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Error while creating NullModel #15

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RxLoutre opened this issue Sep 7, 2017 · 0 comments
Open

Error while creating NullModel #15

RxLoutre opened this issue Sep 7, 2017 · 0 comments

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@RxLoutre
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RxLoutre commented Sep 7, 2017

I've encourtered an issue using svelter.

First, I initialized the tool with the following command :
svelter.py Setup --reference '/media/loutre/SUZUKII/assembly/Drosophila-suzukii-p.fasta' --workdir '/media/loutre/SUZUKII/rearrangment/svelter' --support '/media/loutre/SUZUKII/rearrangment/svelter'

And then tried to create the NullModel using :
svelter.py NullModel --sample '/media/loutre/SUZUKII/alignement/bowtie2-illumina/polished/quiverEssai1/assemblyVSIllumina-sorted.bam' --workdir '/media/loutre/SUZUKII/rearrangment/svelter'

I got this error after a while running :

temp files produced under: /media/loutre/SUZUKII/rearrangment/svelter/
Fatal error: impossible d'ouvrir le fichier '/media/loutre/SUZUKII/rearrangment/svelter/reference_SVelter/SVelter1.NullModel.Figure.a.r' : Aucun fichier ou dossier de ce type
Fatal error: impossible d'ouvrir le fichier '/media/loutre/SUZUKII/rearrangment/svelter/reference_SVelter/SVelter1.NullModel.Figure.a.r' : Aucun fichier ou dossier de ce type
Fatal error: impossible d'ouvrir le fichier '/media/loutre/SUZUKII/rearrangment/svelter/reference_SVelter/SVelter1.NullModel.Figure.a.r' : Aucun fichier ou dossier de ce type
Fatal error: impossible d'ouvrir le fichier '/media/loutre/SUZUKII/rearrangment/svelter/reference_SVelter/SVelter1.NullModel.Figure.b.r' : Aucun fichier ou dossier de ce type
Traceback (most recent call last):
  File "/home/loutre/.local/bin/svelter.py", line 4, in <module>
    __import__('pkg_resources').run_script('SVelter==1.1.0', 'svelter.py')
  File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 719, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1512, in run_script
    exec(script_code, namespace, namespace)
  File "/home/loutre/.local/lib/python2.7/site-packages/SVelter-1.1.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/svelter.py", line 681, in <module>
    
  File "function.pyx", line 3234, in svelter_sv.function.RDNullfigure2_Modify (svelter_sv/function.c:95003)
IOError: [Errno 2] No such file or directory: '/media/loutre/SUZUKII/rearrangment/svelter/NullModel.assemblyVSIllumina-sorted.bam/RDNull.assemblyVSIllumina-sorted.genome.NegativeBinomial'

This is really strange because the directory exist and has all right (write, read even execute). He is trying to access a file that I thought it was supposed to create. Isn't the NullModel phase supposed to create all /SVelter1.NullModel.Figure.* files ?

Did I made a mistake ?

Thanks for your help !

Roxane

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