These are chat archives for dereneaton/ipyrad

May 2018
May 31 2018 18:57
Screenshot from 2018-05-31 14-56-00.png
I'm having a new issue when running iPyrad on one of our machines. When I get to step 3 after dereplicating I get a vsearch error.
I looked at the vsearch documentation and it seems to be a known issue that has been fixed on their latest release, but I can't get the version that comes with ipyrad to go.
It also only happens on this specific machine, even though the two others that are exactly the same can make it through the whole process with no issues.
May 31 2018 19:07

Hi Isaac:
I tried to import some python libraries via a jupyter notebook and got the following error:

import ipyrad.analysis as ipa      ## ipyrad analysis toolkit
import ipyparallel as ipp              ## parallel processing
import toyplot                                  ## plotting library
ImportErrorTraceback (most recent call last)
<ipython-input-6-93992b7be745> in <module>()
----> 1 import ipyrad.analysis as ipa      ## ipyrad analysis toolkit
      2 import ipyparallel as ipp          ## parallel processing
      3 import toyplot                     ## plotting library

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/ in <module>()
     19 ## main ip.functions
---> 20 from . import load as _load
     21 from . import assemble
     22 from ipyrad.core.parallel import get_client as _get_client

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/load/ in <module>()
     12 """
---> 14 from .load import test_assembly
     15 from .load import save_json
     16 from .load import load_json

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/load/ in <module>()
     11 import ipyrad as ip
     12 from copy import deepcopy
---> 13 from ipyrad.assemble.util import *
     14 from collections import OrderedDict

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/ in <module>()
      3 """ import assembly funcs """
----> 5 from . import demultiplex
      6 from . import rawedit
      7 from . import cluster_within

ImportError: cannot import name demultiplex

I think there may be some incompatibility between the system install of python2 and the local version installed via conda. I tried running 'module unload python2' before running the command, which resolves some errors when running the ipyrad cli, but this didn't work here. Any suggestions?

May 31 2018 20:11

HI @isaacovercast. I downloaded ipyrad in a new maching and I am getting the following error. I have uninstall and reinstall everything again, and even follow this old post (!topic/pyrad-users/914y_5p5u8Y), but I am still getting the same error, and I am not even able to type ipyrad -h

-Traceback (most recent call last):
File "/home1/02202/lmv498/miniconda2/bin/ipyrad", line 11, in <module>
load_entry_point('ipyrad==0.6.21', 'console_scripts', 'ipyrad')()
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/pkg_resources/", line 480, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/pkg_resources/", line 2693, in load_entry_point
return ep.load()
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/pkg_resources/", line 2324, in load
return self.resolve()
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/pkg_resources/", line 2330, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/ipyrad/", line 20, in <module>
from . import load as _load
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/ipyrad/load/", line 14, in <module>
from .load import test_assembly
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/ipyrad/load/", line 14, in <module>
from ipyrad.assemble.util import
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/", line 8, in <module>
from . import jointestimate
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/", line 10, in <module>
import numba
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/numba/", line 10, in <module>
from . import config, errors, runtests, types
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/numba/", line 11, in <module>
import llvmlite.binding as ll
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/llvmlite/binding/", line 6, in <module>
from .dylib import

File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/llvmlite/binding/", line 4, in <module>
from . import ffi
File "/home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/llvmlite/binding/", line 127, in <module>
raise e
OSError: /lib64/ version `GLIBC_2.12' not found (required by /home1/02202/lmv498/miniconda2/lib/python2.7/site-packages/llvmlite/binding/

May 31 2018 21:41
I also try installing gilb using conda install -c asmeurer glibc, but get the following error:
/home1/02202/lmv498/miniconda2/bin/python: error while loading shared libraries: __vdso_time: invalid mode for dlopen(): Invalid argument
Isaac Overcast
May 31 2018 22:34
Hi @LinaValencia85 This is a version issue between llvmlite and the version of glibc installed on your computer. I assume this is a cluster, as it seems to have a very old version of glibc installed. The old issue you mention is about numpy, but you might be able to fix this issue in the same way by trying to roll back to an older version of llvmlite. Or you could try installing llvmlite by hand on your cluster. I think you could try 'pip install llvmlite' and that might work.
Isaac Overcast
May 31 2018 22:48
@nidrews It looks like your computer only has ~16GB of RAM, so that's why you're seeing the error. One thing you could try is reducing the number of cores you're running on, this will split up the available ram among fewer cores. The other thing you could try is jacking the newest version of vsearch into the ipyrad/bins directory. This is a desperate move, though and I wouldn't recommend it as it'd be tricky. On the whole, 4 cores and 16GB of RAM is a pretty resource poor system, so if you have access to a computer with more cores and more ram, that would be the better option.
@tommydevitt Hm, yeah that looks weird, it's failing to load some very critical and what should be non-controversial imports. Check your $PYTHONPATH? Might be an option to just blast conda and reinstall rm -rf /home1/02745/tdevitt/miniconda2, reinstall miniconda and then reinstall ipyrad. This sometimes fixes weird behavior.
What happens if you just do python and then do import ipyrad?