Error in system building

[vecos1990]

Dear @philbiggin
I just tried running a job again and it fails.
Here is the complete log file

"**Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 64
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

abfe_recptor_result 1 1 1
build_ligand_system 1 1 1
calculate_ABFE 3 1 1
fep_complex 3 1 1
fep_ligand 3 1 1
gather_receptor_results 1 1 1
total 12 1 1

Select jobs to execute...

[Thu Dec 18 20:41:02 2025]
rule build_ligand_system:
input: /home/disk6/homes/cveranso/ABFE_workflow/examples/dnmt3a_mr046978a_105_Pro_noH.pdb, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input
output: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top
jobid: 4
reason: Missing output files: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top
wildcards: ligand_name=dnmt3a_mr046978a_105_Lig
resources: tmpdir=/tmp

[Thu Dec 18 20:41:05 2025]
Error in rule build_ligand_system:
jobid: 4
output: /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/ligand/ligand.top, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.gro, /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input/complex/complex.top
shell:

        python /homes/cveranso/miniconda3/envs/abfe_bi_11dec/lib/python3.10/site-packages/abfe/scripts/preparation/generate_ABFE_systems.py --ligand_sdf_dir /home/disk6/homes/cveranso/ABFE_workflow/examples/output/orig_input/dnmt3a_mr046978a_105_Lig.sdf             --protein_pdb_path /home/disk6/homes/cveranso/ABFE_workflow/examples/dnmt3a_mr046978a_105_Pro_noH.pdb             --cofactor_sdf_path None --output_dir_path /home/disk6/homes/cveranso/ABFE_workflow/examples/output/dnmt3a_mr046978a_105_Lig/input -ff gaff

    (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/2025-12-18T204101.233253.snakemake.log**
"

[philbiggin]

Do the examples work for you? I

[vecos1990]

Dear @philbiggin
Unfortunately, the examples also fail.
I have attached the log file for a trial run using ligands 2 and 27 from the example set.

The complete log file is attached to this

error_example.log

[philbiggin]

please post or pm me with - ./ABFE_workflow/examples/output/ligand-2/1/ligand/job_ligand.sh

[vecos1990]

Here is the requested file.
I am beginning to see some lines that could cause an error.

job_ligand.sh

[philbiggin]

Unless by some miracle you have the same queue names as us then

--partition=gpu4-biggin

is certainly one problem for sure.

You should edit ./src/abfe/template/cluster_configs/default_slurm_template.json to reflect your local queueing system.