MultiQC: ModuleNotFoundError: No module named 'imp' - MultiQC

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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?

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:

github.com/ewels/MultiQC

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'

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: