[ensembl-dev] Error on using parse_ncbi_gff3.pl

[Daniel Barrell]

Odd, D. rerio should have also failed then if my suspicions were correct.
Guess there must be something else going on here.

Dan





*Daniel Barrell*
Platform Specialist
*eagle*discover Best of Show Winner at Bio-IT World 2016

*Eagle Genomics Ltd*
T: +44 (0)1223 654481
http://www.eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

https://youtu.be/rPdgFTo0FZM

On 20 September 2016 at 12:14, Herzig, David <david.herzig at roche.com> wrote:

> Hi Daniel
>
> Thx for the feedback.
>
> I was able to use it for:
> - d rerio
> - m musculus
> - r norvegicus
>
> regards,
> David
>
>
> On Tue, Sep 20, 2016 at 1:11 PM, Daniel Barrell <
> daniel.barrell at eaglegenomics.com> wrote:
>
>> Hi David,
>>
>> Line 1184334 is the last line of the GFF3 file and contains '###'. There
>> used to be code to ignore lines like these:
>>
>> + next if $line =~ /^#/;
>>
>> When the script moved to use ensembl-io I think it may have lost this
>> check, however I would expect ensembl-io to handle the '###'. Which species
>> files worked? I checked on NCBI and other species (e.g. horse) would also
>> fail in the same way.
>>
>> Dan
>>
>>
>>
>>
>>
>>
>> *Daniel Barrell*
>> Platform Specialist
>> *eagle*discover Best of Show Winner at Bio-IT World 2016
>>
>> *Eagle Genomics Ltd*
>> T: +44 (0)1223 654481
>> http://www.eaglegenomics.com
>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>>
>> https://youtu.be/rPdgFTo0FZM
>>
>> On 20 September 2016 at 11:16, Herzig, David <david.herzig at roche.com>
>> wrote:
>>
>>> Hi Ensembl Users
>>>
>>> I have setup the ensembl environment for several species. Everything is
>>> ok.
>>> After that I imported data from NCBI by using the parse_ncbi_gff3.pl
>>> script. Works fine for almost all species. But for the specie sus scrofa I
>>> have the following issue:
>>>
>>> I downloaded the file from NCBI:
>>> /ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ref_Sscrofa10.2
>>> _top_level.gff3
>>>
>>> I used the parse_ncbi_gff3.pl script to import it.
>>>
>>> The process starts successfully but after a while I get the following
>>> error message and the process stops:
>>>
>>> Can't call method "phase" on an undefined value at
>>> /home/ensembl/release-85/ensembl-pipeline/scripts/refseq_import/
>>> parse_ncbi_gff3.pl line 882, <__ANONIO__> line 1184334.
>>>
>>> Any ideas?
>>>
>>> regards,
>>> David
>>>
>>>
>>> --
>>>
>>> David Herzig
>>> Scientist, pRED Informatics
>>> Roche Pharma Research and Early Development
>>>
>>> Roche Innovation Center Basel
>>>
>>> F. Hoffmann-La Roche Ltd
>>> Grenzacherstrasse 124
>>> 4070 Basel
>>> Switzerland
>>> Phone +41 61 687 31 70
>>>
>>> Learn more about pRED Informatics at http://go.roche.com/*pREDi*
>>> <http://go.roche.com/pREDi>
>>>
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>>>
>>
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>>
>
>
> --
>
> David Herzig
> Scientist, pRED Informatics
> Roche Pharma Research and Early Development
>
> Roche Innovation Center Basel
>
> F. Hoffmann-La Roche Ltd
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
> Phone +41 61 687 31 70
>
> Learn more about pRED Informatics at http://go.roche.com/*pREDi*
> <http://go.roche.com/pREDi>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
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