Snakemake fails to produce output

Question

I'm trying to run fastqc on two paired files (1.fq.gz and 2.fq.gz). Running:

snakemake --use-conda -np newenv/1_fastqc.html

...produces what looks like a sensible DAG:

Building DAG of jobs...
Job stats:
job           count    min threads    max threads
----------  -------  -------------  -------------
curlewtest        1              1              1
total             1              1              1


[Sat May 21 11:27:40 2022]
rule curlewtest:
    input: 1.fq.gz, 2.fq.gz
    output: newenv/1_fastqc.html, newenv/2_fastqc.html
    jobid: 0
    resources: tmpdir=/tmp

fastqc 1.fq.gz 2.fq.gz
Job stats:
job           count    min threads    max threads
----------  -------  -------------  -------------
curlewtest        1              1              1
total             1              1              1

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

When I run the job snakemake --use-conda --cores all newenv/1_fastqc.html , the analysis runs, but the output files fail to appear. Snakemake also throws the following error:

Waiting at most 5 seconds for missing files.
MissingOutputException in line 2 of /mnt/data/kcollier/snakemake-workspace/snakefile:
Job Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
newenv/1_fastqc.html
newenv/2_fastqc.html completed successfully, but some output files are missing. 0
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Increasing latency does not help. The output directory I created beforehand (newenv) also disappears. Does anyone else know why this is?