MissingOutputException in rule download_genome_annotations

[biocclh]

Hi,

I'm using SCENICPLUS version 1.0a2 and encountering an import error:

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Job stats:
job                             count
----------------------------  -------
AUCell_direct                       1
AUCell_extended                     1
all                                 1
download_genome_annotations         1
eGRN_direct                         1
eGRN_extended                       1
get_search_space                    1
motif_enrichment_dem                1
prepare_GEX_ACC_non_multiome        1
prepare_menr                        1
region_to_gene                      1
scplus_mudata                       1
tf_to_gene                          1
total                              13

Select jobs to execute...
Execute 2 jobs...

[Tue Nov 18 09:41:50 2025]
localrule prepare_GEX_ACC_non_multiome:
    input: /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/NK_ATAC_cistopic_obj_with_model.pkl, /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/sub_NK.h5ad
    output: /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/ACC_GEX.h5mu
    jobid: 2
    reason: Missing output files: /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/ACC_GEX.h5mu
    resources: tmpdir=/tmp


[Tue Nov 18 09:41:50 2025]
localrule download_genome_annotations:
    output: /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/genome_annotation.tsv, /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/chromsizes.tsv
    jobid: 8
    reason: Missing output files: /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/chromsizes.tsv, /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/genome_annotation.tsv
    resources: tmpdir=/tmp

Waiting at most 5 seconds for missing files.
MissingOutputException in rule download_genome_annotations in file /project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/scplus_pipeline/Snakemake/workflow/Snakefile, line 221:
Job 8  completed successfully, but some output files are missing. 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:
/project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/chromsizes.tsv
Removing output files of failed job download_genome_annotations since they might be corrupted:
/project_res/hail/kefu/RPyyb240812A1012027-2/scATAC/SCENICPlus/data/NK/out/genome_annotation.tsv
[Tue Nov 18 09:43:16 2025]
Finished job 2.
1 of 13 steps (8%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-11-18T094150.024276.snakemake.log
WorkflowError:
At least one job did not complete successfully.

Thank you for your help!
Thank you for your help and for developing this great tool!