ModuleNotFoundError: No module named 'imp'

[jackieway]

Hello, I'm trying to use the command atlas run genomes (I ran QC, assembly, binning, and genecatalog separately), but keep getting the following error message. I've tried to run conda install -c conda-forge imp to manually install imp, but this hasn't worked. Is there any way to fix this? Thanks!

    input: genomes/alignments/stats/W197-1.stats, genomes/alignments/stats/W197-10.stats, genomes/alignments/stats/W197-11.stats, genomes/alignments/stats/W197-12.stats, genomes/alignments/stats/W197-2.stats, genomes/alignments/stats/W197-3.stats, genomes/alignments/stats/W197-4.stats, genomes/alignments/stats/W197-5.stats, genomes/alignments/stats/W197-6.stats, genomes/alignments/stats/W197-7.stats, genomes/alignments/stats/W197-8.stats, genomes/alignments/stats/W197-9.stats
    output: reports/genome_mapping/results.html
    log: logs/genomes/alignment/multiqc.log
    jobid: 303
    reason: Missing output files: reports/genome_mapping/results.html
    resources: tmpdir=/tmp, mem_mb=30358, mem_mib=28952, time_min=300, runtime=300

Activating conda environment: databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_
Activating conda environment: databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_
Traceback (most recent call last):
  File "/home/.snakemake/scripts/tmp2d7oexmc.wrapper.py", line 32, in <module>
    shell(
  File "/root/mambaforge/lib/python3.10/site-packages/snakemake/shell.py", line 294, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  multiqc  --force -o reports/genome_mapping -n results.html genomes/alignments/stats  > logs/genomes/alignment/multiqc.log 2>&1' returned non-zero exit status 1.
[Mon Dec 18 17:25:18 2023]
Error in rule multiqc_mapping_genome:
    jobid: 303
    input: genomes/alignments/stats/W197-1.stats, genomes/alignments/stats/W197-10.stats, genomes/alignments/stats/W197-11.stats, genomes/alignments/stats/W197-12.stats, genomes/alignments/stats/W197-2.stats, genomes/alignments/stats/W197-3.stats, genomes/alignments/stats/W197-4.stats, genomes/alignments/stats/W197-5.stats, genomes/alignments/stats/W197-6.stats, genomes/alignments/stats/W197-7.stats, genomes/alignments/stats/W197-8.stats, genomes/alignments/stats/W197-9.stats
    output: reports/genome_mapping/results.html
    log: logs/genomes/alignment/multiqc.log (check log file(s) for error details)
    conda-env: /home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_
Logfile logs/genomes/alignment/multiqc.log:
================================================================================
Traceback (most recent call last):
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import run_multiqc
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/multiqc/__init__.py", line 16, in <module>
    from .multiqc import run
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/multiqc/multiqc.py", line 29, in <module>
    from .plots import table
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/multiqc/plots/table.py", line 9, in <module>
    from multiqc.utils import config, report, util_functions, mqc_colour
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/multiqc/utils/report.py", line 13, in <module>
    import lzstring
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/lzstring/__init__.py", line 11, in <module>
    from future import standard_library
  File "/home/databases/conda_envs/b1385549c4a116a0a0235ec42cff7acd_/lib/python3.12/site-packages/future/standard_library/__init__.py", line 65, in <module>
    import imp
ModuleNotFoundError: No module named 'imp'
================================================================================

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Note the path to the log file for debugging.
Documentation is available at: https://metagenome-atlas.readthedocs.io
Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues
Complete log: .snakemake/log/2023-12-18T172513.129169.snakemake.log
[Atlas] CRITICAL: Command 'snakemake --snakefile /root/mambaforge/lib/python3.10/site-packages/atlas/workflow/Snakefile --directory /home  --rerun-triggers mtime --jobs 16 --rerun-incomplete --configfile '/home/config.yaml' --nolock  --show-failed-logs   --use-conda --conda-prefix /home/databases/conda_envs    --resources mem=29 mem_mb=30358 java_mem=25   --scheduler greedy  genomes   ' returned non-zero exit status 1.```

[SilasK]

There is a solution here #702