I'm testing the transflow installation by running the example sequences. First, I followed the one-step way, but if failed during the 5.Transmission analysis step. Then, I tried the step-by-step way, and gave me the same error. Something related with the snakemake rules.
I used this command:
bash transflow.sh --configfile config/configfile.yaml --cores 4 -k
The last lines of the error message:
[Wed May 8 19:03:01 2024]
Error in rule transmission_network:
jobid: 4
input: 5.Transmission_cluster/SNP_based_method/samples_cluster_SNP_12.csv, 4.SNP_distance/samples_pairwise_distance_matrix.txt
output: 5.Transmission_cluster/SNP_based_method/transmission_clusters.txt, 5.Transmission_cluster/SNP_based_method/transmission_detection_run_info.txt
log: 5.Transmission_cluster/SNP_based_method/transmission_detection.log (check log file(s) for error details)
shell:
python3 /home/paumayell/transflow/workflow/scripts/run_transmission_detection.py --cluster 5.Transmission_cluster/SNP_based_method/samples_cluster_SNP_12.csv --distance 4.SNP_distance/samples_pairwise_distance_matrix.txt --network True --output 5.Transmission_cluster/SNP_based_method --date /home/paumayell/transflow/example/samples.txt --coord True --method SNP 2> 5.Transmission_cluster/SNP_based_method/transmission_detection.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-05-08T190143.361895.snakemake.log
Dear developers,
I'm testing the transflow installation by running the example sequences. First, I followed the one-step way, but if failed during the 5.Transmission analysis step. Then, I tried the step-by-step way, and gave me the same error. Something related with the snakemake rules.
I used this command:
bash transflow.sh --configfile config/configfile.yaml --cores 4 -kThe last lines of the error message:
Complete log file: 2024-05-08T190143.361895.snakemake.log
Thank you very much for your help
Paulina