Assuming unrestricted shared filesystem usage.
host: hos76216
Building DAG of jobs...
Pulling singularity image docker://quay.io/biocontainers/cutadapt:4.9--py39hff71179_0.
Using shell: /usr/bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job         count
--------  -------
cutadapt        1
total           1

Select jobs to execute...
Execute 1 jobs...

[Tue Nov 12 14:13:43 2024]
localrule cutadapt:
    input: subset.fasta
    output: output.fasta
    log: cutadapt.log
    jobid: 0
    reason: Missing output files: output.fasta
    resources: tmpdir=/tmp

Activating singularity image /home/fchaaban/tests/snakemake/test/.snakemake/singularity/7a81fdea5f528dce1de6f54c1cb2878f.simg
/usr/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
/usr/bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
/usr/bin/sh: line 1: conda: command not found
WorkflowError:
Error running conda info. Is conda installed and accessible? Error: Command ' singularity --quiet --silent exec --home '/home/fchaaban/tests/snakemake/test'  /home/fchaaban/tests/snakemake/test/.snakemake/singularity/7a81fdea5f528dce1de6f54c1cb2878f.simg sh -c 'conda info --json'' returned non-zero exit status 127.
Removing output files of failed job cutadapt since they might be corrupted:
output.fasta
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-11-12T141342.658077.snakemake.log
WorkflowError:
At least one job did not complete successfully.

❯ tar -xzvf test.tar.gz && cd test
❯ snakemake --snakefile Snakefile --sdm apptainer

❯ conda install snakemake=8.24
❯ snakemake --snakefile Snakefile --sdm apptainer
Assuming unrestricted shared filesystem usage.
host: hos76216
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job         count
--------  -------
cutadapt        1
total           1

Select jobs to execute...
Execute 1 jobs...

[Tue Nov 12 14:21:46 2024]
localrule cutadapt:
    input: subset.fasta
    output: output.fasta
    log: cutadapt.log
    jobid: 0
    reason: Missing output files: output.fasta
    resources: tmpdir=/tmp

Activating singularity image /home/fchaaban/tests/snakemake/test/.snakemake/singularity/7a81fdea5f528dce1de6f54c1cb2878f.simg
/usr/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
[Tue Nov 12 14:21:47 2024]
Finished job 0.
1 of 1 steps (100%) done
Complete log: .snakemake/log/2024-11-12T142146.888985.snakemake.log