why snakemake error showing up when executing polish workflow

[akshaydinesh26]

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.

[akshaydinesh26]

I reinstalled it with python version 3.9 and snakemak version 7.32.4 it worked.

[lcoombe]

Hi @akshaydinesh26,

Do you know which version of snakemake you were using before you changed the version?

Your error looks like this error which I previously reported upstream: https://github.com/snakemake/snakemake/issues/3015

Thanks for your interest in ntEdit and for reporting which snakemake version worked for you! Lauren