and so it begins… running the ZEN data through my IPython notebook

1. Downloaded the notebook from here:

http://jennomics.github.io/QIIMEbyJennomics/

2. immediate failure:

!validate_mapping_file.py -m $mapping_file
Traceback (most recent call last):
  File "/macqiime/QIIME/bin/validate_mapping_file.py", line 14, in <module>
    from qiime.util import parse_command_line_parameters, get_options_lookup,\
  File "/macqiime/lib/python2.7/site-packages/qiime/util.py", line 26, in <module>
    import gzip
  File "/Users/Jenna/anaconda/lib/python2.7/gzip.py", line 10, in <module>
    import io
  File "/Users/Jenna/anaconda/lib/python2.7/io.py", line 51, in <module>
    import _io
ImportError: dlopen(/Users/Jenna/anaconda/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyInt_AsInt
  Referenced from: /Users/Jenna/anaconda/lib/python2.7/lib-dynload/_io.so
  Expected in: dynamic lookup

2. because my computer is so shiny and new, I don’t have any microsoft applications installed (yet?). I’m using “Numbers,” which I’ve never used before and does not have tab-delimited format as an export option. I’m hoping that the problem was that I was trying to use a .csv file for my mapping file. So, I converted it:

perl -pi -e ‘s/\,/\t/g’ ZEN.csv

and tried again. Nope!

3. tried googling this:

ImportError: dlopen Symbol not found

cannot understand what I see there, but it does convince me that it’s probably an anaconda problem

tried googling this:

Expected in: dynamic lookup anaconda

I felt pretty hopeful when the first hit was this:

issues with starting ipython notebook – Google Groups

but, that was an unresolved issue. I did notice that the issue might actually be with lib-dynload, whatever the hell that is.

So, googled this:

anaconda lib-dynload

and ended up here:

http://stackoverflow.com/questions/19124436/linking-problems-with-anaconda-when-using-ld-library-path

something in there made it click that the path to python should be via macqiime, and you can see in the traceback that it starts off with the macqiime python, but then switches to the anaconda python. I always feel better about asking the community a question if I have some sense of what might be going on. So, I’ll post it on the QIIME forum now.

While I was writing the post, I thought to try to run the command from the command line instead of the notebook, and it worked, so that really helps narrow things down…

ALSO, while posting it, I realized that I haven’t update to QIIME 1.9 yet. Blach.

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