[ensembl-dev] Error on using parse_ncbi_gff3.pl

[Herzig, David]

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>
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