Question on RNA STAR Revision: 13:850f3679b9b4

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Question on RNA STAR Revision: 13:850f3679b9b4

Sarah Maman-2
?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

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Re: Question on RNA STAR Revision: 13:850f3679b9b4

Björn Grüning-3
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/
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Question on RNA STAR Revision: 13:850f3679b9b4

Sarah Maman-2
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 <[hidden email]>
Envoyé : lundi 25 novembre 2019 22:50
À : Sarah Maman; [hidden email]
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/