[maker-devel] Maker Bio::Root Error

[Timothy Stitt (TGAC)]

Thanks Carson. Much appreciated.

I've passed on your recommendations to the user and I'll let you know the outcome.

Tim.

---

Timothy Stitt PhD / Head of Scientific Computing

The Genome Analysis Centre (TGAC)

http://www.tgac.ac.uk/


p: +44 1603 450378

e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Tuesday, 7 October 2014 17:17
To: Timothy Stitt <timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Maker Bio::Root Error

His file is not formatted correctly. Values should be tab delimited, but in several cases he has leading space characters contaminating the values. He needs to find and remove the contaminating white space.
Here is the GFF3 specification just for reference --> http://www.sequenceontology.org/gff3.shtml.

Here is an example perl script that could do this (cut and paste it into a file if you want)-->

#!/usr/bin/perl
use strict;
my $file = shift;
open(IN, "< $file");
while(my $line = <IN>){
    my @F = split(/\t/, $line);
    chomp($F[-1]);
    @F = map {s/^\s|\s$//g; $_} @F;
    print join("\t", @F)."\n";
}
close(IN);


Then run it as follows -->
perl fixgff3_script.pl old_file.gff > new_file.gff


Thanks,
Carson


From: "Timothy Stitt (TGAC)" <Timothy.Stitt at tgac.ac.uk<mailto:Timothy.Stitt at tgac.ac.uk>>
Date: Tuesday, October 7, 2014 at 1:34 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Subject: Re: [maker-devel] Maker Bio::Root Error

Hi Carson,

I spoke with the user and it does seem they have some confusion over what is a well-formed GFF3 file (they mention there is no example template for them to copy on the MAKER website). I am attaching the user's GFF3 file. Could you have a quick scan to determine if they are using an incorrect format?

Any advice greatly received.

Thanks,

Tim.

---

Timothy Stitt PhD / Head of Scientific Computing

The Genome Analysis Centre (TGAC)

http://www.tgac.ac.uk/


p: +44 1603 450378

e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Sunday, 5 October 2014 23:58
To: Timothy Stitt <timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>>, "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 Bio::Root Error

The location of the error is when MAKER tries to read a user provided GFF3 file, and then BioPerl is saying one of the values is invalid. Looking at the single quotes around the value, it appears that there is some contaminating whitespace.  There may be other problems with the GFF3 file as well.  I could take  look if you want.

Thanks,
Carson



From: "Timothy Stitt (TGAC)" <Timothy.Stitt at tgac.ac.uk<mailto:Timothy.Stitt at tgac.ac.uk>>
Date: Saturday, October 4, 2014 at 9:14 AM
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 Bio::Root Error

Dear Maker Developers,

One of my Maker users is observing the following error when running maker on our systems:

------------- EXCEPTION: Bio::Root::BadParameter -------------
MSG: ' 9.1' is not a valid score
VALUE:  9.1
STACK: Error::throw
STACK: Bio::Root::Root::throw /tgac/software/testing/perl_activeperl/5.18.2.1802/x86_64/site/lib/Bio/Root/Root.pm:449
STACK: Bio::SeqFeature::Generic::score /tgac/software/testing/perl_activeperl/5.18.2.1802/x86_64/site/lib/Bio/SeqFeature/Generic.pm:468
STACK: GFFDB::_ary_to_features /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/GFFDB.pm:891
STACK: GFFDB::phathits_on_chunk /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/GFFDB.pm:534
STACK: Process::MpiChunk::_go /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:756
STACK: Process::MpiChunk::run /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiTiers.pm:287
STACK: /tgac/software/testing/bin/core/../..//maker/2.31.6/x86_64/bin/maker:686
--------------------------------------------------------------
--> rank=NA, hostname=UV00000010-P002
ERROR: Failed while doing repeat masking

When the user runs with the '-RM_off' option, everything is fine but fails with the above error when not applying that option. I was just wondering if anyone had any insight into what might be causing this?

Regards,

Tim.

---

Timothy Stitt PhD / Head of Scientific Computing

The Genome Analysis Centre (TGAC)

http://www.tgac.ac.uk/


p: +44 1603 450378

e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>

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