FoldTree snakemake workflow crashes because it cannot copy a file

[Cydhra]

I am trying to run the foldtree snakemake workflow with an identifiers.txt file in a custom folder. The structs download successfully and all, but the foldseek allvall step crashes with an error:

Could not copy file ../datasets/CATH/1.10.10.10/tmp/3015592231757429187/search_tmp/12975415917271705121/aln to ../datasets/CATH/1.10.10.10/tmp/3015592231757429187/result!
Error: Search died
[Thu Feb 19 16:46:53 2026]
Error in rule foldseek_allvall_1:
    jobid: 8
    input: ../datasets/CATH/1.10.10.10/finalset.csv
    output: ../datasets/CATH/1.10.10.10/allvall_1.csv
    log: ../datasets/CATH/1.10.10.10/logs/foldseekallvall.log (check log file(s) for error details)
    conda-env: foldtree
    shell:
        foldseek easy-search ../datasets/CATH/1.10.10.10/structs/ ../datasets/CATH/1.10.10.10/structs/ ../datasets/CATH/1.10.10.10/allvall_1.csv ../datasets/CATH/1.10.10.10/tmp --format-output 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore' --exhaustive-search --alignment-type 2 -e inf --threads 1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

The exact command line is snakemake -s ./workflow/fold_tree --config folder=../datasets/CATH/1.10.10.10 filter=False --cores 48

I have verified that both the ../datasets/CATH/1.10.10.10/tmp/3015592231757429187/search_tmp/12975415917271705121/aln file and the ../datasets/CATH/1.10.10.10/tmp/3015592231757429187/result folder exist, so I don't know what prevents this from working.

Looking forward for suggestions because I am kindof lost on how to handle this.