Error in install_wild_pbwt

[fawaz-dabbaghieh]

Hi,

I am trying to run the example provided, but I got the following error at rule install_wild_pbwt.

I am using conda 24.9.0 and followed the instruction in README to make a pangeblocks environment

Your conda installation is not configured to use strict channel priorities. This is however important for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Creating conda environment envs/wild-pbwt.yml...
Downloading and installing remote packages.
Environment for /home/fawaz/projects/pangeblocks/envs/wild-pbwt.yml created (location: .snakemake/conda/2531f729280f749ae90cb08ddbe916b3_)
Creating conda environment envs/pggb.yml...
Downloading and installing remote packages.
Environment for /home/fawaz/projects/pangeblocks/envs/pggb.yml created (location: .snakemake/conda/73c822e7b455a871d4d465c058116b99_)
Creating conda environment envs/pangeblocks.yml...
Downloading and installing remote packages.
Environment for /home/fawaz/projects/pangeblocks/envs/pangeblocks.yml created (location: .snakemake/conda/c2d3fd8e95bc46226b42128dc207dbed_)
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job stats:
job                        count
-----------------------  -------
all                            1
compute_vertical_blocks        1
coverage_to_graph              1
ilp                            1
install_wild_pbwt              1
postprocessing_gfa             1
submsa_index                   1
unchop_gfa                     1
total                          8

Select jobs to execute...
Execute 2 jobs...

[Mon Dec  9 15:49:16 2024]
localrule compute_vertical_blocks:
    input: test/sars-cov-2-subMSA/sars-cov-2.fa
    output: output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json
    log: output-sars-cov-2/logs/sars-cov-2-rule-compute_blocks_alpha50.err.log
    jobid: 6
    reason: Missing output files: output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json
    wildcards: alpha=50, name_msa=sars-cov-2
    resources: tmpdir=/tmp

/usr/bin/time --verbose src/greedy_vertical_blocks.py test/sars-cov-2-subMSA/sars-cov-2.fa --output output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json         --threshold-vertical-blocks 50 --log-level ERROR > output-sars-cov-2/logs/sars-cov-2-rule-compute_blocks_alpha50.err.log 2>&1
Activating conda environment: .snakemake/conda/c2d3fd8e95bc46226b42128dc207dbed_

[Mon Dec  9 15:49:16 2024]
localrule install_wild_pbwt:
    output: Wild-pBWT/bin/wild-pbwt
    log: output-sars-cov-2/logs/rule-install_wild_pbwt.err.log
    jobid: 7
    reason: Missing output files: Wild-pBWT/bin/wild-pbwt
    resources: tmpdir=/tmp


        if ! [ -f "Wild-pBWT/bin/wild-pbwt"]; then
            rm -rf Wild-pBWT/
            git clone https://github.com/illoxian/Wild-pBWT.git && cd Wild-pBWT
            make wild-pbwt
        else
            echo "wild-pbwt already installed"
        fi
        
Activating conda environment: .snakemake/conda/2531f729280f749ae90cb08ddbe916b3_
[Mon Dec  9 15:49:16 2024]
Finished job 6.
1 of 8 steps (12%) done
Select jobs to execute...
Execute 1 jobs...

[Mon Dec  9 15:49:16 2024]
localrule submsa_index:
    input: test/sars-cov-2-subMSA/sars-cov-2.fa, output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json
    output: output-sars-cov-2/submsas/sars-cov-2_alpha50.txt
    log: output-sars-cov-2/logs/sars-cov-2-alpha50-rule-submsa_index.out.log
    jobid: 5
    reason: Missing output files: output-sars-cov-2/submsas/sars-cov-2_alpha50.txt; Input files updated by another job: output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json
    wildcards: alpha=50, name_msa=sars-cov-2
    resources: tmpdir=/tmp

/usr/bin/time --verbose src/submsas.py --path-msa test/sars-cov-2-subMSA/sars-cov-2.fa         --path-vertical-blocks output-sars-cov-2/maximal-blocks/sars-cov-2/vertical_blocks_alpha50.json --threshold-vertical-blocks 50         --max-positions-submsas 80000 --output output-sars-cov-2/submsas/sars-cov-2_alpha50.txt > output-sars-cov-2/logs/sars-cov-2-alpha50-rule-submsa_index.out.log 2>&1
        
Activating conda environment: .snakemake/conda/c2d3fd8e95bc46226b42128dc207dbed_
[Mon Dec  9 15:49:17 2024]
Finished job 5.
2 of 8 steps (25%) done
[Mon Dec  9 15:49:18 2024]
Error in rule install_wild_pbwt:
    jobid: 7
    output: Wild-pBWT/bin/wild-pbwt
    log: output-sars-cov-2/logs/rule-install_wild_pbwt.err.log (check log file(s) for error details)
    conda-env: /home/fawaz/projects/pangeblocks/.snakemake/conda/2531f729280f749ae90cb08ddbe916b3_
    shell:
        
        if ! [ -f "Wild-pBWT/bin/wild-pbwt"]; then
            rm -rf Wild-pBWT/
            git clone https://github.com/illoxian/Wild-pBWT.git && cd Wild-pBWT
            make wild-pbwt
        else
            echo "wild-pbwt already installed"
        fi
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-12-09T154802.677552.snakemake.log
WorkflowError:
At least one job did not complete successfully.```