From ABoyher at danforthcenter.org  Wed Jan 15 18:56:47 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 01:56:47 +0000
Subject: [maker-devel] Maker failing
Message-ID: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From cjfields at illinois.edu  Thu Jan 16 08:03:46 2020
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 Jan 2020 15:03:46 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
Message-ID: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From ABoyher at danforthcenter.org  Thu Jan 16 08:42:53 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 15:42:53 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>,
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
Message-ID: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>

Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.

Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: Fields, Christopher J <cjfields at illinois.edu>
Sent: Thursday, January 16, 2020 9:03:46 AM
To: Boyher, Adam <ABoyher at danforthcenter.org>; maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Maker failing

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From carsonhh at gmail.com  Wed Jan 22 10:53:37 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 10:53:37 -0700
Subject: [maker-devel] Maker installation-RepeatMasker (or running
 RepeatMasker outside maker)
In-Reply-To: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
References: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
Message-ID: <5E517EE3-4AF1-4205-88EC-599AF01C7128@gmail.com>

You can manually specify a path in maker_exe.ctl

?Carson


> On Dec 29, 2019, at 3:03 PM, Linnie Linnie <peachandolives at gmail.com> wrote:
> 
> Dear Maker team,
> 
> I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly.  
> However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? 
> 
> I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error:
> 
> Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.
> Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> ERROR: RepeatMasker failed
> --> rank=NA, hostname=loma
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:NQYS01000001.1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:NQYS01000001.1
> 
> examining contents of the fasta file and run log
> 
> As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? 
> 
> 
> Thank you so much for all your help (and Happy New Year to everyone!)
> L. 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From ovidiu.paun at univie.ac.at  Wed Jan 22 01:23:20 2020
From: ovidiu.paun at univie.ac.at (Ovidiu Paun)
Date: Wed, 22 Jan 2020 09:23:20 +0100
Subject: [maker-devel] Illegal division by zero while polishing ESTs
Message-ID: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>

Hi

I have been using maker to annotate a genome and all went fine. However I
have obtained a new transcriptome (from a Trinity assembly) and implemented
it as a EST fasta file. Since then I get errors for some of the contigs (but
not all!):

 

Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.

--> rank=NA, hostname=8767v89

ERROR: Failed while polishig ESTs

ERROR: Chunk failed at level:2, tier_type:3

FAILED CONTIG:scaffold21

 

I checked the transcriptome fasta file and apart from the fact that it is
pretty large (ca 500k contigs), I do not see any errors.

I would greatly appreaciate any help.

Best wishes

Ovidiu Paun

 

Assoc.-Prof. Dr. Ovidiu Paun

Department of Botany and Biodiversity Research

University of Vienna

 <http://plantgenomics.univie.ac.at> http://plantgenomics.univie.ac.at 

 

 

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From carsonhh at gmail.com  Wed Jan 22 11:31:59 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:31:59 -0700
Subject: [maker-devel] Maker failing
In-Reply-To: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
	<BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
Message-ID: <F9686BDC-D3E6-4CDA-9F22-7A6BA113A70E@gmail.com>

The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward.  Let TMP= in the maker_opts.ctl file be the default of /tmp.

?Carson



> On Jan 16, 2020, at 8:42 AM, Boyher, Adam <ABoyher at danforthcenter.org> wrote:
> 
> Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.
> 
> Get Outlook for Android <https://aka.ms/ghei36>
> From: Fields, Christopher J <cjfields at illinois.edu <mailto:cjfields at illinois.edu>>
> Sent: Thursday, January 16, 2020 9:03:46 AM
> To: Boyher, Adam <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>; 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] Maker failing
>  
> It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.
>  
> chris
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>
> Date: Wednesday, January 15, 2020 at 7:57 PM
> To: "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: [maker-devel] Maker failing
>  
> Hi
> I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:
>  
> ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
> MAKER will need to delete the file, before trying again
>  
> --> rank=12, hostname=pacifica.datasci.danforthcenter.org <http://pacifica.datasci.danforthcenter.org/>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:Chromosome10_0
>  
>  
> Any idea what could cause that?
> 
> Adam
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Wed Jan 22 11:38:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:38:45 -0700
Subject: [maker-devel] maker-devel post from
 david.carlson@stonybrook.edu requires approval
In-Reply-To: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <2A9D6FC3-A1D5-498D-9A02-0C0DE420200F@gmail.com>

Try both ways (run in same maker directory to avoid reprocessing of evidence alignments). Then look at the output in a browser. Really the best way to decide which works best id manual evaluation.

?Carson



> From: David Carlson <david.carlson at stonybrook.edu>
> Subject: Training Augustus using Transdecoder output
> Date: January 7, 2020 at 1:47:23 PM MST
> To: maker-devel at yandell-lab.org
> 
> 
> Hi Maker users and developers,
> I'm currently in the process of annotating a new genome, and I have a question regarding training Augustus.
> 
> I have RNA-Seq data from my organism, which I've mapped to my genome assembly with Hisat2 and assembled into transcripts with StringTie.  
> 
> I've used these transcripts to predict proteining coding genes with Transdecoder (using homology evidence from the swissprot and Pfam databases).
> 
> I was thinking about taking the Transdecoder output, (after removing sequences that are not full length) and using these as the initial training set for Augustus.
> 
> In the past, I've used Busco for the initial Augustus training, but my thought is that these Transdecoder predicted genes might be a better source of evidence for my particular species.
> 
> Do any of you have experience trying this approach, or thoughts regarding its merits?
> Thanks!
> Dave
> 
> -- 
> Dave Carlson
> PhD Candidate
> Ecology and Evolution Department
> Stony Brook University

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From carsonhh at gmail.com  Wed Jan 22 11:56:27 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:56:27 -0700
Subject: [maker-devel] Illegal division by zero while polishing ESTs
In-Reply-To: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
References: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
Message-ID: <051E102E-4F07-4212-9201-309E96243B1D@gmail.com>

It?s obtaining a sequence length of zero. You may have empty entries in your sequence file. Look at the STDERR and the ID of the sequence causing the issue will be in the command name. It may be as simple as editing and removing it from your input file.

?Carson



> On Jan 22, 2020, at 1:23 AM, Ovidiu Paun <ovidiu.paun at univie.ac.at> wrote:
> 
> Hi
> I have been using maker to annotate a genome and all went fine. However I have obtained a new transcriptome (from a Trinity assembly) and implemented it as a EST fasta file. Since then I get errors for some of the contigs (but not all!):
>  
> Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.
> --> rank=NA, hostname=8767v89
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:scaffold21
>  
> I checked the transcriptome fasta file and apart from the fact that it is pretty large (ca 500k contigs), I do not see any errors.
> I would greatly appreaciate any help.
> Best wishes
> Ovidiu Paun
>  
> Assoc.-Prof. Dr. Ovidiu Paun
> Department of Botany and Biodiversity Research
> University of Vienna
> http://plantgenomics.univie.ac.at <http://plantgenomics.univie.ac.at/>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From Robin.Haw at oicr.on.ca  Tue Jan 28 14:15:42 2020
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Tue, 28 Jan 2020 21:15:42 +0000
Subject: [maker-devel] [GSoC 2020] [Open Genome Informatics] Google Summer
 of Code 2020 Participation
Message-ID: <A4A4DF77-BBCF-45B6-9F09-9095C1458696@oicr.on.ca>

Dear All,
Sorry for the multiple postings!

The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2020 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.

For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>

Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org

Collaborate. Translate. Change lives.

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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From scott at scottcain.net  Fri Jan 31 11:05:32 2020
From: scott at scottcain.net (Scott Cain)
Date: Fri, 31 Jan 2020 10:05:32 -0800
Subject: [maker-devel] Google Summer of Code
Message-ID: <CA+JTaoyWRKrNvXPJ_WmJhr=Vcnq+0WfzFNU6k-SNCZpigZYdxg@mail.gmail.com>

Hi all,

It's that time of year to be putting together Google Summer of Code project
ideas.  The deadline is fast approaching.  The application is due on Feb 5,
so if you'd like to get some ideas on the wiki page, now is the time:

http://gmod.org/wiki/GSOC_Project_Ideas_2020

If you need an account to edit the page, please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From had38 at cam.ac.uk  Wed Jan 29 07:42:24 2020
From: had38 at cam.ac.uk (H.DENISE)
Date: Wed, 29 Jan 2020 14:42:24 +0000
Subject: [maker-devel] Avoiding re-indexing the same file
Message-ID: <BF8AF51A-8D0A-4AC3-8D1B-223C5CE2D218@cam.ac.uk>

Hi,
I?m new to Maker and need to compare the annotations with different features (+/- RepeatMasker, using different protein files etc ?). However the first step seems to be the indexing of my files and the RNASeq file I?m using is large, therefore Maker seems to take ages at this step,. As it is a constant file for my applications, is there a way to provide the indexing file in order to avoid repeating this step?
Thanks in advance, Hubert



Hubert DENISE, PhD

Genome Data Analyst
R.Durbin's group
Department of Genetics
University of Cambridge

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From eabernathy at ucdavis.edu  Fri Jan 31 14:50:22 2020
From: eabernathy at ucdavis.edu (Emily Abernathy)
Date: Fri, 31 Jan 2020 13:50:22 -0800
Subject: [maker-devel] Error: FASTA header doesn't match '>(\S+)'
Message-ID: <CACWrxM1a8FpLnQnmEQOvX1MiZP7CK7adgbCZrM0yyf2ghhzWcA@mail.gmail.com>

Hello,
    I am running MAKER for the first time and I have been unable to resolve
an error. The error is as follows:
[image: image.png]
I am using a genome that I assembled in Supernova v2 with headers that
resemble this:
>1 edges=1057764..867844 left=488686 right=145511 ver=1.10 style=3

and I downloaded two fasta files from ENSEMBL whose headers resemble this:
>ENSTGUT00000018018.1 cdna
chromosome:taeGut3.2.4:8_random:2849599:2959678:-1
gene:ENSTGUG00000017338.1 gene_biotype:protein_coding
transcript_biotype:protein_coding

and

>ENSTGUP00000017615.1 pep chromosome:taeGut3.2.4:23_random:205321:209117:1
gene:ENSTGUG00000017337.1 transcript:ENSTGUT00000018017.1
gene_biotype:protein_coding transcript_biotype:protein_coding

These are my only input FASTA files and I have been struggling to fix this
error for almost a month now. Any and all advice on how to fix this error
is much appreciated!

Thanks in advance,
E. Abernathy



-- 
Emily Abernathy
Graduate Group in Ecology
University of California, Davis
http://hulllabucd.wix.com/hulllab
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From ABoyher at danforthcenter.org  Wed Jan 15 18:56:47 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 01:56:47 +0000
Subject: [maker-devel] Maker failing
Message-ID: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From cjfields at illinois.edu  Thu Jan 16 08:03:46 2020
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 Jan 2020 15:03:46 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
Message-ID: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From ABoyher at danforthcenter.org  Thu Jan 16 08:42:53 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 15:42:53 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>,
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
Message-ID: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>

Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.

Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: Fields, Christopher J <cjfields at illinois.edu>
Sent: Thursday, January 16, 2020 9:03:46 AM
To: Boyher, Adam <ABoyher at danforthcenter.org>; maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Maker failing

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From carsonhh at gmail.com  Wed Jan 22 10:53:37 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 10:53:37 -0700
Subject: [maker-devel] Maker installation-RepeatMasker (or running
 RepeatMasker outside maker)
In-Reply-To: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
References: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
Message-ID: <5E517EE3-4AF1-4205-88EC-599AF01C7128@gmail.com>

You can manually specify a path in maker_exe.ctl

?Carson


> On Dec 29, 2019, at 3:03 PM, Linnie Linnie <peachandolives at gmail.com> wrote:
> 
> Dear Maker team,
> 
> I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly.  
> However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? 
> 
> I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error:
> 
> Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.
> Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> ERROR: RepeatMasker failed
> --> rank=NA, hostname=loma
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:NQYS01000001.1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:NQYS01000001.1
> 
> examining contents of the fasta file and run log
> 
> As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? 
> 
> 
> Thank you so much for all your help (and Happy New Year to everyone!)
> L. 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From ovidiu.paun at univie.ac.at  Wed Jan 22 01:23:20 2020
From: ovidiu.paun at univie.ac.at (Ovidiu Paun)
Date: Wed, 22 Jan 2020 09:23:20 +0100
Subject: [maker-devel] Illegal division by zero while polishing ESTs
Message-ID: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>

Hi

I have been using maker to annotate a genome and all went fine. However I
have obtained a new transcriptome (from a Trinity assembly) and implemented
it as a EST fasta file. Since then I get errors for some of the contigs (but
not all!):

 

Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.

--> rank=NA, hostname=8767v89

ERROR: Failed while polishig ESTs

ERROR: Chunk failed at level:2, tier_type:3

FAILED CONTIG:scaffold21

 

I checked the transcriptome fasta file and apart from the fact that it is
pretty large (ca 500k contigs), I do not see any errors.

I would greatly appreaciate any help.

Best wishes

Ovidiu Paun

 

Assoc.-Prof. Dr. Ovidiu Paun

Department of Botany and Biodiversity Research

University of Vienna

 <http://plantgenomics.univie.ac.at> http://plantgenomics.univie.ac.at 

 

 

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From carsonhh at gmail.com  Wed Jan 22 11:31:59 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:31:59 -0700
Subject: [maker-devel] Maker failing
In-Reply-To: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
	<BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
Message-ID: <F9686BDC-D3E6-4CDA-9F22-7A6BA113A70E@gmail.com>

The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward.  Let TMP= in the maker_opts.ctl file be the default of /tmp.

?Carson



> On Jan 16, 2020, at 8:42 AM, Boyher, Adam <ABoyher at danforthcenter.org> wrote:
> 
> Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.
> 
> Get Outlook for Android <https://aka.ms/ghei36>
> From: Fields, Christopher J <cjfields at illinois.edu <mailto:cjfields at illinois.edu>>
> Sent: Thursday, January 16, 2020 9:03:46 AM
> To: Boyher, Adam <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>; 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] Maker failing
>  
> It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.
>  
> chris
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>
> Date: Wednesday, January 15, 2020 at 7:57 PM
> To: "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: [maker-devel] Maker failing
>  
> Hi
> I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:
>  
> ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
> MAKER will need to delete the file, before trying again
>  
> --> rank=12, hostname=pacifica.datasci.danforthcenter.org <http://pacifica.datasci.danforthcenter.org/>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:Chromosome10_0
>  
>  
> Any idea what could cause that?
> 
> Adam
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Wed Jan 22 11:38:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:38:45 -0700
Subject: [maker-devel] maker-devel post from
 david.carlson@stonybrook.edu requires approval
In-Reply-To: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <2A9D6FC3-A1D5-498D-9A02-0C0DE420200F@gmail.com>

Try both ways (run in same maker directory to avoid reprocessing of evidence alignments). Then look at the output in a browser. Really the best way to decide which works best id manual evaluation.

?Carson



> From: David Carlson <david.carlson at stonybrook.edu>
> Subject: Training Augustus using Transdecoder output
> Date: January 7, 2020 at 1:47:23 PM MST
> To: maker-devel at yandell-lab.org
> 
> 
> Hi Maker users and developers,
> I'm currently in the process of annotating a new genome, and I have a question regarding training Augustus.
> 
> I have RNA-Seq data from my organism, which I've mapped to my genome assembly with Hisat2 and assembled into transcripts with StringTie.  
> 
> I've used these transcripts to predict proteining coding genes with Transdecoder (using homology evidence from the swissprot and Pfam databases).
> 
> I was thinking about taking the Transdecoder output, (after removing sequences that are not full length) and using these as the initial training set for Augustus.
> 
> In the past, I've used Busco for the initial Augustus training, but my thought is that these Transdecoder predicted genes might be a better source of evidence for my particular species.
> 
> Do any of you have experience trying this approach, or thoughts regarding its merits?
> Thanks!
> Dave
> 
> -- 
> Dave Carlson
> PhD Candidate
> Ecology and Evolution Department
> Stony Brook University

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From carsonhh at gmail.com  Wed Jan 22 11:56:27 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:56:27 -0700
Subject: [maker-devel] Illegal division by zero while polishing ESTs
In-Reply-To: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
References: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
Message-ID: <051E102E-4F07-4212-9201-309E96243B1D@gmail.com>

It?s obtaining a sequence length of zero. You may have empty entries in your sequence file. Look at the STDERR and the ID of the sequence causing the issue will be in the command name. It may be as simple as editing and removing it from your input file.

?Carson



> On Jan 22, 2020, at 1:23 AM, Ovidiu Paun <ovidiu.paun at univie.ac.at> wrote:
> 
> Hi
> I have been using maker to annotate a genome and all went fine. However I have obtained a new transcriptome (from a Trinity assembly) and implemented it as a EST fasta file. Since then I get errors for some of the contigs (but not all!):
>  
> Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.
> --> rank=NA, hostname=8767v89
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:scaffold21
>  
> I checked the transcriptome fasta file and apart from the fact that it is pretty large (ca 500k contigs), I do not see any errors.
> I would greatly appreaciate any help.
> Best wishes
> Ovidiu Paun
>  
> Assoc.-Prof. Dr. Ovidiu Paun
> Department of Botany and Biodiversity Research
> University of Vienna
> http://plantgenomics.univie.ac.at <http://plantgenomics.univie.ac.at/>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From Robin.Haw at oicr.on.ca  Tue Jan 28 14:15:42 2020
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Tue, 28 Jan 2020 21:15:42 +0000
Subject: [maker-devel] [GSoC 2020] [Open Genome Informatics] Google Summer
 of Code 2020 Participation
Message-ID: <A4A4DF77-BBCF-45B6-9F09-9095C1458696@oicr.on.ca>

Dear All,
Sorry for the multiple postings!

The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2020 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.

For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>

Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org

Collaborate. Translate. Change lives.

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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From scott at scottcain.net  Fri Jan 31 11:05:32 2020
From: scott at scottcain.net (Scott Cain)
Date: Fri, 31 Jan 2020 10:05:32 -0800
Subject: [maker-devel] Google Summer of Code
Message-ID: <CA+JTaoyWRKrNvXPJ_WmJhr=Vcnq+0WfzFNU6k-SNCZpigZYdxg@mail.gmail.com>

Hi all,

It's that time of year to be putting together Google Summer of Code project
ideas.  The deadline is fast approaching.  The application is due on Feb 5,
so if you'd like to get some ideas on the wiki page, now is the time:

http://gmod.org/wiki/GSOC_Project_Ideas_2020

If you need an account to edit the page, please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From had38 at cam.ac.uk  Wed Jan 29 07:42:24 2020
From: had38 at cam.ac.uk (H.DENISE)
Date: Wed, 29 Jan 2020 14:42:24 +0000
Subject: [maker-devel] Avoiding re-indexing the same file
Message-ID: <BF8AF51A-8D0A-4AC3-8D1B-223C5CE2D218@cam.ac.uk>

Hi,
I?m new to Maker and need to compare the annotations with different features (+/- RepeatMasker, using different protein files etc ?). However the first step seems to be the indexing of my files and the RNASeq file I?m using is large, therefore Maker seems to take ages at this step,. As it is a constant file for my applications, is there a way to provide the indexing file in order to avoid repeating this step?
Thanks in advance, Hubert



Hubert DENISE, PhD

Genome Data Analyst
R.Durbin's group
Department of Genetics
University of Cambridge

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From eabernathy at ucdavis.edu  Fri Jan 31 14:50:22 2020
From: eabernathy at ucdavis.edu (Emily Abernathy)
Date: Fri, 31 Jan 2020 13:50:22 -0800
Subject: [maker-devel] Error: FASTA header doesn't match '>(\S+)'
Message-ID: <CACWrxM1a8FpLnQnmEQOvX1MiZP7CK7adgbCZrM0yyf2ghhzWcA@mail.gmail.com>

Hello,
    I am running MAKER for the first time and I have been unable to resolve
an error. The error is as follows:
[image: image.png]
I am using a genome that I assembled in Supernova v2 with headers that
resemble this:
>1 edges=1057764..867844 left=488686 right=145511 ver=1.10 style=3

and I downloaded two fasta files from ENSEMBL whose headers resemble this:
>ENSTGUT00000018018.1 cdna
chromosome:taeGut3.2.4:8_random:2849599:2959678:-1
gene:ENSTGUG00000017338.1 gene_biotype:protein_coding
transcript_biotype:protein_coding

and

>ENSTGUP00000017615.1 pep chromosome:taeGut3.2.4:23_random:205321:209117:1
gene:ENSTGUG00000017337.1 transcript:ENSTGUT00000018017.1
gene_biotype:protein_coding transcript_biotype:protein_coding

These are my only input FASTA files and I have been struggling to fix this
error for almost a month now. Any and all advice on how to fix this error
is much appreciated!

Thanks in advance,
E. Abernathy



-- 
Emily Abernathy
Graduate Group in Ecology
University of California, Davis
http://hulllabucd.wix.com/hulllab
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From ABoyher at danforthcenter.org  Wed Jan 15 18:56:47 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 01:56:47 +0000
Subject: [maker-devel] Maker failing
Message-ID: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From cjfields at illinois.edu  Thu Jan 16 08:03:46 2020
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 Jan 2020 15:03:46 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
Message-ID: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From ABoyher at danforthcenter.org  Thu Jan 16 08:42:53 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 15:42:53 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>,
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
Message-ID: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>

Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.

Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: Fields, Christopher J <cjfields at illinois.edu>
Sent: Thursday, January 16, 2020 9:03:46 AM
To: Boyher, Adam <ABoyher at danforthcenter.org>; maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Maker failing

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From carsonhh at gmail.com  Wed Jan 22 10:53:37 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 10:53:37 -0700
Subject: [maker-devel] Maker installation-RepeatMasker (or running
 RepeatMasker outside maker)
In-Reply-To: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
References: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
Message-ID: <5E517EE3-4AF1-4205-88EC-599AF01C7128@gmail.com>

You can manually specify a path in maker_exe.ctl

?Carson


> On Dec 29, 2019, at 3:03 PM, Linnie Linnie <peachandolives at gmail.com> wrote:
> 
> Dear Maker team,
> 
> I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly.  
> However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? 
> 
> I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error:
> 
> Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.
> Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> ERROR: RepeatMasker failed
> --> rank=NA, hostname=loma
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:NQYS01000001.1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:NQYS01000001.1
> 
> examining contents of the fasta file and run log
> 
> As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? 
> 
> 
> Thank you so much for all your help (and Happy New Year to everyone!)
> L. 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From ovidiu.paun at univie.ac.at  Wed Jan 22 01:23:20 2020
From: ovidiu.paun at univie.ac.at (Ovidiu Paun)
Date: Wed, 22 Jan 2020 09:23:20 +0100
Subject: [maker-devel] Illegal division by zero while polishing ESTs
Message-ID: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>

Hi

I have been using maker to annotate a genome and all went fine. However I
have obtained a new transcriptome (from a Trinity assembly) and implemented
it as a EST fasta file. Since then I get errors for some of the contigs (but
not all!):

 

Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.

--> rank=NA, hostname=8767v89

ERROR: Failed while polishig ESTs

ERROR: Chunk failed at level:2, tier_type:3

FAILED CONTIG:scaffold21

 

I checked the transcriptome fasta file and apart from the fact that it is
pretty large (ca 500k contigs), I do not see any errors.

I would greatly appreaciate any help.

Best wishes

Ovidiu Paun

 

Assoc.-Prof. Dr. Ovidiu Paun

Department of Botany and Biodiversity Research

University of Vienna

 <http://plantgenomics.univie.ac.at> http://plantgenomics.univie.ac.at 

 

 

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From carsonhh at gmail.com  Wed Jan 22 11:31:59 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:31:59 -0700
Subject: [maker-devel] Maker failing
In-Reply-To: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
	<BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
Message-ID: <F9686BDC-D3E6-4CDA-9F22-7A6BA113A70E@gmail.com>

The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward.  Let TMP= in the maker_opts.ctl file be the default of /tmp.

?Carson



> On Jan 16, 2020, at 8:42 AM, Boyher, Adam <ABoyher at danforthcenter.org> wrote:
> 
> Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.
> 
> Get Outlook for Android <https://aka.ms/ghei36>
> From: Fields, Christopher J <cjfields at illinois.edu <mailto:cjfields at illinois.edu>>
> Sent: Thursday, January 16, 2020 9:03:46 AM
> To: Boyher, Adam <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>; 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] Maker failing
>  
> It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.
>  
> chris
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>
> Date: Wednesday, January 15, 2020 at 7:57 PM
> To: "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: [maker-devel] Maker failing
>  
> Hi
> I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:
>  
> ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
> MAKER will need to delete the file, before trying again
>  
> --> rank=12, hostname=pacifica.datasci.danforthcenter.org <http://pacifica.datasci.danforthcenter.org/>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:Chromosome10_0
>  
>  
> Any idea what could cause that?
> 
> Adam
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Wed Jan 22 11:38:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:38:45 -0700
Subject: [maker-devel] maker-devel post from
 david.carlson@stonybrook.edu requires approval
In-Reply-To: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <2A9D6FC3-A1D5-498D-9A02-0C0DE420200F@gmail.com>

Try both ways (run in same maker directory to avoid reprocessing of evidence alignments). Then look at the output in a browser. Really the best way to decide which works best id manual evaluation.

?Carson



> From: David Carlson <david.carlson at stonybrook.edu>
> Subject: Training Augustus using Transdecoder output
> Date: January 7, 2020 at 1:47:23 PM MST
> To: maker-devel at yandell-lab.org
> 
> 
> Hi Maker users and developers,
> I'm currently in the process of annotating a new genome, and I have a question regarding training Augustus.
> 
> I have RNA-Seq data from my organism, which I've mapped to my genome assembly with Hisat2 and assembled into transcripts with StringTie.  
> 
> I've used these transcripts to predict proteining coding genes with Transdecoder (using homology evidence from the swissprot and Pfam databases).
> 
> I was thinking about taking the Transdecoder output, (after removing sequences that are not full length) and using these as the initial training set for Augustus.
> 
> In the past, I've used Busco for the initial Augustus training, but my thought is that these Transdecoder predicted genes might be a better source of evidence for my particular species.
> 
> Do any of you have experience trying this approach, or thoughts regarding its merits?
> Thanks!
> Dave
> 
> -- 
> Dave Carlson
> PhD Candidate
> Ecology and Evolution Department
> Stony Brook University

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From carsonhh at gmail.com  Wed Jan 22 11:56:27 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:56:27 -0700
Subject: [maker-devel] Illegal division by zero while polishing ESTs
In-Reply-To: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
References: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
Message-ID: <051E102E-4F07-4212-9201-309E96243B1D@gmail.com>

It?s obtaining a sequence length of zero. You may have empty entries in your sequence file. Look at the STDERR and the ID of the sequence causing the issue will be in the command name. It may be as simple as editing and removing it from your input file.

?Carson



> On Jan 22, 2020, at 1:23 AM, Ovidiu Paun <ovidiu.paun at univie.ac.at> wrote:
> 
> Hi
> I have been using maker to annotate a genome and all went fine. However I have obtained a new transcriptome (from a Trinity assembly) and implemented it as a EST fasta file. Since then I get errors for some of the contigs (but not all!):
>  
> Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.
> --> rank=NA, hostname=8767v89
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:scaffold21
>  
> I checked the transcriptome fasta file and apart from the fact that it is pretty large (ca 500k contigs), I do not see any errors.
> I would greatly appreaciate any help.
> Best wishes
> Ovidiu Paun
>  
> Assoc.-Prof. Dr. Ovidiu Paun
> Department of Botany and Biodiversity Research
> University of Vienna
> http://plantgenomics.univie.ac.at <http://plantgenomics.univie.ac.at/>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From Robin.Haw at oicr.on.ca  Tue Jan 28 14:15:42 2020
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Tue, 28 Jan 2020 21:15:42 +0000
Subject: [maker-devel] [GSoC 2020] [Open Genome Informatics] Google Summer
 of Code 2020 Participation
Message-ID: <A4A4DF77-BBCF-45B6-9F09-9095C1458696@oicr.on.ca>

Dear All,
Sorry for the multiple postings!

The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2020 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.

For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>

Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org

Collaborate. Translate. Change lives.

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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From scott at scottcain.net  Fri Jan 31 11:05:32 2020
From: scott at scottcain.net (Scott Cain)
Date: Fri, 31 Jan 2020 10:05:32 -0800
Subject: [maker-devel] Google Summer of Code
Message-ID: <CA+JTaoyWRKrNvXPJ_WmJhr=Vcnq+0WfzFNU6k-SNCZpigZYdxg@mail.gmail.com>

Hi all,

It's that time of year to be putting together Google Summer of Code project
ideas.  The deadline is fast approaching.  The application is due on Feb 5,
so if you'd like to get some ideas on the wiki page, now is the time:

http://gmod.org/wiki/GSOC_Project_Ideas_2020

If you need an account to edit the page, please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From had38 at cam.ac.uk  Wed Jan 29 07:42:24 2020
From: had38 at cam.ac.uk (H.DENISE)
Date: Wed, 29 Jan 2020 14:42:24 +0000
Subject: [maker-devel] Avoiding re-indexing the same file
Message-ID: <BF8AF51A-8D0A-4AC3-8D1B-223C5CE2D218@cam.ac.uk>

Hi,
I?m new to Maker and need to compare the annotations with different features (+/- RepeatMasker, using different protein files etc ?). However the first step seems to be the indexing of my files and the RNASeq file I?m using is large, therefore Maker seems to take ages at this step,. As it is a constant file for my applications, is there a way to provide the indexing file in order to avoid repeating this step?
Thanks in advance, Hubert



Hubert DENISE, PhD

Genome Data Analyst
R.Durbin's group
Department of Genetics
University of Cambridge

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From eabernathy at ucdavis.edu  Fri Jan 31 14:50:22 2020
From: eabernathy at ucdavis.edu (Emily Abernathy)
Date: Fri, 31 Jan 2020 13:50:22 -0800
Subject: [maker-devel] Error: FASTA header doesn't match '>(\S+)'
Message-ID: <CACWrxM1a8FpLnQnmEQOvX1MiZP7CK7adgbCZrM0yyf2ghhzWcA@mail.gmail.com>

Hello,
    I am running MAKER for the first time and I have been unable to resolve
an error. The error is as follows:
[image: image.png]
I am using a genome that I assembled in Supernova v2 with headers that
resemble this:
>1 edges=1057764..867844 left=488686 right=145511 ver=1.10 style=3

and I downloaded two fasta files from ENSEMBL whose headers resemble this:
>ENSTGUT00000018018.1 cdna
chromosome:taeGut3.2.4:8_random:2849599:2959678:-1
gene:ENSTGUG00000017338.1 gene_biotype:protein_coding
transcript_biotype:protein_coding

and

>ENSTGUP00000017615.1 pep chromosome:taeGut3.2.4:23_random:205321:209117:1
gene:ENSTGUG00000017337.1 transcript:ENSTGUT00000018017.1
gene_biotype:protein_coding transcript_biotype:protein_coding

These are my only input FASTA files and I have been struggling to fix this
error for almost a month now. Any and all advice on how to fix this error
is much appreciated!

Thanks in advance,
E. Abernathy



-- 
Emily Abernathy
Graduate Group in Ecology
University of California, Davis
http://hulllabucd.wix.com/hulllab
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From ABoyher at danforthcenter.org  Wed Jan 15 18:56:47 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 01:56:47 +0000
Subject: [maker-devel] Maker failing
Message-ID: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From cjfields at illinois.edu  Thu Jan 16 08:03:46 2020
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 Jan 2020 15:03:46 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
Message-ID: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From ABoyher at danforthcenter.org  Thu Jan 16 08:42:53 2020
From: ABoyher at danforthcenter.org (Boyher, Adam)
Date: Thu, 16 Jan 2020 15:42:53 +0000
Subject: [maker-devel] Maker failing
In-Reply-To: <590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>,
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
Message-ID: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>

Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.

Get Outlook for Android<https://aka.ms/ghei36>
________________________________
From: Fields, Christopher J <cjfields at illinois.edu>
Sent: Thursday, January 16, 2020 9:03:46 AM
To: Boyher, Adam <ABoyher at danforthcenter.org>; maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Maker failing

It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.

chris

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] Maker failing

Hi
I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:

ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
MAKER will need to delete the file, before trying again

--> rank=12, hostname=pacifica.datasci.danforthcenter.org
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3
FAILED CONTIG:Chromosome10_0


Any idea what could cause that?

Adam

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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From carsonhh at gmail.com  Wed Jan 22 10:53:37 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 10:53:37 -0700
Subject: [maker-devel] Maker installation-RepeatMasker (or running
 RepeatMasker outside maker)
In-Reply-To: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
References: <CAL5jVczDpesrfGVc3BoyxSgdNU_YxAkYHVjp=nu==m+gfX5EaA@mail.gmail.com>
Message-ID: <5E517EE3-4AF1-4205-88EC-599AF01C7128@gmail.com>

You can manually specify a path in maker_exe.ctl

?Carson


> On Dec 29, 2019, at 3:03 PM, Linnie Linnie <peachandolives at gmail.com> wrote:
> 
> Dear Maker team,
> 
> I am analyzing a number of genomes in a cluster. I had previously installed RepeatMasker and RepeatModeler independently without problem in order to obtain the repeat libraries that are required by maker. This installation runs perfectly.  
> However, when I install maker, it does not recognize that a successful installation of RepeatMasker is already available. How can tell maker where RepeatMasker is already located? 
> 
> I have alternatively tried to install RepeatMasker from within maker and then try to run maker. But it gives me the following error:
> 
> Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at /data1/home/maker/exe/RepeatMasker/TRF.pm line 1.
> Compilation failed in require at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> BEGIN failed--compilation aborted at /data1/home/maker/exe/RepeatMasker/RepeatMasker line 339.
> ERROR: RepeatMasker failed
> --> rank=NA, hostname=loma
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:NQYS01000001.1
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:NQYS01000001.1
> 
> examining contents of the fasta file and run log
> 
> As a last option, I think I could run RepeatMasker with the installation I already have and then pass its .gff file to maker. In this case, which parameters should I pass in the maker_opts.ctl file? 
> 
> 
> Thank you so much for all your help (and Happy New Year to everyone!)
> L. 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From ovidiu.paun at univie.ac.at  Wed Jan 22 01:23:20 2020
From: ovidiu.paun at univie.ac.at (Ovidiu Paun)
Date: Wed, 22 Jan 2020 09:23:20 +0100
Subject: [maker-devel] Illegal division by zero while polishing ESTs
Message-ID: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>

Hi

I have been using maker to annotate a genome and all went fine. However I
have obtained a new transcriptome (from a Trinity assembly) and implemented
it as a EST fasta file. Since then I get errors for some of the contigs (but
not all!):

 

Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.

--> rank=NA, hostname=8767v89

ERROR: Failed while polishig ESTs

ERROR: Chunk failed at level:2, tier_type:3

FAILED CONTIG:scaffold21

 

I checked the transcriptome fasta file and apart from the fact that it is
pretty large (ca 500k contigs), I do not see any errors.

I would greatly appreaciate any help.

Best wishes

Ovidiu Paun

 

Assoc.-Prof. Dr. Ovidiu Paun

Department of Botany and Biodiversity Research

University of Vienna

 <http://plantgenomics.univie.ac.at> http://plantgenomics.univie.ac.at 

 

 

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From carsonhh at gmail.com  Wed Jan 22 11:31:59 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:31:59 -0700
Subject: [maker-devel] Maker failing
In-Reply-To: <BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
References: <386dfe6d4dc441fb88bfb1d897f58cff@danforthcenter.org>
	<590B3FB7-6953-43EB-8F10-2E4CF8334B1E@illinois.edu>
	<BL0PR05MB4594F63DA23ECA0BBEB4251EFA360@BL0PR05MB4594.namprd05.prod.outlook.com>
Message-ID: <F9686BDC-D3E6-4CDA-9F22-7A6BA113A70E@gmail.com>

The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward.  Let TMP= in the maker_opts.ctl file be the default of /tmp.

?Carson



> On Jan 16, 2020, at 8:42 AM, Boyher, Adam <ABoyher at danforthcenter.org> wrote:
> 
> Genome size is about 1.5Gbp and transcripts are around 22Gbp ?. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.
> 
> Get Outlook for Android <https://aka.ms/ghei36>
> From: Fields, Christopher J <cjfields at illinois.edu <mailto:cjfields at illinois.edu>>
> Sent: Thursday, January 16, 2020 9:03:46 AM
> To: Boyher, Adam <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>; 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] Maker failing
>  
> It?s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.
>  
> chris
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>
> Date: Wednesday, January 15, 2020 at 7:57 PM
> To: "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: [maker-devel] Maker failing
>  
> Hi
> I?ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I?ve recently started annotating a larger genome with more evidence. But I?m not sure that?s the issue anymore. The most recent run yielded this error:
>  
> ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
> MAKER will need to delete the file, before trying again
>  
> --> rank=12, hostname=pacifica.datasci.danforthcenter.org <http://pacifica.datasci.danforthcenter.org/>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:Chromosome10_0
>  
>  
> Any idea what could cause that?
> 
> Adam
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Wed Jan 22 11:38:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:38:45 -0700
Subject: [maker-devel] maker-devel post from
 david.carlson@stonybrook.edu requires approval
In-Reply-To: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.224.1578430065.1009042.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <2A9D6FC3-A1D5-498D-9A02-0C0DE420200F@gmail.com>

Try both ways (run in same maker directory to avoid reprocessing of evidence alignments). Then look at the output in a browser. Really the best way to decide which works best id manual evaluation.

?Carson



> From: David Carlson <david.carlson at stonybrook.edu>
> Subject: Training Augustus using Transdecoder output
> Date: January 7, 2020 at 1:47:23 PM MST
> To: maker-devel at yandell-lab.org
> 
> 
> Hi Maker users and developers,
> I'm currently in the process of annotating a new genome, and I have a question regarding training Augustus.
> 
> I have RNA-Seq data from my organism, which I've mapped to my genome assembly with Hisat2 and assembled into transcripts with StringTie.  
> 
> I've used these transcripts to predict proteining coding genes with Transdecoder (using homology evidence from the swissprot and Pfam databases).
> 
> I was thinking about taking the Transdecoder output, (after removing sequences that are not full length) and using these as the initial training set for Augustus.
> 
> In the past, I've used Busco for the initial Augustus training, but my thought is that these Transdecoder predicted genes might be a better source of evidence for my particular species.
> 
> Do any of you have experience trying this approach, or thoughts regarding its merits?
> Thanks!
> Dave
> 
> -- 
> Dave Carlson
> PhD Candidate
> Ecology and Evolution Department
> Stony Brook University

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From carsonhh at gmail.com  Wed Jan 22 11:56:27 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jan 2020 11:56:27 -0700
Subject: [maker-devel] Illegal division by zero while polishing ESTs
In-Reply-To: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
References: <017901d5d0fd$3523f570$9f6be050$@univie.ac.at>
Message-ID: <051E102E-4F07-4212-9201-309E96243B1D@gmail.com>

It?s obtaining a sequence length of zero. You may have empty entries in your sequence file. Look at the STDERR and the ID of the sequence causing the issue will be in the command name. It may be as simple as editing and removing it from your input file.

?Carson



> On Jan 22, 2020, at 1:23 AM, Ovidiu Paun <ovidiu.paun at univie.ac.at> wrote:
> 
> Hi
> I have been using maker to annotate a genome and all went fine. However I have obtained a new transcriptome (from a Trinity assembly) and implemented it as a EST fasta file. Since then I get errors for some of the contigs (but not all!):
>  
> Illegal division by zero at /usr/local/maker/bin/../lib/GI.pm line 1695.
> --> rank=NA, hostname=8767v89
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:scaffold21
>  
> I checked the transcriptome fasta file and apart from the fact that it is pretty large (ca 500k contigs), I do not see any errors.
> I would greatly appreaciate any help.
> Best wishes
> Ovidiu Paun
>  
> Assoc.-Prof. Dr. Ovidiu Paun
> Department of Botany and Biodiversity Research
> University of Vienna
> http://plantgenomics.univie.ac.at <http://plantgenomics.univie.ac.at/>
>  
>  
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From Robin.Haw at oicr.on.ca  Tue Jan 28 14:15:42 2020
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Tue, 28 Jan 2020 21:15:42 +0000
Subject: [maker-devel] [GSoC 2020] [Open Genome Informatics] Google Summer
 of Code 2020 Participation
Message-ID: <A4A4DF77-BBCF-45B6-9F09-9095C1458696@oicr.on.ca>

Dear All,
Sorry for the multiple postings!

The Open Genome Informatics team serves as an ?umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.

Call for 2020 Project Ideas and Mentors:  We are seeking project ideas to post and attract talented students to this year?s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.

For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.

Please forward this to others who might be interested in taking part.

If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>

Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org

Collaborate. Translate. Change lives.

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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From scott at scottcain.net  Fri Jan 31 11:05:32 2020
From: scott at scottcain.net (Scott Cain)
Date: Fri, 31 Jan 2020 10:05:32 -0800
Subject: [maker-devel] Google Summer of Code
Message-ID: <CA+JTaoyWRKrNvXPJ_WmJhr=Vcnq+0WfzFNU6k-SNCZpigZYdxg@mail.gmail.com>

Hi all,

It's that time of year to be putting together Google Summer of Code project
ideas.  The deadline is fast approaching.  The application is due on Feb 5,
so if you'd like to get some ideas on the wiki page, now is the time:

http://gmod.org/wiki/GSOC_Project_Ideas_2020

If you need an account to edit the page, please let me know.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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From had38 at cam.ac.uk  Wed Jan 29 07:42:24 2020
From: had38 at cam.ac.uk (H.DENISE)
Date: Wed, 29 Jan 2020 14:42:24 +0000
Subject: [maker-devel] Avoiding re-indexing the same file
Message-ID: <BF8AF51A-8D0A-4AC3-8D1B-223C5CE2D218@cam.ac.uk>

Hi,
I?m new to Maker and need to compare the annotations with different features (+/- RepeatMasker, using different protein files etc ?). However the first step seems to be the indexing of my files and the RNASeq file I?m using is large, therefore Maker seems to take ages at this step,. As it is a constant file for my applications, is there a way to provide the indexing file in order to avoid repeating this step?
Thanks in advance, Hubert



Hubert DENISE, PhD

Genome Data Analyst
R.Durbin's group
Department of Genetics
University of Cambridge

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From eabernathy at ucdavis.edu  Fri Jan 31 14:50:22 2020
From: eabernathy at ucdavis.edu (Emily Abernathy)
Date: Fri, 31 Jan 2020 13:50:22 -0800
Subject: [maker-devel] Error: FASTA header doesn't match '>(\S+)'
Message-ID: <CACWrxM1a8FpLnQnmEQOvX1MiZP7CK7adgbCZrM0yyf2ghhzWcA@mail.gmail.com>

Hello,
    I am running MAKER for the first time and I have been unable to resolve
an error. The error is as follows:
[image: image.png]
I am using a genome that I assembled in Supernova v2 with headers that
resemble this:
>1 edges=1057764..867844 left=488686 right=145511 ver=1.10 style=3

and I downloaded two fasta files from ENSEMBL whose headers resemble this:
>ENSTGUT00000018018.1 cdna
chromosome:taeGut3.2.4:8_random:2849599:2959678:-1
gene:ENSTGUG00000017338.1 gene_biotype:protein_coding
transcript_biotype:protein_coding

and

>ENSTGUP00000017615.1 pep chromosome:taeGut3.2.4:23_random:205321:209117:1
gene:ENSTGUG00000017337.1 transcript:ENSTGUT00000018017.1
gene_biotype:protein_coding transcript_biotype:protein_coding

These are my only input FASTA files and I have been struggling to fix this
error for almost a month now. Any and all advice on how to fix this error
is much appreciated!

Thanks in advance,
E. Abernathy



-- 
Emily Abernathy
Graduate Group in Ecology
University of California, Davis
http://hulllabucd.wix.com/hulllab
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