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Description
i was executing the code example given in the github page
this is my code:
run-ntedit polish --draft filt_contig_assembly.fa --reads filtered_P1 -k 71 -t 8
but it is showing an error and based on my search its because of snakemake
run-ntedit polish --draft filt_contig_assembly.fa --reads filtered_P1 -k 71 -t 8
Running ntEdit...
Parameter settings:
--draft filt_contig_assembly.fa
--reads filtered_P1
-k 71
-t 8
-z 100
-y 9.0
-j 3
--cutoff 2
-i 5
-d 5
-x 5.0
-m 0
-a 0
Running snakemake -s /home/centyle-biotech/miniconda3/envs/ntedit/bin/ntedit_run_pipeline.smk ntedit -p --cores 8 --config draft=filt_contig_assembly.fa k=71 t=8 z=100 y=9.0 v=False j=3 reads=filtered_P1 cutoff=2 v=0 i=5 d=5 x=5.0 m=0 a=0 --rerun-trigger mtime
Traceback (most recent call last):
File "/home/centyle-biotech/miniconda3/envs/ntedit/lib/python3.12/site-packages/snakemake/cli.py", line 1977, in args_to_api
config=parse_config(args.config),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/centyle-biotech/miniconda3/envs/ntedit/lib/python3.12/site-packages/snakemake/cli.py", line 256, in parse_config
raise ValueError(
ValueError: Invalid config definition: Config entry must start with a valid identifier.
Traceback (most recent call last):
File "/home/centyle-biotech/miniconda3/envs/ntedit/bin/run-ntedit", line 248, in
main()
File "/home/centyle-biotech/miniconda3/envs/ntedit/bin/run-ntedit", line 243, in main
raise subprocess.SubprocessError("ntEdit failed - check the logs for the error.")
subprocess.SubprocessError: ntEdit failed - check the logs for the error.