Hi Bjoern,
Thanks for your help.
Actually, every exon line has a transcript_id:
$ grep --color -i transcript_id dm6.gtf | wc -l
409159
$ wc -l dm6.gtf
409159 dm6.gtf
Paired fastq and fasta input files seems to be well formated too.
Cheers,
Sarah
INRA | SIGENAE | GenPhySE | INRA Occitanie-Toulouse
Tél. : +33(0)5.61.28.57.08
Télétravail lundi / vendredi
De : Björn Grüning
Envoyé : lundi 25 novembre 2019 22:50
À : Sarah Maman; galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Question on RNA STAR Revision: 13:850f3679b9b4
Hi Sarah,
which GTF file are you using? Please make sure every exon line has a
transcript_id.
Cheers,
Bjoern
Am 25.11.19 um 10:53 schrieb Sarah Maman:
> ?Hello,
>
>
> Please could you help me to run this wrapper : RNA STAR Gapped-read mapper
> for RNA-seq data (Galaxy Version 2.7.2b)
>
> without this error:
>
> terminate called after throwing an instance of 'std::out_of_range'
>what(): basic_string::at
> /galaxydata/galaxy-prod/my_job_working_directory/000/282/282124/tool_script.sh:
> line 9: 48744 Aborted (core dumped) STAR --runThreadN
> ${GALAXY_SLOTS:-4}...
>
>
> Even if I increase the number of genome bins for coordinate-sorting, output
> files are all empty and I read this stderr above.
>
>
> Thanks in advance,
>
> Sarah Maman
>
>
> INRA | SIGENAE | GenPhySE | INRA Occitanie-Toulouse
>
> Tél. : +33(0)5.61.28.57.08
>
> Télétravail lundi / vendredi
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>%(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>http://galaxyproject.org/search/
>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
%(web_page_url)s
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
