[*] Error: run seqtrack R script failed. #8
Description
Dear developers,
I am having a weird problem while running Transflow. In the past, I made a successful run but after changing the snp_threshold I am having an error in the transmission analysis module. My dataset has 1,652 samples, it works fine with smaller datasets.
Here is a piece of the error message :
=> Using SeqTrack to infer transmission events for all clusters with at least 4 samples.
==> Cluster 1 ... Using longitude and latitude information data.
Done
==> Cluster 2 ... Using longitude and latitude information data.
Done
==> Cluster 3 ... Using longitude and latitude information data.
[*] Error: run seqtrack R script failed.
Full Traceback (most recent call last):
File "/hpc/home/user/miniconda3/envs/transflow/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 2576, in run_wrapper
run(
File "/work/user/transflow/L2/workflow/rules/transmission_detection.smk", line 76, in __rule_transmission_network
File "/hpc/home/user/miniconda3/envs/transflow/lib/python3.10/site-packages/snakemake/shell.py", line 294, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail; python3 /work/user/transflow/L2/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 /work/user/transflow/L2/metadata_date_L2_genomes.tsv --coord True --method trans 2> 5.Transmission_cluster/SNP_based_method/transmission_detection.log' returned non-zero exit status 1.
The complete log
The configfile
The command I am running:
snakemake --snakefile workflow/transmission_analysis.snakefile --configfile configfile.yaml --verbose -c 16
The resources:
A SLURM cluster, using #SBATCH --mem-per-cpu=32G and #SBATCH -c 16
Thank you,
Claudia