Multiqc raises the "cannot import name 'gcd' from 'fractions'" error

Question

[sabbirakhand25]

I installed multiqc. But whenever I try to run it this happens.

Please help....

(rna-seq) sabbir@sabbir-VirtualBox:~/Share/week4$ multiqc -h
Traceback (most recent call last):
  File "/home/sabbir/miniconda3/envs/rna-seq/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import multiqc
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/__init__.py", line 16, in <module>
    from .multiqc import run
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/multiqc.py", line 39, in <module>
    from .plots import table
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/plots/table.py", line 9, in <module>
    from multiqc.utils import config, report, util_functions, mqc_colour
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/utils/mqc_colour.py", line 7, in <module>
    import spectra
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/spectra/__init__.py", line 1, in <module>
    from .core import COLOR_SPACES, Color, Scale
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/spectra/core.py", line 1, in <module>
    from colormath import color_objects, color_conversions
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/colormath/color_conversions.py", line 13, in <module>
    import networkx
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/__init__.py", line 114, in <module>
    import networkx.generators
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/generators/__init__.py", line 14, in <module>
    from networkx.generators.intersection import *
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/generators/intersection.py", line 13, in <module>
    from networkx.algorithms import bipartite
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/algorithms/__init__.py", line 16, in <module>
    from networkx.algorithms.dag import *
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/algorithms/dag.py", line 23, in <module>
    from fractions import gcd
ImportError: cannot import name 'gcd' from 'fractions' (/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/fractions.py)

[Kevin Blighe]

Hi, what happens? Please post status, warning, and / or error messages. Please describe that data that you are QCing.

[sabbirakhand25]

(rna-seq) sabbir@sabbir-VirtualBox:~/Share/week4$ multiqc -h
Traceback (most recent call last):
  File "/home/sabbir/miniconda3/envs/rna-seq/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import multiqc
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/__init__.py", line 16, in <module>
    from .multiqc import run
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/multiqc.py", line 39, in <module>
    from .plots import table
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/plots/table.py", line 9, in <module>
    from multiqc.utils import config, report, util_functions, mqc_colour
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/multiqc/utils/mqc_colour.py", line 7, in <module>
    import spectra
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/spectra/__init__.py", line 1, in <module>
    from .core import COLOR_SPACES, Color, Scale
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/spectra/core.py", line 1, in <module>
    from colormath import color_objects, color_conversions
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/colormath/color_conversions.py", line 13, in <module>
    import networkx
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/__init__.py", line 114, in <module>
    import networkx.generators
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/generators/__init__.py", line 14, in <module>
    from networkx.generators.intersection import *
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/generators/intersection.py", line 13, in <module>
    from networkx.algorithms import bipartite
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/algorithms/__init__.py", line 16, in <module>
    from networkx.algorithms.dag import *
  File "/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/site-packages/networkx/algorithms/dag.py", line 23, in <module>
    from fractions import gcd
ImportError: cannot import name 'gcd' from 'fractions' (/home/sabbir/miniconda3/envs/rna-seq/lib/python3.9/fractions.py)

[sabbirakhand25]

It shows this error.. Sorry I'm new here, I'm trying but couldn't upload the screenshot

[Ram]

Hi, you're doing the right thing by copy-pasting the error. Uploading a screenshot of plain text is counter-productive. Copy-pasting it here is the right way to go. GenoMax and I have formatted your error so it can be read easier. You can do it yourself with the 101010 button on the toolbar.

[sabbirakhand25]

Thanks for the help.

[sabbirakhand25]

Thank you guys problem solved!

[Ram]

I've moved the helpful comments to answers. Please accept the answer(s) that helped you solve your problem. To accept an answer, click the grey check mark on the left side of the answer.

[Devon Ryan]

Can you post the output of conda list? That will help me track down the versions of networkx that need to have their metadata patched.

[Phil Ewels]

x-ref MultiQC GitHub issue about this: https://github.com/ewels/MultiQC/issues/1413 - I guess that we just have to wait for the next release of networkx. But it would still be good to hear what version people are running when they hit this problem. Help very welcome! :)

Answer 1

[Carambakaracho]

This is most likely a simple dependency problem due to python 3.9: https://stackoverflow.com/questions/66174862/import-error-cant-import-name-gcd-from-fractions

Easiest would be if you install a virtual environment with Python 3.8 or earlier...

Answer 2

[GenoMax]

It appears that python 3.9 may not be working with multiqc. You may need to specify python=3.7 when you install with conda.

Answer 3

[Phil Ewels]

This appears to be a problem with the networkx dependency for MultiQC. Upgrading to version 2.5.1 solves the problem (conda install networkx=2.5.1).

See https://github.com/ewels/MultiQC/issues/1413 for discussion. I've updated the package version pin in MultiQC which will go out in the next release.