one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!

[ahsusohail]

I am trying to run vesselexpress (Ver 1.1.0) via the browser version (with Chrome or Safari) through Docker Desktop (Ver 4.33.0) installation.

I am using MacSonoma.

I followed this for the installation of vesselexpress.
docker pull phispa1812/vesselexpress
docker run -p 5000:5000 phispa1812/vesselexpress
Type: localhost:5000 in your browser

It gives the following error message: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!

Would you be able to help me with this?

Thank you.
-Ahsan

[ahsusohail]

The browser is not letting me download the logs but I have copied/pasted the entire log here:

Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count

---

all 1
graphAnalysis 1
makeImgDir 1
segmentation_3D 1
skeletonize 1
total 5

Select jobs to execute...
Execute 1 jobs...

[Tue Aug 13 23:49:27 2024]
localrule makeImgDir:
input: data/CD31_23-0142_Substack16-25-0006.tiff
output: data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff
jobid: 4
reason: Missing output files: data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff
wildcards: img=CD31_23-0142_Substack16-25-0006, ext=tiff
resources: tmpdir=/tmp

[Tue Aug 13 23:49:27 2024]
Finished job 4.
1 of 5 steps (20%) done
Select jobs to execute...
Execute 1 jobs...

[Tue Aug 13 23:49:27 2024]
localrule segmentation_3D:
input: data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff
output: data/CD31_23-0142_Substack16-25-0006/Binary_CD31_23-0142_Substack16-25-0006.tiff
jobid: 3
reason: Missing output files: data/CD31_23-0142_Substack16-25-0006/Binary_CD31_23-0142_Substack16-25-0006.tiff; Input files updated by another job: data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff
wildcards: img=CD31_23-0142_Substack16-25-0006, ext=tiff
resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/0a3b21b85f62992132147e08d91a7f9f_
[Tue Aug 13 23:49:50 2024]
Error in rule segmentation_3D:
jobid: 3
input: data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff
output: data/CD31_23-0142_Substack16-25-0006/Binary_CD31_23-0142_Substack16-25-0006.tiff
conda-env: /home/user/VesselExpress_server/VesselExpress/.snakemake/conda/0a3b21b85f62992132147e08d91a7f9f_
shell:
python workflow/scripts/segmentation3D.py -input "data/CD31_23-0142_Substack16-25-0006/CD31_23-0142_Substack16-25-0006.tiff" -small_RAM_mode 0 -smoothing 1 -core_threshold 3.0 -core_vessel_1 1 -core_vessel_2 1 -post_closing 5 -post_thinning 1 -post_cleaning 100 -gamma_1 5 -sigma_1 1.0 -cutoff_method_1 threshold_triangle -gamma_2 5 -sigma_2 2.0 -cutoff_method_2 threshold_li -min_thickness 1 -thin 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/2024-08-13T234924.930801.snakemake.log
WorkflowError:
At least one job did not complete successfully.▮