Question on RNA STAR Revision: 13:850f3679b9b4
?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
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
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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 <bjoern.gruening@gmail.com> 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/
participants (2)
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Björn Grüning -
Sarah Maman