error running script: cannot execute foldseek binary file

[ruthalee]

Hello, I am trying to run the script with a custom database. I get the error below.

`(foldtree) rulee@infra04-wg324 fold_tree % snakemake --cores 4 --use-conda -s workflow/fold_tree --config folder=decaheme custom_structs=True /Users/ruthlee/fold_tree/ Config file /Users/ruthlee/fold_tree/workflow/config/config_vars.yaml is extended by additional config specified via the command line. Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Job stats: job count

---

all 1 foldseek2distmat 1 foldseek_allvall_1 1 mad_root_post 3 postprocess 3 quicktree 3 total 12

Select jobs to execute...

[Wed Jan 24 16:54:30 2024] rule foldseek_allvall_1: input: decaheme/finalset.csv output: decaheme/allvall_1.csv log: decaheme/logs/foldseekallvall.log jobid: 7 reason: Missing output files: decaheme/allvall_1.csv wildcards: folder=decaheme resources: tmpdir=/var/folders/c8/9q8d9t1x4yz69_zzdytq4bww0000gn/T

Activating conda environment: foldtree /bin/bash: /Users/ruthlee/fold_tree/foldseek/foldseek: cannot execute binary file [Wed Jan 24 16:54:30 2024] Error in rule foldseek_allvall_1: jobid: 7 input: decaheme/finalset.csv output: decaheme/allvall_1.csv log: decaheme/logs/foldseekallvall.log (check log file(s) for error details) conda-env: foldtree shell: /Users/ruthlee/fold_tree/foldseek/foldseek easy-search decaheme/structs/ decaheme/structs/ decaheme/allvall_1.csv decaheme/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!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-01-24T165429.787296.snakemake.log`

I followed the instructions for the installation. The only hiccup I had was with some bioconda dependencies. I have an M1 Mac, so I had force an osx-64 environment to configure the foldtree environment. I don't know if that would do anything. Any ideas? Thank so much for your help!

[aamirrr-m]

I think i may have found a resolution for my linux vm installation:

head to your config_vars.yaml file in fold_tree/workflow/config

find the line foldseek_path: provided

and replace provided with foldseek (all lowercase)

and try it again.

I had this issue starting from yesterday, let me know if it works for you too.

[cactuskid]

I've changed the configfile variable to default to just use the latest foldseek instead of the binary included in the repo ( I wanted my results to be replicable so I was using the same version throughout all my benchmarking experiments ). This shouldn't impact results though.

[ruthalee]

Thank you aamirr-m and cactuskid. I installed on my university's linux computing system and it ran perfectly. I'll try again on my mac with the new change, but I have something working regardless. Thank you!