Here is another issue, with a dataset including aDNA samples. I am not sure if an insufficient coverage is the cause of the problem here, as there is a division by zero error at the locus selection step of the pipeline.
I am using secapr 2.1.1.
Not sufficiently many loci (2500) were found that have an average read-coverage of 3.000000 for all samples. Extracting all 0 loci that fulfil this requirement.
Traceback (most recent call last):
File "/mnt/shared/scratch/tmichel/apps/conda/envs/secapr_env/bin/secapr", line 10, in <module>
sys.exit(main())
File "/mnt/shared/scratch/tmichel/apps/conda/envs/secapr_env/lib/python3.8/site-packages/secapr/__main__.py", line 55, in main
args.func(args)
File "/mnt/shared/scratch/tmichel/apps/conda/envs/secapr_env/lib/python3.8/site-packages/secapr/locus_selection.py", line 352, in main
target_loci = extract_best_loci(subfolder_file_dict,sample_bam_dict,output_folder,n,threshold,input_type,input_dir,new_file_plot)
File "/mnt/shared/scratch/tmichel/apps/conda/envs/secapr_env/lib/python3.8/site-packages/secapr/locus_selection.py", line 215, in extract_best_loci
average = sum(selection[column])/no_of_loci
ZeroDivisionError: division by zero
Hello Tobias,
Here is another issue, with a dataset including aDNA samples. I am not sure if an insufficient coverage is the cause of the problem here, as there is a division by zero error at the locus selection step of the pipeline.
I am using secapr 2.1.1.
Kind regards,
Thibauld