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" 'module' has no attribute 'which' "after installation #11
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Hello, Thanks for checking out the program. I can see from the log you pasted above that dRep is running from python2.7, while it needs to be installed in python3. As you already have pyenv setup, this should be very easy to do, involving just two commands-
Please let me know if this is unclear, or if the problem still persists. Best, |
Thanks for pointing that out!
The test_suite is still failing, though, because the nonexistent 'test_backend/ecoli_wd' directory. I ran it manually, as suggested in another thread, and it seems to work |
Great! Thank you for troubleshooting and posting the solution for others.
I'll work on getting the test_suite to work, but if it's working for you
when run it manually, everything is almost definitely working correctly.
You can also run the "check dependencies" test to make sure dRep is able to
access and call all the necessary programs for the operation you'd like to
perform.
Thanks again for help troubleshooting, and don't hesitate to post again if
you encounter any other problems.
…-Matt
On Aug 10, 2017, at 12:19, German BonillaRosso <notifications@github.com> wrote:
Thanks for pointing that out!
It seems that if pip is installed under python2, in order to install
packages under python3 then we need to either make a virtual environment
under python3 or install with pip3 (for Ubuntu). I'm leaving this here as
reference:
sudo apt-get install python3-pip sudo pip3 install .
The test_suite is still failing, though, because the nonexistent
'test_backend/ecoli_wd' directory. I ran it manually, as suggested in
another thread, and it seems to work ./bin/dRep compare_wf outputdir/ -g
./tests/genomes/*
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Hello. [zjs@www bins]$ pyenv global but I still fail down the step when DREP call CheckM, [CheckM - qa] Tabulating genome statistics. Calculating AAI between multi-copy marker genes. Reading HMM info from file. Unexpected error: <type 'exceptions.IOError'> How can I solve this problem? |
Hello, Has checkM been properly installed? There are some steps that have to be run for it to work properly, like running the command:
See https://github.com/Ecogenomics/CheckM/wiki/Installation for more detailed instructions. What is the response when you try the command:
? What about the command:
? Best, |
Hello.
The test suite is failing with:
And I can see that subdirectory "test_backend" is indeed not in there, and not in the github repo.
However, dRep is also failing while running the test dataset on its own as:
I get this exact last error when running with my data too, which leads me this should be related ti an overall installation problem. I also reinstalled it through pip and have the same result.
I am running on Ubuntu 16.04, and set pyenv to run globally with python 2.7.9 and 3.5.1...
Any idea what might be going wrong?
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