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Old 06-06-2017, 05:47 PM   #1
crh
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Default bowtie2-build python error

Hi

We installed bowtie2-2.3.2 on an ubuntu system.
Running bowtie2-build we received the following error that I think indicates problems with the python installation??

./bowtie2-build /home/charlesh/binf/sto1/seq/genome/chlre/chlre5.5/Creinhardtii_281_v5.0.fa cre_281_v5.0
File "/usr/lib/python3.4/site.py", line 182
file=sys.stderr)
^
SyntaxError: invalid syntax

Suggestions?

Charles
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Old 06-06-2017, 10:43 PM   #2
wdecoster
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Which python version are you using?
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Old 06-07-2017, 05:10 AM   #3
crh
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Python 3.4.3 and 2.7 are installed on the system.

Python 3.4.3 appears to be the default.

charlesh@~/binf/src/bowtie2-2.3.2 => python
Python 3.4.3 (default, Nov 17 2016, 01:08:31)
[GCC 4.8.4] on linux

I downloaded what I believe was the binary for bowtie2:
bowtie2-2.3.2-linux-x86_64.zip

however, for both bowtie2 and bowtie2-build they are not binaries I can see the python code.

Charles
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Old 06-07-2017, 08:22 AM   #4
alec
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The line in question is: print("\nRemainder of file ignored", file=sys.stderr)

This is valid syntax in python 3 but not 2. It looks like bowtie is using python 2.7 but it is trying to load modules for 3.4.3.

What does `/usr/bin/env python --version` print? What are your PATH and PYTHONPATH environment variables?
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Old 06-07-2017, 09:43 AM   #5
crh
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Here is what /env is set to:

charlesh@~/binf/src/bowtie2-2.3.2 => /usr/bin/env python --version
Python 2.7.6

PYTHONPATH
PYTHONPATH=/usr/lib/python3.4/:/usr/local/lib/python3.4/dist-packages:/home/charlesh/binf/lib:/home/charlesh/binf/bin/drive5_py/:/home/charlesh/binf/lib/drive5_py:/home/charlesh/binf/bin/galaxy_tools/:/home/charlesh/lib/:/home/charlesh/binf/src/biopython-1.61:/home/charlesh/binf/src/PyCogent-1.5.3:/home/charlesh/binf/src/RNASeqReadSimulator-master/src:/home/charlesh/binf/lib/uparse:/home/charlesh/binf/src/scikit-bio:/home/charlesh/binf/src/picrust:/home/charlesh/binf/src/hdf5-1.8.1

PATH:
PATH=/home/charlesh/binf/R/bin:/usr/bin:/bin::/home/charlesh/binf/lib:/usr/games:/usr/bin:/usr/sbin:/sbin:/usr/local/sbin:/usr/local/bin:/home/charlesh/binf/bin:/home/charlesh/binf/bin/galaxy_tools/:/home/charlesh/binf/bin/drive5_py/:/home/charlesh/bin:/home/charlesh/bin/x86_64:/home/charlesh/bin/x86_64:/home/charlesh/binf/lib:/home/charlesh/binf/bin:/home/charlesh/binf/src/blat_33:/home/charlesh/binf/src/clustalx1.82.linux:/usr/lib/phylip/bin:/home/charlesh/binf/lib/drive5:/home/charlesh/bin/misassembly_tools:/home/charlesh/binf/lib/drive5_py:/home/charlesh/binf/src/microbiomeutil-r20110519/ChimeraSlayer:/home/charlesh/binf/src/bedtools2-2.19.1/bin:/usr/lib/phylip/bin:/home/charlesh/bin/misassembly_tools:/home/charlesh/binf/src/PASA_r20130907/misc_utilities/:/home/charlesh/binf/src/PASA_r20130907/scripts:/home/charlesh/binf/src/ucsc/bin/:/home/charlesh/binf/src/bowtie2-2.3.2/:/home/charlesh/binf/src/tophat-2.0.13.Linux_x86_64/:/home/charlesh/binf/bin/drive5_py/:/usr/lib/qiime/bin/:/home/charlesh/binf/src/ncbi-blast-2.2.30+/bin:/home/charlesh/binf/src/TransDecoder/:/home/charlesh/binf/src/inparanoid_4.1:/home/charlesh/binf/src/Trimmomatic-0.36/:/seu/cs/home/user/c/charlesh/bin/misassembly_tools
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Old 06-07-2017, 10:01 AM   #6
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Removing "/usr/lib/python3.4/:/usr/local/lib/python3.4/dist-packages" from the start of your PYTHONPATH should fix your immediate problem.

The problem is that bowtie2-build is using python 2.7 (because the first line is #!/usr/bin/env python). However, your PYTHONPATH is causing it to try to load python 3 libraries.

Alternatively, you could make sure that the location of python 3 is on your PATH variable. I'm not sure why `/usr/bin/env python` is launching 2.7 while in your earlier post you indicated that just typing `python` launches 3.4
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Old 06-07-2017, 10:44 AM   #7
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Alec

Moving the python3.4 info into PATH and out of PYTHONPATH solved the problem.

Thanks!
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