I am running fastqc and multiqc in ubuntu linux terminal. fastqc runs perfectly without any issues but multiqc fails to run, showing the message. No idea how to fix the missing ‘imp’ module. I tried to read and apply every solution found in the internet or google.
I used the command ‘conda install multiqc’ to install multiqc in the existing conda environment. I tried to install it in a new conda environment. Still, its showing the same message.The python version currently running is 3.12.0
Could anyone help to fix the issue?
ewels
October 12, 2023, 10:38am
2
Ooh, that’s not good. I managed to replicate it locally so it’s not just you. I guess you’re one of the first to try running with Python 3.12 - seems specific to this version of Python.
I made an issue on the MultiQC repo to track this:
opened 10:37AM - 12 Oct 23 UTC
priority: high
installation
Looks like MultiQC is having some problems running in Conda with Python 3.12, du… e to a dependency error of some kind:
```console
❯ conda create --name py3.12 python=3.12 multiqc --yes --quiet
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/ewels/.miniconda3/miniconda3/envs/py3.12
added / updated specs:
- multiqc
- python=3.12
The following packages will be downloaded:
```
<details>
```
package | build
---------------------------|-----------------
brotli-1.1.0 | hb547adb_1 19 KB conda-forge
brotli-bin-1.1.0 | hb547adb_1 17 KB conda-forge
brotli-python-1.1.0 | py312h9f69965_1 335 KB conda-forge
ca-certificates-2023.7.22 | hf0a4a13_0 146 KB conda-forge
certifi-2023.7.22 | pyhd8ed1ab_0 150 KB conda-forge
charset-normalizer-3.3.0 | pyhd8ed1ab_0 45 KB conda-forge
click-8.1.7 |unix_pyh707e725_0 82 KB conda-forge
contourpy-1.1.1 | py312h389731b_1 222 KB conda-forge
cycler-0.12.1 | pyhd8ed1ab_0 13 KB conda-forge
fonttools-4.43.1 | py312he37b823_0 2.5 MB conda-forge
freetype-2.12.1 | hadb7bae_2 582 KB conda-forge
humanfriendly-10.0 | pyhd8ed1ab_6 72 KB conda-forge
importlib-metadata-6.8.0 | pyha770c72_0 25 KB conda-forge
kiwisolver-1.4.5 | py312h389731b_1 60 KB conda-forge
lcms2-2.15 | hf2736f0_3 210 KB conda-forge
libblas-3.9.0 |18_osxarm64_openblas 15 KB conda-forge
libbrotlicommon-1.1.0 | hb547adb_1 67 KB conda-forge
libbrotlidec-1.1.0 | hb547adb_1 28 KB conda-forge
libbrotlienc-1.1.0 | hb547adb_1 274 KB conda-forge
libcblas-3.9.0 |18_osxarm64_openblas 14 KB conda-forge
libcxx-16.0.6 | h4653b0c_0 1.1 MB conda-forge
libdeflate-1.19 | hb547adb_0 52 KB conda-forge
libgfortran-5.0.0 |13_2_0_hd922786_1 108 KB conda-forge
libgfortran5-13.2.0 | hf226fd6_1 972 KB conda-forge
libjpeg-turbo-3.0.0 | hb547adb_1 535 KB conda-forge
liblapack-3.9.0 |18_osxarm64_openblas 14 KB conda-forge
libopenblas-0.3.24 |openmp_hd76b1f2_0 2.7 MB conda-forge
libsqlite-3.43.2 | h091b4b1_0 790 KB conda-forge
libtiff-4.6.0 | ha8a6c65_2 240 KB conda-forge
libwebp-base-1.3.2 | hb547adb_0 267 KB conda-forge
libxcb-1.15 | hf346824_0 327 KB conda-forge
llvm-openmp-17.0.2 | h1c12783_0 269 KB conda-forge
markdown-3.5 | pyhd8ed1ab_0 75 KB conda-forge
markdown-it-py-3.0.0 | pyhd8ed1ab_0 63 KB conda-forge
markupsafe-2.1.3 | py312h02f2b3b_1 26 KB conda-forge
matplotlib-base-3.8.0 | py312hba9b818_2 7.5 MB conda-forge
multiqc-1.16 | pyhdfd78af_0 1.0 MB bioconda
networkx-3.1 | pyhd8ed1ab_0 1.4 MB conda-forge
numpy-1.26.0 | py312h696b312_0 5.9 MB conda-forge
openjpeg-2.5.0 | h4c1507b_3 316 KB conda-forge
openssl-3.1.3 | h53f4e23_0 2.1 MB conda-forge
packaging-23.2 | pyhd8ed1ab_0 48 KB conda-forge
pillow-10.0.1 | py312hb653a51_2 43.8 MB conda-forge
pip-23.2.1 | pyhd8ed1ab_0 1.3 MB conda-forge
pthread-stubs-0.4 | h27ca646_1001 6 KB conda-forge
pygments-2.16.1 | pyhd8ed1ab_0 833 KB conda-forge
pyparsing-3.1.1 | pyhd8ed1ab_0 87 KB conda-forge
python-3.12.0 |h47c9636_0_cpython 12.7 MB conda-forge
python_abi-3.12 | 4_cp312 6 KB conda-forge
pyyaml-6.0.1 | py312h02f2b3b_1 178 KB conda-forge
requests-2.31.0 | pyhd8ed1ab_0 55 KB conda-forge
rich-13.6.0 | pyhd8ed1ab_0 179 KB conda-forge
rich-click-1.7.0 | pyhd8ed1ab_0 32 KB conda-forge
setuptools-68.2.2 | pyhd8ed1ab_0 454 KB conda-forge
simplejson-3.19.2 | py312he37b823_0 126 KB conda-forge
tk-8.6.13 | hb31c410_0 3.1 MB conda-forge
typing_extensions-4.8.0 | pyha770c72_0 34 KB conda-forge
urllib3-2.0.6 | pyhd8ed1ab_0 96 KB conda-forge
wheel-0.41.2 | pyhd8ed1ab_0 56 KB conda-forge
xorg-libxau-1.0.11 | hb547adb_0 13 KB conda-forge
zipp-3.17.0 | pyhd8ed1ab_0 19 KB conda-forge
zstd-1.5.5 | h4f39d0f_0 391 KB conda-forge
------------------------------------------------------------
Total: 94.0 MB
The following NEW packages will be INSTALLED:
brotli conda-forge/osx-arm64::brotli-1.1.0-hb547adb_1
brotli-bin conda-forge/osx-arm64::brotli-bin-1.1.0-hb547adb_1
brotli-python conda-forge/osx-arm64::brotli-python-1.1.0-py312h9f69965_1
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h3422bc3_4
ca-certificates conda-forge/osx-arm64::ca-certificates-2023.7.22-hf0a4a13_0
certifi conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.3.0-pyhd8ed1ab_0
click conda-forge/noarch::click-8.1.7-unix_pyh707e725_0
coloredlogs conda-forge/noarch::coloredlogs-15.0.1-pyhd8ed1ab_3
colormath conda-forge/noarch::colormath-3.0.0-py_2
contourpy conda-forge/osx-arm64::contourpy-1.1.1-py312h389731b_1
cycler conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0
fonttools conda-forge/osx-arm64::fonttools-4.43.1-py312he37b823_0
freetype conda-forge/osx-arm64::freetype-2.12.1-hadb7bae_2
future conda-forge/noarch::future-0.18.3-pyhd8ed1ab_0
humanfriendly conda-forge/noarch::humanfriendly-10.0-pyhd8ed1ab_6
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
importlib-metadata conda-forge/noarch::importlib-metadata-6.8.0-pyha770c72_0
jinja2 conda-forge/noarch::jinja2-3.1.2-pyhd8ed1ab_1
kiwisolver conda-forge/osx-arm64::kiwisolver-1.4.5-py312h389731b_1
lcms2 conda-forge/osx-arm64::lcms2-2.15-hf2736f0_3
lerc conda-forge/osx-arm64::lerc-4.0.0-h9a09cb3_0
libblas conda-forge/osx-arm64::libblas-3.9.0-18_osxarm64_openblas
libbrotlicommon conda-forge/osx-arm64::libbrotlicommon-1.1.0-hb547adb_1
libbrotlidec conda-forge/osx-arm64::libbrotlidec-1.1.0-hb547adb_1
libbrotlienc conda-forge/osx-arm64::libbrotlienc-1.1.0-hb547adb_1
libcblas conda-forge/osx-arm64::libcblas-3.9.0-18_osxarm64_openblas
libcxx conda-forge/osx-arm64::libcxx-16.0.6-h4653b0c_0
libdeflate conda-forge/osx-arm64::libdeflate-1.19-hb547adb_0
libexpat conda-forge/osx-arm64::libexpat-2.5.0-hb7217d7_1
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_1
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_1
libjpeg-turbo conda-forge/osx-arm64::libjpeg-turbo-3.0.0-hb547adb_1
liblapack conda-forge/osx-arm64::liblapack-3.9.0-18_osxarm64_openblas
libopenblas conda-forge/osx-arm64::libopenblas-0.3.24-openmp_hd76b1f2_0
libpng conda-forge/osx-arm64::libpng-1.6.39-h76d750c_0
libsqlite conda-forge/osx-arm64::libsqlite-3.43.2-h091b4b1_0
libtiff conda-forge/osx-arm64::libtiff-4.6.0-ha8a6c65_2
libwebp-base conda-forge/osx-arm64::libwebp-base-1.3.2-hb547adb_0
libxcb conda-forge/osx-arm64::libxcb-1.15-hf346824_0
libzlib conda-forge/osx-arm64::libzlib-1.2.13-h53f4e23_5
llvm-openmp conda-forge/osx-arm64::llvm-openmp-17.0.2-h1c12783_0
lzstring conda-forge/noarch::lzstring-1.0.4-py_1001
markdown conda-forge/noarch::markdown-3.5-pyhd8ed1ab_0
markdown-it-py conda-forge/noarch::markdown-it-py-3.0.0-pyhd8ed1ab_0
markupsafe conda-forge/osx-arm64::markupsafe-2.1.3-py312h02f2b3b_1
matplotlib-base conda-forge/osx-arm64::matplotlib-base-3.8.0-py312hba9b818_2
mdurl conda-forge/noarch::mdurl-0.1.0-pyhd8ed1ab_0
multiqc bioconda/noarch::multiqc-1.16-pyhdfd78af_0
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
ncurses conda-forge/osx-arm64::ncurses-6.4-h7ea286d_0
networkx conda-forge/noarch::networkx-3.1-pyhd8ed1ab_0
numpy conda-forge/osx-arm64::numpy-1.26.0-py312h696b312_0
openjpeg conda-forge/osx-arm64::openjpeg-2.5.0-h4c1507b_3
openssl conda-forge/osx-arm64::openssl-3.1.3-h53f4e23_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pillow conda-forge/osx-arm64::pillow-10.0.1-py312hb653a51_2
pip conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0
pthread-stubs conda-forge/osx-arm64::pthread-stubs-0.4-h27ca646_1001
pygments conda-forge/noarch::pygments-2.16.1-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.1.1-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python conda-forge/osx-arm64::python-3.12.0-h47c9636_0_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-arm64::python_abi-3.12-4_cp312
pyyaml conda-forge/osx-arm64::pyyaml-6.0.1-py312h02f2b3b_1
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
rich conda-forge/noarch::rich-13.6.0-pyhd8ed1ab_0
rich-click conda-forge/noarch::rich-click-1.7.0-pyhd8ed1ab_0
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
simplejson conda-forge/osx-arm64::simplejson-3.19.2-py312he37b823_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
spectra conda-forge/noarch::spectra-0.0.11-py_1
tk conda-forge/osx-arm64::tk-8.6.13-hb31c410_0
typing_extensions conda-forge/noarch::typing_extensions-4.8.0-pyha770c72_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
urllib3 conda-forge/noarch::urllib3-2.0.6-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.41.2-pyhd8ed1ab_0
xorg-libxau conda-forge/osx-arm64::xorg-libxau-1.0.11-hb547adb_0
xorg-libxdmcp conda-forge/osx-arm64::xorg-libxdmcp-1.1.3-h27ca646_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
yaml conda-forge/osx-arm64::yaml-0.2.5-h3422bc3_2
zipp conda-forge/noarch::zipp-3.17.0-pyhd8ed1ab_0
zstd conda-forge/osx-arm64::zstd-1.5.5-h4f39d0f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
```
</details>
```console
❯ conda activate py3.12
❯ multiqc --help
Traceback (most recent call last):
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/bin/multiqc", line 6, in <module>
from multiqc.__main__ import run_multiqc
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/__init__.py", line 16, in <module>
from .multiqc import run
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/multiqc.py", line 30, in <module>
from .plots import table
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/plots/table.py", line 9, in <module>
from multiqc.plots import beeswarm, table_object
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/plots/beeswarm.py", line 9, in <module>
from multiqc.plots import table_object
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/plots/table_object.py", line 9, in <module>
from multiqc.utils import config, report
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/multiqc/utils/report.py", line 18, in <module>
import lzstring
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/lzstring/__init__.py", line 11, in <module>
from future import standard_library
File "/Users/ewels/.miniconda3/miniconda3/envs/py3.12/lib/python3.12/site-packages/future/standard_library/__init__.py", line 65, in <module>
import imp
ModuleNotFoundError: No module named 'imp'
```
Thank you so much ewels for the reply. You are absolutely right. It has some issue with the python 3.12. I fixed the issue with the installation of phython 3.11. Now, MultiQC is working.
ewels
October 14, 2023, 8:08pm
4
Great stuff. Thanks for letting us know! We have a fix in the works. Hoping to release on Monday.
ewels
October 21, 2023, 3:46pm
5
MultiQC v1.17 went out a few days ago and fixed the Python 3.12 problems, so for anyone landing here I’d recommend upgrading to both the latest stable releases of MultiQC + Python
You can find the release notes here:
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