Fatal error with bowtie2 when running metaphlan2

Issue #26 new
Former user created an issue


I have installed metaphlan2 and bowtie2 successfully, but when tried it for the first time using the example fasta file, I got this error: [eazhar@klogin2 test]$ metaphlan2.py SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile1.txt /home/eazhar/.conda/envs/py2env01/lib/python2.7/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters Help message for read_fastx.py OSError: fatal error running BowTie2. Is BowTie2 in the system path? (py2env01) [eazhar@klogin2 test]$ close failed in file object destructor: sys.excepthook is missing lost sys.stderr

Bowtie2 is already in the path. [eazhar@klogin2 test]$ echo $PATH /home/eazhar/.conda/envs/py2env01/bin:/app/Genome/bowtie2-2.2.9/:/app/utils/anaconda2/bin:/fefs1/generic/eazhar/app/metaphlan2:/usr/lib64/qt-3.3/bin:/opt/kusu/bin:/opt/kusu/sbin:/usr/pgsql-9.0/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bin:/home/eazhar/bin eazhar@klogin2 test]$ which bowtie2 /app/Genome/bowtie2-2.2.9/bowtie2

Can you help me please..

Thanks Nada

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