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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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I got an Intel MKL FATAL ERROR #16

Closed zhangbw3187 closed 5 years ago

zhangbw3187 commented 5 years ago

Hi Dr. Zwaenepoel, I successfully installed the software, but got an error when I tried to ran "wgd ksd" as: wgd ksd -o ./ -n 12 ./blabla.blast.tsv.mcl blabla.cds.fa The mcl file is produced by "wgd mcl"

the error said it cannot load /root/anaconda3/lib/python3.7/site-packages/sklearn/metrics/../../../../libmkl_core.so.

But I can see there is a file called libmkl_core.so in that path, and the r+x authority of the file (as well as the whole path to the file) has been given to every user.

Could you please help me to see what's wrong with it? Many thanks, Bowen

2019-03-15 10:38:08: INFO   Performing analysis on gene family GF_006004
2019-03-15 10:38:08: INFO   Performing analysis on gene family GF_006005
2019-03-15 10:38:08: INFO   Performing analysis on gene family GF_006006
2019-03-15 10:38:08: INFO   Performing analysis on gene family GF_006007
2019-03-15 11:44:23: INFO   Analysis done
2019-03-15 11:44:23: INFO   Making results data frame
2019-03-15 11:45:55: INFO   Removing tmp directory
2019-03-15 11:45:57: INFO   Computing weights, outlier cut-off at Ks > 5
Intel MKL FATAL ERROR: Cannot load /root/anaconda3/lib/python3.7/site-packages/sklearn/metrics/../../../../libmkl_core.so.
arzwa commented 5 years ago

Hi Bowen,

That's weird, so the analyses all went correctly but then the last step failed? From the looks of it, it's some problem with your python packages. From similar issues (e.g. here), I think you might want to try reinstalling numpy using conda install -f numpy, (or perhaps conda install -f sklearn, just guessing). You might want to retry then on a subset of your gene families (e.g. use 10 random lines from your mcl file instead of the full mcl file) to see if it works.

If that doesn't work, than I would advise you to install wgd in a different environment (e.g. using virtualenv or (mini)conda) with python3.6 (I see you are using python3.7, which I haven't tested yet).

Let me know if that solves your troubles,

Arthur (not a 'Dr.' yet BTW ;)

zhangbw3187 commented 5 years ago

Thank you Arthur, I tried to reinstalled numpy and sklearn, but it still doesn't work. Same error.

I couldn't reinstall the python of this system, but I will try to borrow another machine with different environment. I will follow up after I got it.

Best, Bowen

zhangbw3187 commented 5 years ago

Hi Arthur, I got Python3.6, it works fine now.

Thank you and best wishes!

Bowen

arzwa commented 5 years ago

OK, great! I'll have to get a look at possible issues with Python3.7. Thanks!