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Alyce Fowler


-----Original Message-----
From: maker-devel [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: Monday, August 14, 2017 1:31 PM
To: [hidden email]
Subject: maker-devel Digest, Vol 111, Issue 3

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Today's Topics:

   1. Problem with MAKER installation ([hidden email])
   2. split_fasta script (Patrick Michael Chiuco)
   3. Inconsistent RepeatMasker error on draft assembly (Zach Cohen)
   4. Re: split_fasta script (Carson Holt)
   5. Re: Problem with MAKER installation (Carson Holt)
   6. Re: Inconsistent RepeatMasker error on draft assembly
      (Carson Holt)


----------------------------------------------------------------------

Message: 1
Date: Tue, 8 Aug 2017 15:33:01 +0800
From: [hidden email]
To: [hidden email]
Subject: [maker-devel] Problem with MAKER installation
Message-ID:
        <[hidden email]>
Content-Type: text/plain;charset=iso-8859-1

Hi,

I am installing MAKER to annotate a fungus genome. However, I experienced
issue with
"Argument "2.53_01" isn't numeric in numeric ge (>=) at
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/forks.pm line 1570." .

I aware that the issue arise because of the "_" in the "2.53_01" however I
have no idea on how to solve it.

Would you mind to give advice on this matter?

Thank you.



Best regards,

Dr. Joon Liang Tan
PhD, Bsc (Hons)
Lecturer (Bioinformatics Programme)
Faculty of Information Science and Technology (FIST)
Multimedia University
75450 Melaka
Malaysia
Phone: +60 62524813






------------------------------

Message: 2
Date: Thu, 10 Aug 2017 19:35:47 +0800
From: Patrick Michael Chiuco <[hidden email]>
To: [hidden email]
Subject: [maker-devel] split_fasta script
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

 

Hi!

 Good day! Is there anyway to download a previous version of Maker (<=
v2.31.0) or get deprecated accessory scripts? One of the accessory
scripts included in the previous versions (split_fasta) is a dependency
of an annotation pipeline [1] we're currently using. Thanks!

 Patrick
 

Links:
------
[1]
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1426-6
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Message: 3
Date: Fri, 11 Aug 2017 18:43:58 +0000
From: Zach Cohen <[hidden email]>
To: [hidden email]
Subject: [maker-devel] Inconsistent RepeatMasker error on draft
        assembly
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hello All,
I'm receiving a RepeatMasker on some (not all) of my scaffolds.

*Widget::RepeatMasker:*

*cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker
/scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb
-species all -dir
/scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0
-pa 2*

*#-------------------------------#*

*ERROR: RepeatMasker failed*

*--> rank=NA, hostname=82853d8df2a5*

*ERROR: Failed while doing repeat masking*

*ERROR: Chunk failed at level:0, tier_type:1*

FAILED CONTIG:scaffold2852_size18614

*ERROR: Chunk failed at level:2, tier_type:0*

*FAILED CONTIG:scaffold2852_size18614*

*examining contents of the fasta file and run log*


I'm not sure if there is an issue with the widget itself, as this doesn't
come up for all the scaffolds and the example data seemed to run fine, or a
problem with these particular scaffolds. Thanks for any assistance you can
provide!

Best,

Z
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Message: 4
Date: Fri, 11 Aug 2017 23:53:49 -0600
From: Carson Holt <[hidden email]>
To: Patrick Michael Chiuco <[hidden email]>
Cc: [hidden email]
Subject: Re: [maker-devel] split_fasta script
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

split_fasta was deprecated quite a while ago (2010) and replaced by fasta_tool. I was able to find an old copy in the subversion repository, I can?t guarantee it will work as expected though with how much other libraries in maker have changed since then.

?Carson






> On Aug 10, 2017, at 5:35 AM, Patrick Michael Chiuco <[hidden email]> wrote:
>
>  
> Hi!
>
>      Good day! Is there anyway to download a previous version of Maker (<= v2.31.0) or get deprecated accessory scripts? One of the accessory scripts included in the previous versions (split_fasta) is a dependency of an annotation pipeline <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1426-6> we're currently using. Thanks!
>
> Patrick
>  
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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------------------------------

Message: 5
Date: Sat, 12 Aug 2017 00:00:24 -0600
From: Carson Holt <[hidden email]>
To: [hidden email]
Cc: [hidden email]
Subject: Re: [maker-devel] Problem with MAKER installation
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=utf-8

You may need to reinstall your forks and forks::shared modules. If you use CPAN, you can use the ?force? option to do this. Also if forks is broken, other modules may be as well, so you may get another error in another module after the reinstall (then you will have to reinstall that module). This can possibly be caused by a processor version issue if this is a cluster with mixed architectures (old vs new Intel chips or AMD vs Intel), or it can be due to a system update breaking dynamically linked C libraries.

?Carson


> On Aug 8, 2017, at 1:33 AM, [hidden email] wrote:
>
> Hi,
>
> I am installing MAKER to annotate a fungus genome. However, I experienced
> issue with
> "Argument "2.53_01" isn't numeric in numeric ge (>=) at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/forks.pm line 1570." .
>
> I aware that the issue arise because of the "_" in the "2.53_01" however I
> have no idea on how to solve it.
>
> Would you mind to give advice on this matter?
>
> Thank you.
>
>
>
> Best regards,
>
> Dr. Joon Liang Tan
> PhD, Bsc (Hons)
> Lecturer (Bioinformatics Programme)
> Faculty of Information Science and Technology (FIST)
> Multimedia University
> 75450 Melaka
> Malaysia
> Phone: +60 62524813
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




------------------------------

Message: 6
Date: Mon, 14 Aug 2017 11:30:33 -0600
From: Carson Holt <[hidden email]>
To: Zach Cohen <[hidden email]>
Cc: [hidden email]
Subject: Re: [maker-devel] Inconsistent RepeatMasker error on draft
        assembly
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

If running under MPI, you can get messages from multiple processes (slightly out of order), in which case the more descript cause of the error may be further upstream in the STDERR log. If running without MPI, and the error you see is matched with the Widget::RepeatMasker command used, then you can simply copy it and run it outside of MAKER. If there are installation issues with your RepeatMasker copy then the cause will become more apparent.

i.e. Run the command by itself ?> /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2

?Carson


> On Aug 11, 2017, at 12:43 PM, Zach Cohen <[hidden email]> wrote:
>
> Hello All,
> I'm receiving a RepeatMasker on some (not all) of my scaffolds.
> Widget::RepeatMasker:
>
> cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2
>
> #-------------------------------#
>
> ERROR: RepeatMasker failed
>
> --> rank=NA, hostname=82853d8df2a5
>
> ERROR: Failed while doing repeat masking
>
> ERROR: Chunk failed at level:0, tier_type:1
>
> FAILED CONTIG:scaffold2852_size18614
>
> ERROR: Chunk failed at level:2, tier_type:0
>
> FAILED CONTIG:scaffold2852_size18614
>
> examining contents of the fasta file and run log
>
>
>
> I'm not sure if there is an issue with the widget itself, as this doesn't come up for all the scaffolds and the example data seemed to run fine, or a problem with these particular scaffolds. Thanks for any assistance you can provide!
>
> Best,
>
> Z
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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