atlas: maxbin binning fails - Can't locate LWP/Simple.pm in @INC

Hi, Running a fresh conda install of metagenome atlas 2.4.3 on CentOS Linux 7, when trying to do binning maxbin keeps crashing with the following error:

Activating conda environment: /bio/kembel_s/atlas-databases/conda_envs/b9530507
Can't locate LWP/Simple.pm in @INC (you may need to install the LWP::Simple module) (@INC contains: /home/kembel_s/perl5/lib/perl5/x86_64-linux-thread-multi /home/kembel_s/perl5/lib/perl5 /bio/kembel_s/atlas-databases/conda_envs/b9530507/lib/site_perl/5.30.3/x86_64-linux-thread-multi /bio/kembel_s/atlas-databases/conda_envs/b9530507/lib/site_perl/5.30.3 /bio/kembel_s/atlas-databases/conda_envs/b9530507/lib/5.30.3/x86_64-linux-thread-multi /bio/kembel_s/atlas-databases/conda_envs/b9530507/lib/5.30.3 .) at /bio/kembel_s/atlas-databases/conda_envs/b9530507/bin/run_MaxBin.pl line 5.
BEGIN failed--compilation aborted at /bio/kembel_s/atlas-databases/conda_envs/b9530507/bin/run_MaxBin.pl line 5.
[Tue Oct 27 10:20:42 2020]
Error in rule maxbin:
    jobid: 45
    output: r1t1-2018AT-NP/binning/maxbin/intermediate_files, r1t1-2018AT-NP/binning/maxbin/r1t1-2018AT-NP.summary, r1t1-2018AT-NP/binning/maxbin/r1t1-2018AT-NP.marker, r1t1-2018AT-NP/binning/maxbin/r1t1-2018AT-NP.marker_of_each_bin.tar.gz, r1t1-2018AT-NP/binning/maxbin/r1t1-2018AT-NP.log
    log: r1t1-2018AT-NP/logs/binning/maxbin.log (check log file(s) for error message)
    conda-env: /bio/kembel_s/atlas-databases/conda_envs/b9530507
    shell:

I have installed both the LWP::Simple module and maxbin2 using conda. 2020-10-27T101506.554610.snakemake.log

Sorry if this is a stupid question but I’m at a loss as to how to get maxbin to see the LWP::Simple dependency. Binning works fine with metabat and DASTool.

About this issue

  • Original URL
  • State: closed
  • Created 4 years ago
  • Comments: 17 (10 by maintainers)

Most upvoted comments

Ok I tested my solution and it works. The bioconda package should be updated soon, so this fix is no longer needed. Thankyou all for your bug reports and your help.