>

From dmacguig at buffalo.edu  Wed Oct 20 09:28:28 2021
From: dmacguig at buffalo.edu (Macguigan, Daniel)
Date: Wed, 20 Oct 2021 15:28:28 +0000
Subject: [maker-devel] Maker Repeat Masking model_org option with D
Message-ID: <1634743709431.3974@buffalo.edu>

Hello,


I have a straightforward question, but I can't seem to find the answer anywhere. Is it possible to specify a species/clade for Dfam masking using the model_org option in the *maker_opts.ctl file? The comment on this option says "select a model organism for RepBase masking in RepeatMasker."


As an example, I currently have RepeatMasker configured to use Dfam. It works fine when I run RepeatMasker on its own with a command like this.


RepeatMasker -gff -species Arthropoda -dir ./RMask_dir


However, when I specify "model_org=Arthropoda" in the maker_opts.ctl file, I get a message "ERROR: Could not determine if RepBase is installed"


I am using RepeatMasker v.4.1.1 and Maker v.3.01.03.


Thanks,

Dan


--
Dan MacGuigan, PhD
he-him-his
Postdoctoral Fellow
Department of Biological Sciences
University at Buffalo
@DMacGuig
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/90eb2bd8/attachment-0001.html>

From ggirmate at purdue.edu  Fri Oct 29 08:10:01 2021
From: ggirmate at purdue.edu (Gezahegn Girma)
Date: Fri, 29 Oct 2021 10:10:01 -0400
Subject: [maker-devel] Support on maker
In-Reply-To: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
	<BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
Message-ID: <3DD1C99A-FCDD-4AC2-894F-0BB8DFEF6883@purdue.edu>

Hi Barry,

Thank you so much for the kind reply and suggestion to join mailing list.

Looking forward for support to resolve the issues.

Regards,
Gez

> On Oct 29, 2021, at 02:24, Marvin B Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Gez,
>  
> I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:
>  
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
>  
> Cheers,
>  
> Barry
>  
> From: Gezahegn Girma <ggirmate at purdue.edu>
> Date: Thursday, October 28, 2021 at 12:19 PM
> To: Marvin B Moore <barry.moore at genetics.utah.edu>
> Subject: Support on maker
> 
> Hi Barry,
>  
> I am using maker for genome annotation of sorghum genotype.
>  
> Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.
>  
> =========================================================
> STATUS: Now running MAKER...
> WARNING: Cannot find >0, trying to re-index the fasta.
> stop here: 0
> ERROR: Fasta index error
>  at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
>         Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
> 10-nompi/bin/../lib/Process/MpiTiers.pm line 73
>           Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
>          eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
>           Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
> iers.pm line 79
>         Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
> Process/MpiTiers.pm line 56
>          Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
> 1.10-nompi/bin/maker line 669
> --> rank=NA, hostname=bell-a105.rcac.purdue.edu <http://bell-a105.rcac.purdue.edu/>
> ERROR: Failed in tier preparation
> examining contents of the fasta file and run log
> .
> .
> .
> Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its 
> translation. Please verify the query sequence(s) and/or filtering options
> deleted:0 hits
> ================================================================================
> Regards,
> Gez

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/96e9e4f1/attachment-0001.html>

From Fungi at uwyo.edu  Tue Oct  5 14:48:13 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Tue, 5 Oct 2021 20:48:13 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
Message-ID: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!


Sincerely,
Steve Miller
Botany
University of Wyoming
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211005/1a05caf5/attachment-0002.html>

From jason.stajich at gmail.com  Wed Oct  6 10:33:50 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 09:33:50 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
Message-ID: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To
gain better help you might specify the problems you are having in running
or installing?

I'll also point out a parallel genome annotation tool we have built called
funannotate which does the prediction training automatically from BUSCO or
RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda
https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Sorry to say probably not a new issue.  I saw that MAKER is an
> easy-to-use genome annotation pipeline designed to be usable by small
> research groups with little bioinformatics experience.  That statement
> describes me to a t.  I am new to Whole Genome Sequencing and associated
> analysis, and have a limited skill set with computers.  I have a a 1.52
> GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I
> would like to predict functional genes.  I have tried to follow the
> tutorial that you have posted for Winter School 2018 to see if I can
> duplicate your installation and implementation for my HPC.  I doubt that
> you will be impressed, but I recently received a ?certificate? for
> completing our HPC Linux course path the University of Wyoming. .  I
> realize now how much I don?t know and how much work it will take to
> complete an annotation, but I am needing to generate at least some
> preliminary data to include in an upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/6e71c865/attachment-0002.html>

From myandell at genetics.utah.edu  Wed Oct  6 11:11:47 2021
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Wed, 6 Oct 2021 17:11:47 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
Message-ID: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Jason Stajich <jason.stajich at gmail.com>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming
_______________________________________________
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/a0ebc1b3/attachment-0002.html>

From jason.stajich at gmail.com  Wed Oct  6 18:53:42 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 17:53:42 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <CALf8LpzFGsrV7DFAP19WaUNBx80XeDuCzmGZKEkPrvbgAeDdAQ@mail.gmail.com>

It?s just a genome assembly as input. Nothing more.

On Wed, Oct 6, 2021 at 1:28 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach
> and as you predicted my dataset is too large to run an annotation locally
> on my laptop - about 157 x too large by my calculations.  I would be happy
> to try your funannotate tool, but my dataset is in Fasta, and I would have
> to run BUSCO to get my Fasta data into a different format?  Because of the
> size of my WGS, that would likely have to be done on the HPC?
>
> Although I do not have all the experience necessary to pull this off
> quickly, I am thinking about my experimental design and the steps that I
> will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this
> plant functions differently from its fully photosynthetic cousin and if all
> related non-photosynthetic plants function in the same way.  There are two
> annotated genomes of closely related plants in NCBI: 1.  another fairly
> closely related non-photosynthetic plant and 2. a fairly closely related
> fully photosynthetic plant.  I do not have a clue as to how good either
> these annotations are.
>
> For the annotation portion of my WGS, I can understand using the fairly
> closely related fully photosynthetic plant to train my annotation gene
> prediction, assuming that all functional genes required for photosynthesis
> and metabolism are present in this plant.  Once my WGS is annotated, I can
> then move on to compare the functional genes in both non-photosynthetic
> plants.
>
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version
> 2.31.10 is installed on my HPC, but I don?t know if all the associated
> tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I
> would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI
> (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again
> in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER
> (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from
> InterProScan and a BLAST report of homology and script maker_map_ids to
> make pretty graphics
>
> Thanks again for any help you can provide.  I wish there was an upcoming
> workshop I could attend to get into this process in a hurry!
>
>
>
> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu>
> wrote:
>
> ? This message was sent from a non-UWYO address. Please exercise caution
> when clicking links or opening attachments from external sources.
>
>
> Thanks, Jason!
>
> *From: *maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of
> Jason Stajich <jason.stajich at gmail.com>
> *Date: *Wednesday, October 6, 2021 at 10:35 AM
> *To: *"Steven L. Miller" <Fungi at uwyo.edu>
> *Cc: *"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> *Subject: *Re: [maker-devel] Adapting MAKER pipeline for my HPC
>
> Steven -
>
> You might start with the galaxy install and tutorial or the cyverse one.
>
> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
>
> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
> http://gmod.org/wiki/MAKER_Tutorial
> Not sure if the space needed will be too much for your large genome.  To
> gain better help you might specify the problems you are having in running
> or installing?
>
> I'll also point out a parallel genome annotation tool we have built called
> funannotate which does the prediction training automatically from BUSCO or
> RNASeq datasets.
> https://funannotate.readthedocs.io/en/latest/ -
>
> installation with conda
> https://funannotate.readthedocs.io/en/latest/install.html
>  also docker image.
> https://hub.docker.com/r/nextgenusfs/funannotate
> https://github.com/reslp/funannotate-docker
>
> Jason Stajich
>
>
> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:
>
> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use
> genome annotation pipeline designed to be usable by small research groups
> with little bioinformatics experience.  That statement describes me to a t.
>   I am new to Whole Genome Sequencing and associated analysis, and have a
> limited skill set with computers.  I have a a 1.52 GB, 75k unitigs,
> non-photosynthetic vascular plant assembly for which I would like to
> predict functional genes.  I have tried to follow the tutorial that you
> have posted for Winter School 2018 to see if I can duplicate your
> installation and implementation for my HPC.  I doubt that you will be
> impressed, but I recently received a ?certificate? for completing our HPC
> Linux course path the University of Wyoming. .  I realize now how much I
> don?t know and how much work it will take to complete an annotation, but I
> am needing to generate at least some preliminary data to include in an
> upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> --
Jason Stajich
jason.stajich at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/426fb22f/attachment-0002.html>

From Fungi at uwyo.edu  Wed Oct  6 14:28:16 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Wed, 6 Oct 2021 20:28:16 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
Message-ID: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>

Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?

Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
My experimental design is this:
I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.

For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.

So, these are the steps I must figure out to run this analysis on my HPC:
1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics

Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!



On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).


 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming

_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/2396e851/attachment-0002.html>

From Fungi at uwyo.edu  Thu Oct 14 14:22:33 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Thu, 14 Oct 2021 20:22:33 +0000
Subject: [maker-devel] failed to run MAKER tutorial test data
Message-ID: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>

As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module?
Thanks,
Steve Miller
University of Wyoming

[fungi at tlog2 testdata]$ maker
Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
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:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: contig-dpp-500-500
Length: 32156
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased


Maker is now finished!!!



Start_time: 1634230718
End_time:   1634230724
Elapsed:    6
[fungi at tlog2 testdata]$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211014/de5af1c9/attachment-0002.html>

From carsonhh at gmail.com  Tue Oct 19 21:33:05 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 21:33:05 -0600
Subject: [maker-devel] failed to run MAKER tutorial test data
In-Reply-To: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
References: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
Message-ID: <EA18D7B7-BE1C-4354-A03A-889D24EAE8C6@gmail.com>

RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER install it for you.

*Delete the MAKER installed copy ?> /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker
*Then download and install it yourself following the instructions here ?> https://www.repeatmasker.org/RepeatMasker/
*Then change the location of RepeatMasker= in the maker_exe.ctl file to point to the new installation

At the very least you will be able to see any failure messages during the RepeatMasker install that will indicate what is happening on your local system.

?Carson


> On Oct 14, 2021, at 2:22 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module? 
> Thanks,
> Steve Miller
> University of Wyoming
> 
> [fungi at tlog2 testdata]$ maker
> 
> Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
> 
> 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:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore
> 
>  
> To access files for individual sequences use the datastore index:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
>  
> STATUS: Now running MAKER...
> 
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> #---------------------------------------------------------------------
> 
> Now starting the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
> #---------------------------------------------------------------------
> 
> Now retrying the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> Tries: 2!!
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
>  
>  
> Maker is now finished!!!
> 
>  
>  
>  
> Start_time: 1634230718
> 
> End_time:   1634230724
> 
> Elapsed:    6
> 
> [fungi at tlog2 testdata]$
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0002.p7s>

From carsonhh at gmail.com  Tue Oct 19 23:40:56 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 23:40:56 -0600
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <A34FA21F-F20B-4EE1-95C7-513D2586F09F@gmail.com>

Funnanotate takes FASTA as input. But if you still choose the MAKER route, BUSCO can train Augustus for you (BUSCO also runs much faster than MAKER). Once you have trained Augustus, you could use MAKER to annotate just a few contigs (not the whole genome). That might give you something to work with, since you are only looking for some preliminary data.

?Carson


> On Oct 6, 2021, at 2:28 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?
> 
> Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.
> 
> For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.
> 
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics
> 
> Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!
> 
> 
> 
>> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>> wrote:
>> 
>> ? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.
>> 
>> Thanks, Jason!
>>  
>> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>>
>> Date: Wednesday, October 6, 2021 at 10:35 AM
>> To: "Steven L. Miller" <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>>
>> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC
>>  
>> Steven - 
>>  
>> You might start with the galaxy install and tutorial or the cyverse one.
>> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html <https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html>
>> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html <https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html>
>> http://gmod.org/wiki/MAKER_Tutorial <http://gmod.org/wiki/MAKER_Tutorial>
>> Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?
>>  
>> I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets. 
>> https://funannotate.readthedocs.io/en/latest/ <https://funannotate.readthedocs.io/en/latest/> - 
>>  
>> installation with conda https://funannotate.readthedocs.io/en/latest/install.html <https://funannotate.readthedocs.io/en/latest/install.html> 
>>  also docker image.
>> https://hub.docker.com/r/nextgenusfs/funannotate <https://hub.docker.com/r/nextgenusfs/funannotate>
>> https://github.com/reslp/funannotate-docker <https://github.com/reslp/funannotate-docker>
>>  
>> Jason Stajich
>>  
>>  
>> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>> wrote:
>>> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).  
>>>  
>>>  I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.
>>>  
>>> I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!
>>>  
>>> Sincerely,
>>> Steve Miller
>>> Botany
>>> University of Wyoming
>>> _______________________________________________
>>> 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>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0002.p7s>

From carsonhh at gmail.com  Wed Oct 20 00:07:19 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 20 Oct 2021 00:07:19 -0600
Subject: [maker-devel] How do I extract matrix from annotation
In-Reply-To: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
References: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
Message-ID: <3A1F8537-5566-4F98-B507-2EDAC41EAC89@gmail.com>

This is an older email that looks like never got an answer. Briefly you need to use Linux command line tools to evaluate the GFF3 file.

Examples:

#count protein coding transcripts
cat annotations.gff | grep -c -P ?\tmRNA\t"

#count tRNA transcripts
cat annotations.gff | grep -c -P ?\ttRNA\t"

#count snoRNA transcripts
cat annotations.gff | grep -c -P ?\tsnoRNA\t"


You can also pull out the Parent feature and count uniq entries to look at genes instead of transcripts. Example:

#count protein coding genes
cat annotations.gff | grep -c -P ?\tmRNA\t? | perl -ane ?/Parent=([^\;\n]+)/; print "$1\n?? | sort | uniq | grep -c ?"


You can also try tools like SOBA from the Sequence Ontology that give statistics on GFF3 features ?> http://www.sequenceontology.org/cgi-bin/soba.cgi

?Carson



> On Jul 27, 2021, at 9:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Carson, Greetings from Nigeria.
> Please how can I extract these matrix from my annotations?
> 
> Number of  protein-coding genes in the assembled tea plant genome  Those with known proteins and/or domains . Annotation of noncoding RNA genes  ribosomal RNA genes Number of  transfer RNA genes, Number  transcription factor genes and  simple sequence 
> 
> Thanks
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
> 
> https://orcid.org/0000-0002-8424-4859 <https://orcid.org/0000-0002-8424-4859>
> 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment-0002.p7s>

From barry.moore at genetics.utah.edu  Fri Oct 29 00:24:36 2021
From: barry.moore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 29 Oct 2021 06:24:36 +0000
Subject: [maker-devel] Support on maker
In-Reply-To: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
Message-ID: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>

Hi Gez,

I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:

http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

Cheers,

Barry

From: Gezahegn Girma <ggirmate at purdue.edu>
Date: Thursday, October 28, 2021 at 12:19 PM
To: Marvin B Moore <barry.moore at genetics.utah.edu>
Subject: Support on maker
Hi Barry,

I am using maker for genome annotation of sorghum genotype.

Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.

=========================================================
STATUS: Now running MAKER...
WARNING: Cannot find >0, trying to re-index the fasta.
stop here: 0
ERROR: Fasta index error
 at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
        Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
10-nompi/bin/../lib/Process/MpiTiers.pm line 73
          Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
         eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
          Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
iers.pm line 79
        Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
Process/MpiTiers.pm line 56
         Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
1.10-nompi/bin/maker line 669
--> rank=NA, hostname=bell-a105.rcac.purdue.edu<http://bell-a105.rcac.purdue.edu>
ERROR: Failed in tier preparation
examining contents of the fasta file and run log
.
.
.
Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its
translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
================================================================================
Regards,
Gez


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/05ba96d9/attachment-0002.html>

From dmacguig at buffalo.edu  Wed Oct 20 09:28:28 2021
From: dmacguig at buffalo.edu (Macguigan, Daniel)
Date: Wed, 20 Oct 2021 15:28:28 +0000
Subject: [maker-devel] Maker Repeat Masking model_org option with D
Message-ID: <1634743709431.3974@buffalo.edu>

Hello,


I have a straightforward question, but I can't seem to find the answer anywhere. Is it possible to specify a species/clade for Dfam masking using the model_org option in the *maker_opts.ctl file? The comment on this option says "select a model organism for RepBase masking in RepeatMasker."


As an example, I currently have RepeatMasker configured to use Dfam. It works fine when I run RepeatMasker on its own with a command like this.


RepeatMasker -gff -species Arthropoda -dir ./RMask_dir


However, when I specify "model_org=Arthropoda" in the maker_opts.ctl file, I get a message "ERROR: Could not determine if RepBase is installed"


I am using RepeatMasker v.4.1.1 and Maker v.3.01.03.


Thanks,

Dan


--
Dan MacGuigan, PhD
he-him-his
Postdoctoral Fellow
Department of Biological Sciences
University at Buffalo
@DMacGuig
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/90eb2bd8/attachment-0002.html>

From ggirmate at purdue.edu  Fri Oct 29 08:10:01 2021
From: ggirmate at purdue.edu (Gezahegn Girma)
Date: Fri, 29 Oct 2021 10:10:01 -0400
Subject: [maker-devel] Support on maker
In-Reply-To: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
	<BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
Message-ID: <3DD1C99A-FCDD-4AC2-894F-0BB8DFEF6883@purdue.edu>

Hi Barry,

Thank you so much for the kind reply and suggestion to join mailing list.

Looking forward for support to resolve the issues.

Regards,
Gez

> On Oct 29, 2021, at 02:24, Marvin B Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Gez,
>  
> I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:
>  
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
>  
> Cheers,
>  
> Barry
>  
> From: Gezahegn Girma <ggirmate at purdue.edu>
> Date: Thursday, October 28, 2021 at 12:19 PM
> To: Marvin B Moore <barry.moore at genetics.utah.edu>
> Subject: Support on maker
> 
> Hi Barry,
>  
> I am using maker for genome annotation of sorghum genotype.
>  
> Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.
>  
> =========================================================
> STATUS: Now running MAKER...
> WARNING: Cannot find >0, trying to re-index the fasta.
> stop here: 0
> ERROR: Fasta index error
>  at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
>         Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
> 10-nompi/bin/../lib/Process/MpiTiers.pm line 73
>           Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
>          eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
>           Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
> iers.pm line 79
>         Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
> Process/MpiTiers.pm line 56
>          Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
> 1.10-nompi/bin/maker line 669
> --> rank=NA, hostname=bell-a105.rcac.purdue.edu <http://bell-a105.rcac.purdue.edu/>
> ERROR: Failed in tier preparation
> examining contents of the fasta file and run log
> .
> .
> .
> Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its 
> translation. Please verify the query sequence(s) and/or filtering options
> deleted:0 hits
> ================================================================================
> Regards,
> Gez

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/96e9e4f1/attachment-0002.html>

From Fungi at uwyo.edu  Tue Oct  5 14:48:13 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Tue, 5 Oct 2021 20:48:13 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
Message-ID: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!


Sincerely,
Steve Miller
Botany
University of Wyoming
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211005/1a05caf5/attachment-0003.html>

From jason.stajich at gmail.com  Wed Oct  6 10:33:50 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 09:33:50 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
Message-ID: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To
gain better help you might specify the problems you are having in running
or installing?

I'll also point out a parallel genome annotation tool we have built called
funannotate which does the prediction training automatically from BUSCO or
RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda
https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Sorry to say probably not a new issue.  I saw that MAKER is an
> easy-to-use genome annotation pipeline designed to be usable by small
> research groups with little bioinformatics experience.  That statement
> describes me to a t.  I am new to Whole Genome Sequencing and associated
> analysis, and have a limited skill set with computers.  I have a a 1.52
> GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I
> would like to predict functional genes.  I have tried to follow the
> tutorial that you have posted for Winter School 2018 to see if I can
> duplicate your installation and implementation for my HPC.  I doubt that
> you will be impressed, but I recently received a ?certificate? for
> completing our HPC Linux course path the University of Wyoming. .  I
> realize now how much I don?t know and how much work it will take to
> complete an annotation, but I am needing to generate at least some
> preliminary data to include in an upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/6e71c865/attachment-0003.html>

From myandell at genetics.utah.edu  Wed Oct  6 11:11:47 2021
From: myandell at genetics.utah.edu (Mark Yandell)
Date: Wed, 6 Oct 2021 17:11:47 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
Message-ID: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Jason Stajich <jason.stajich at gmail.com>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming
_______________________________________________
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/a0ebc1b3/attachment-0003.html>

From jason.stajich at gmail.com  Wed Oct  6 18:53:42 2021
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 6 Oct 2021 17:53:42 -0700
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <CALf8LpzFGsrV7DFAP19WaUNBx80XeDuCzmGZKEkPrvbgAeDdAQ@mail.gmail.com>

It?s just a genome assembly as input. Nothing more.

On Wed, Oct 6, 2021 at 1:28 PM Steven L. Miller <Fungi at uwyo.edu> wrote:

> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach
> and as you predicted my dataset is too large to run an annotation locally
> on my laptop - about 157 x too large by my calculations.  I would be happy
> to try your funannotate tool, but my dataset is in Fasta, and I would have
> to run BUSCO to get my Fasta data into a different format?  Because of the
> size of my WGS, that would likely have to be done on the HPC?
>
> Although I do not have all the experience necessary to pull this off
> quickly, I am thinking about my experimental design and the steps that I
> will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this
> plant functions differently from its fully photosynthetic cousin and if all
> related non-photosynthetic plants function in the same way.  There are two
> annotated genomes of closely related plants in NCBI: 1.  another fairly
> closely related non-photosynthetic plant and 2. a fairly closely related
> fully photosynthetic plant.  I do not have a clue as to how good either
> these annotations are.
>
> For the annotation portion of my WGS, I can understand using the fairly
> closely related fully photosynthetic plant to train my annotation gene
> prediction, assuming that all functional genes required for photosynthesis
> and metabolism are present in this plant.  Once my WGS is annotated, I can
> then move on to compare the functional genes in both non-photosynthetic
> plants.
>
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version
> 2.31.10 is installed on my HPC, but I don?t know if all the associated
> tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I
> would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI
> (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again
> in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER
> (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from
> InterProScan and a BLAST report of homology and script maker_map_ids to
> make pretty graphics
>
> Thanks again for any help you can provide.  I wish there was an upcoming
> workshop I could attend to get into this process in a hurry!
>
>
>
> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu>
> wrote:
>
> ? This message was sent from a non-UWYO address. Please exercise caution
> when clicking links or opening attachments from external sources.
>
>
> Thanks, Jason!
>
> *From: *maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of
> Jason Stajich <jason.stajich at gmail.com>
> *Date: *Wednesday, October 6, 2021 at 10:35 AM
> *To: *"Steven L. Miller" <Fungi at uwyo.edu>
> *Cc: *"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> *Subject: *Re: [maker-devel] Adapting MAKER pipeline for my HPC
>
> Steven -
>
> You might start with the galaxy install and tutorial or the cyverse one.
>
> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
>
> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
> http://gmod.org/wiki/MAKER_Tutorial
> Not sure if the space needed will be too much for your large genome.  To
> gain better help you might specify the problems you are having in running
> or installing?
>
> I'll also point out a parallel genome annotation tool we have built called
> funannotate which does the prediction training automatically from BUSCO or
> RNASeq datasets.
> https://funannotate.readthedocs.io/en/latest/ -
>
> installation with conda
> https://funannotate.readthedocs.io/en/latest/install.html
>  also docker image.
> https://hub.docker.com/r/nextgenusfs/funannotate
> https://github.com/reslp/funannotate-docker
>
> Jason Stajich
>
>
> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu> wrote:
>
> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use
> genome annotation pipeline designed to be usable by small research groups
> with little bioinformatics experience.  That statement describes me to a t.
>   I am new to Whole Genome Sequencing and associated analysis, and have a
> limited skill set with computers.  I have a a 1.52 GB, 75k unitigs,
> non-photosynthetic vascular plant assembly for which I would like to
> predict functional genes.  I have tried to follow the tutorial that you
> have posted for Winter School 2018 to see if I can duplicate your
> installation and implementation for my HPC.  I doubt that you will be
> impressed, but I recently received a ?certificate? for completing our HPC
> Linux course path the University of Wyoming. .  I realize now how much I
> don?t know and how much work it will take to complete an annotation, but I
> am needing to generate at least some preliminary data to include in an
> upcoming grant submittal (~2 months).
>
>  I read your MAKER wiki page, but it seems that it hasn?t been completed
> in many cases, with many important parts (important parts to me, in any
> case) under construction.
>
> I am writing to get any help I can to find a way forward in my project.
> Any suggestions and any help you can provide would be gratefully accepted!
>
>
>
> Sincerely,
> Steve Miller
> Botany
> University of Wyoming
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> --
Jason Stajich
jason.stajich at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/426fb22f/attachment-0003.html>

From Fungi at uwyo.edu  Wed Oct  6 14:28:16 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Wed, 6 Oct 2021 20:28:16 +0000
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
Message-ID: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>

Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?

Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
My experimental design is this:
I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.

For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.

So, these are the steps I must figure out to run this analysis on my HPC:
1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics

Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!



On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>> wrote:

? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).


 I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming

_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211006/2396e851/attachment-0003.html>

From Fungi at uwyo.edu  Thu Oct 14 14:22:33 2021
From: Fungi at uwyo.edu (Steven L. Miller)
Date: Thu, 14 Oct 2021 20:22:33 +0000
Subject: [maker-devel] failed to run MAKER tutorial test data
Message-ID: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>

As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module?
Thanks,
Steve Miller
University of Wyoming

[fungi at tlog2 testdata]$ maker
Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
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:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: contig-dpp-500-500
Length: 32156
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: contig-dpp-500-500
Length: 32156
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
ERROR: RepeatMasker failed
--> rank=NA, hostname=tlog2
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:contig-dpp-500-500

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
did not finish on the last run and must be erased


Maker is now finished!!!



Start_time: 1634230718
End_time:   1634230724
Elapsed:    6
[fungi at tlog2 testdata]$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211014/de5af1c9/attachment-0003.html>

From carsonhh at gmail.com  Tue Oct 19 21:33:05 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 21:33:05 -0600
Subject: [maker-devel] failed to run MAKER tutorial test data
In-Reply-To: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
References: <FE7169E8-6D77-4A45-8B7B-4C206E0567D5@uwyo.edu>
Message-ID: <EA18D7B7-BE1C-4354-A03A-889D24EAE8C6@gmail.com>

RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER install it for you.

*Delete the MAKER installed copy ?> /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker
*Then download and install it yourself following the instructions here ?> https://www.repeatmasker.org/RepeatMasker/
*Then change the location of RepeatMasker= in the maker_exe.ctl file to point to the new installation

At the very least you will be able to see any failure messages during the RepeatMasker install that will indicate what is happening on your local system.

?Carson


> On Oct 14, 2021, at 2:22 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module? 
> Thanks,
> Steve Miller
> University of Wyoming
> 
> [fungi at tlog2 testdata]$ maker
> 
> Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
> 
> 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:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore
> 
>  
> To access files for individual sequences use the datastore index:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
>  
> STATUS: Now running MAKER...
> 
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> #---------------------------------------------------------------------
> 
> Now starting the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
> #---------------------------------------------------------------------
> 
> Now retrying the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> Tries: 2!!
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
>  
>  
> Maker is now finished!!!
> 
>  
>  
>  
> Start_time: 1634230718
> 
> End_time:   1634230724
> 
> Elapsed:    6
> 
> [fungi at tlog2 testdata]$
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/7e45286f/attachment-0003.p7s>

From carsonhh at gmail.com  Tue Oct 19 23:40:56 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 19 Oct 2021 23:40:56 -0600
Subject: [maker-devel] Adapting MAKER pipeline for my HPC
In-Reply-To: <5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
References: <34B451FB-ACFA-4FEA-B543-818E49C3EB4F@uwyo.edu>
	<CALf8Lpyx6H2CS41UJ6jY110N=PwVdOKPtE=ZxOAUgrhPUXoQnA@mail.gmail.com>
	<DD0D3079-756B-4D41-9A99-A4E16AA5DD28@umail.utah.edu>
	<5DB0986F-11B4-4BBA-B021-CABDB97EC7A1@uwyo.edu>
Message-ID: <A34FA21F-F20B-4EE1-95C7-513D2586F09F@gmail.com>

Funnanotate takes FASTA as input. But if you still choose the MAKER route, BUSCO can train Augustus for you (BUSCO also runs much faster than MAKER). Once you have trained Augustus, you could use MAKER to annotate just a few contigs (not the whole genome). That might give you something to work with, since you are only looking for some preliminary data.

?Carson


> On Oct 6, 2021, at 2:28 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> Yes thank you Jason for responding!  Yes I have tried the Galaxy approach and as you predicted my dataset is too large to run an annotation locally on my laptop - about 157 x too large by my calculations.  I would be happy to try your funannotate tool, but my dataset is in Fasta, and I would have to run BUSCO to get my Fasta data into a different format?  Because of the size of my WGS, that would likely have to be done on the HPC?
> 
> Although I do not have all the experience necessary to pull this off quickly, I am thinking about my experimental design and the steps that I will have to accomplish.
> My experimental design is this:
> I have a non-photosynthetic plant.  I want to eventually find out how this plant functions differently from its fully photosynthetic cousin and if all related non-photosynthetic plants function in the same way.  There are two annotated genomes of closely related plants in NCBI: 1.  another fairly closely related non-photosynthetic plant and 2. a fairly closely related fully photosynthetic plant.  I do not have a clue as to how good either these annotations are.
> 
> For the annotation portion of my WGS, I can understand using the fairly closely related fully photosynthetic plant to train my annotation gene prediction, assuming that all functional genes required for photosynthesis and metabolism are present in this plant.  Once my WGS is annotated, I can then move on to compare the functional genes in both non-photosynthetic plants.
> 
> So, these are the steps I must figure out to run this analysis on my HPC:
> 1.  installation of necessary MAKER related bits of software?  MAKER version 2.31.10 is installed on my HPC, but I don?t know if all the associated tools are also installed (e.g. Augustus)
> 2.  upload my assembled WGS in fasta format (from my limited knowledge I would need to use GlobusFTP?)
> 3.  upload the annotated WGS of the fully photosynthetic plant from NCBI (again in Fasta using Globus FTP?)
> 4.  upload the annotated WGS of the other non-photosynthetic plant (again in Fasta using Globus FTP?)
> 5.  Run MAKER, using one or the other fully annotated WGS to train MAKER (or Augustus)  to predict the genes from my non-photosynthetic plant
> 6.  Use the ugly MAKER output data in GFF3 along with reports from InterProScan and a BLAST report of homology and script maker_map_ids to make pretty graphics
> 
> Thanks again for any help you can provide.  I wish there was an upcoming workshop I could attend to get into this process in a hurry!
> 
> 
> 
>> On Oct 6, 2021, at 11:11 AM, Mark Yandell <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>> wrote:
>> 
>> ? This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources.
>> 
>> Thanks, Jason!
>>  
>> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Jason Stajich <jason.stajich at gmail.com <mailto:jason.stajich at gmail.com>>
>> Date: Wednesday, October 6, 2021 at 10:35 AM
>> To: "Steven L. Miller" <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>>
>> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC
>>  
>> Steven - 
>>  
>> You might start with the galaxy install and tutorial or the cyverse one.
>> https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html <https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html>
>> https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html <https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html>
>> http://gmod.org/wiki/MAKER_Tutorial <http://gmod.org/wiki/MAKER_Tutorial>
>> Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?
>>  
>> I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets. 
>> https://funannotate.readthedocs.io/en/latest/ <https://funannotate.readthedocs.io/en/latest/> - 
>>  
>> installation with conda https://funannotate.readthedocs.io/en/latest/install.html <https://funannotate.readthedocs.io/en/latest/install.html> 
>>  also docker image.
>> https://hub.docker.com/r/nextgenusfs/funannotate <https://hub.docker.com/r/nextgenusfs/funannotate>
>> https://github.com/reslp/funannotate-docker <https://github.com/reslp/funannotate-docker>
>>  
>> Jason Stajich
>>  
>>  
>> On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu <mailto:Fungi at uwyo.edu>> wrote:
>>> Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a ?certificate? for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don?t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).  
>>>  
>>>  I read your MAKER wiki page, but it seems that it hasn?t been completed in many cases, with many important parts (important parts to me, in any case) under construction.
>>>  
>>> I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!
>>>  
>>> Sincerely,
>>> Steve Miller
>>> Botany
>>> University of Wyoming
>>> _______________________________________________
>>> 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>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211019/c113a1ac/attachment-0003.p7s>

From carsonhh at gmail.com  Wed Oct 20 00:07:19 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 20 Oct 2021 00:07:19 -0600
Subject: [maker-devel] How do I extract matrix from annotation
In-Reply-To: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
References: <CAOXM=CVJqKtuSrtw0NaEh1d3yJVL4QwZcWnSL8+uvJevSBQc2A@mail.gmail.com>
Message-ID: <3A1F8537-5566-4F98-B507-2EDAC41EAC89@gmail.com>

This is an older email that looks like never got an answer. Briefly you need to use Linux command line tools to evaluate the GFF3 file.

Examples:

#count protein coding transcripts
cat annotations.gff | grep -c -P ?\tmRNA\t"

#count tRNA transcripts
cat annotations.gff | grep -c -P ?\ttRNA\t"

#count snoRNA transcripts
cat annotations.gff | grep -c -P ?\tsnoRNA\t"


You can also pull out the Parent feature and count uniq entries to look at genes instead of transcripts. Example:

#count protein coding genes
cat annotations.gff | grep -c -P ?\tmRNA\t? | perl -ane ?/Parent=([^\;\n]+)/; print "$1\n?? | sort | uniq | grep -c ?"


You can also try tools like SOBA from the Sequence Ontology that give statistics on GFF3 features ?> http://www.sequenceontology.org/cgi-bin/soba.cgi

?Carson



> On Jul 27, 2021, at 9:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Carson, Greetings from Nigeria.
> Please how can I extract these matrix from my annotations?
> 
> Number of  protein-coding genes in the assembled tea plant genome  Those with known proteins and/or domains . Annotation of noncoding RNA genes  ribosomal RNA genes Number of  transfer RNA genes, Number  transcription factor genes and  simple sequence 
> 
> Thanks
> 
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
> 
> https://orcid.org/0000-0002-8424-4859 <https://orcid.org/0000-0002-8424-4859>
> 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/b8841a68/attachment-0003.p7s>

From barry.moore at genetics.utah.edu  Fri Oct 29 00:24:36 2021
From: barry.moore at genetics.utah.edu (Marvin B Moore)
Date: Fri, 29 Oct 2021 06:24:36 +0000
Subject: [maker-devel] Support on maker
In-Reply-To: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
Message-ID: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>

Hi Gez,

I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:

http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

Cheers,

Barry

From: Gezahegn Girma <ggirmate at purdue.edu>
Date: Thursday, October 28, 2021 at 12:19 PM
To: Marvin B Moore <barry.moore at genetics.utah.edu>
Subject: Support on maker
Hi Barry,

I am using maker for genome annotation of sorghum genotype.

Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.

=========================================================
STATUS: Now running MAKER...
WARNING: Cannot find >0, trying to re-index the fasta.
stop here: 0
ERROR: Fasta index error
 at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
        Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
10-nompi/bin/../lib/Process/MpiTiers.pm line 73
          Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
         eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
          Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
iers.pm line 79
        Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
Process/MpiTiers.pm line 56
         Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
1.10-nompi/bin/maker line 669
--> rank=NA, hostname=bell-a105.rcac.purdue.edu<http://bell-a105.rcac.purdue.edu>
ERROR: Failed in tier preparation
examining contents of the fasta file and run log
.
.
.
Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its
translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
================================================================================
Regards,
Gez


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/05ba96d9/attachment-0003.html>

From dmacguig at buffalo.edu  Wed Oct 20 09:28:28 2021
From: dmacguig at buffalo.edu (Macguigan, Daniel)
Date: Wed, 20 Oct 2021 15:28:28 +0000
Subject: [maker-devel] Maker Repeat Masking model_org option with D
Message-ID: <1634743709431.3974@buffalo.edu>

Hello,


I have a straightforward question, but I can't seem to find the answer anywhere. Is it possible to specify a species/clade for Dfam masking using the model_org option in the *maker_opts.ctl file? The comment on this option says "select a model organism for RepBase masking in RepeatMasker."


As an example, I currently have RepeatMasker configured to use Dfam. It works fine when I run RepeatMasker on its own with a command like this.


RepeatMasker -gff -species Arthropoda -dir ./RMask_dir


However, when I specify "model_org=Arthropoda" in the maker_opts.ctl file, I get a message "ERROR: Could not determine if RepBase is installed"


I am using RepeatMasker v.4.1.1 and Maker v.3.01.03.


Thanks,

Dan


--
Dan MacGuigan, PhD
he-him-his
Postdoctoral Fellow
Department of Biological Sciences
University at Buffalo
@DMacGuig
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211020/90eb2bd8/attachment-0003.html>

From ggirmate at purdue.edu  Fri Oct 29 08:10:01 2021
From: ggirmate at purdue.edu (Gezahegn Girma)
Date: Fri, 29 Oct 2021 10:10:01 -0400
Subject: [maker-devel] Support on maker
In-Reply-To: <BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
References: <F70694A2-F421-4E8D-A54C-5332F9E1EB5F@purdue.edu>
	<BYAPR11MB36382A7BC415D0FE920C05F4AC879@BYAPR11MB3638.namprd11.prod.outlook.com>
Message-ID: <3DD1C99A-FCDD-4AC2-894F-0BB8DFEF6883@purdue.edu>

Hi Barry,

Thank you so much for the kind reply and suggestion to join mailing list.

Looking forward for support to resolve the issues.

Regards,
Gez

> On Oct 29, 2021, at 02:24, Marvin B Moore <barry.moore at genetics.utah.edu> wrote:
> 
> Hi Gez,
>  
> I?m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren?t aleady a member of this mailing list, I?d highly recommend you join here:
>  
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
>  
> Cheers,
>  
> Barry
>  
> From: Gezahegn Girma <ggirmate at purdue.edu>
> Date: Thursday, October 28, 2021 at 12:19 PM
> To: Marvin B Moore <barry.moore at genetics.utah.edu>
> Subject: Support on maker
> 
> Hi Barry,
>  
> I am using maker for genome annotation of sorghum genotype.
>  
> Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.
>  
> =========================================================
> STATUS: Now running MAKER...
> WARNING: Cannot find >0, trying to re-index the fasta.
> stop here: 0
> ERROR: Fasta index error
>  at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
>         Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
> 10-nompi/bin/../lib/Process/MpiTiers.pm line 73
>           Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
>          eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
>           Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
> iers.pm line 79
>         Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
> Process/MpiTiers.pm line 56
>          Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
> 1.10-nompi/bin/maker line 669
> --> rank=NA, hostname=bell-a105.rcac.purdue.edu <http://bell-a105.rcac.purdue.edu/>
> ERROR: Failed in tier preparation
> examining contents of the fasta file and run log
> .
> .
> .
> Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its 
> translation. Please verify the query sequence(s) and/or filtering options
> deleted:0 hits
> ================================================================================
> Regards,
> Gez

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20211029/96e9e4f1/attachment-0003.html>