Error: Missing argument '<analysis directory>'

[LuisGuz]

Dear Alexander Lab.
I'm trying to setup EukHeist for detecting microalgae from snow samples, and I'm having some trouble.
I'd appreciate some help!

After installing and running my samples I'm getting an error in multiqc, showing the following:

Usage: multiqc [OPTIONS]

Error: Missing argument .

This is MultiQC v1.12 (2d5d85c)

For more help, run 'multiqc --help' or visit http://multiqc.info

When running samples after successfully running $ snakemake -s EUKHeist -np --use-conda:
$ snakemake -s EUKHeist --use-conda --cores 60
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 60
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

all 1 1 1
metaG_only 1 1 1
multiqc_metaG 1 1 1
total 3 1 1

Select jobs to execute...

[Fri Feb 24 14:45:23 2023]
rule multiqc_metaG:
output: /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html, /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html
jobid: 2
reason: Missing output files: /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html, /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html
resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/9efd08072f56882cb9f0ca791feda2d7_
Usage: multiqc [OPTIONS]

Error: Missing argument .

This is MultiQC v1.12 (2d5d85c)

For more help, run 'multiqc --help' or visit http://multiqc.info

$less .snakemake/log/2023-02-24T144521.236461.snakemake.log

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 60
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

all 1 1 1
metaG_only 1 1 1
multiqc_metaG 1 1 1
total 3 1 1

Select jobs to execute...

[Fri Feb 24 14:45:23 2023]
rule multiqc_metaG:
output: /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html, /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html
jobid: 2
reason: Missing output files: /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html, /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html
resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/9efd08072f56882cb9f0ca791feda2d7_
[Fri Feb 24 14:45:24 2023]
Error in rule multiqc_metaG:
jobid: 2
output: /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html, /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html
conda-env: /home/luisguzman/EukHeist/.snakemake/conda/9efd08072f56882cb9f0ca791feda2d7_
shell:

    multiqc -f --export -n multiqc_metaG.html -o multiqc_metaG 
    cat multiqc_metaG/multiqc_metaG*.html > /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/trimmedG_multiqc.html
    mv multiqc_metaG/multiqc_metaG_data /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/multiqc_metaG_data
    rm -rf multiqc_metaG/
    
    multiqc -f --export -n multiqc_metaG_raw.html -o multiqc_metaG_raw 
    cat multiqc_metaG_raw/multiqc_metaG_raw*.html > /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/rawG_multiqc.html
    mv multiqc_metaG_raw/multiqc_metaG_raw_data /home/luisguzman/Bioinformatics/metagenomics2/eukheist/output2/qc/multiqc_metaG_raw_data
    rm -rf multiqc_metaG_raw/
    
    (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/2023-02-24T144521.236461.snakemake.log

Here are my input files.
Maybe I'm missing something?

assembly2.txt
metagenomic2.txt

Best regards.

[akrinos]

Hi @LuisGuz ! Thanks so much for trying out EUKHeist, so sorry that this reply is so late - I just received some kind of email about it. I had a question but you've probably moved on to something else by this point. Is this the full log that you received from the program, i.e., no other rules were scheduled to run? This will help me in figuring out where the source of the issue starts - it looks like from my reading that the wildcards are not getting passed through correctly within Snakemake.