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GATB / pyGATB

Python3 wrapper for GATB-Core.
GNU Affero General Public License v3.0
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Seg Fault when try to use Graph Module #6

Open nhvanlie opened 4 years ago

nhvanlie commented 4 years ago

Hello, I installed pyGATB using pip and python v3.5.6 on our cluster. I was playing around with the data and while I could reproduce the sample code for the Bank module, the code kept causing a segmentation fault when I tried to read the data into Graph (whether it was a h5 or fastq file):

~/gatbTest$ python
Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 21:41:56) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from gatb import Graph
>>> graph = Graph('-in ./celegans_reads.h5')
Input is h5 or _gatb/ (we assume that kmer counting has already been done), we will complete it into a graph if necessary.
Segmentation fault
~/gatbTest$ python
Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 21:41:56) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from gatb import Graph
>>> graph = Graph('-in ./colombaTestBig_R2.fq')
Segmentation fault