Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error on result/reads/../input_files.txt #38

Open
ChristianDina opened this issue Sep 11, 2024 · 0 comments
Open

Error on result/reads/../input_files.txt #38

ChristianDina opened this issue Sep 11, 2024 · 0 comments

Comments

@ChristianDina
Copy link

Did anyone meet this error. This seems to happen on reads that have run with kgwasflow and happened several times (throught this may be an incomplete result).
And the log file is empty

Error in rule kmc_canonical:
jobid: 1021
input: results/reads/B00HOQU/input_files.txt
output: results/kmers_count/B00HOQU/output_kmc_canon.kmc_suf, results/kmers_count/B00HOQU/output_kmc_canon.kmc_pre, results/kmers_count/B00HOQU/kmc_canonical.done
log: logs/count_kmers/kmc/B00HOQU/kmc_canon.log (check log file(s) for error details)
conda-env: /CONDAS/users/dina-c/snmk-env-default/8cf2dd55151db0fd70913609e8931b24_
shell:

    kmc -t8  -v -k31 -ci2         @results/reads/B00HOQU/input_files.txt results/kmers_count/B00HOQU/output_kmc_canon results/kmers_count/B00HOQU         1> results/kmers_count/B00HOQU/kmc_canon.1 2> results/kmers_count/B00HOQU/kmc_canon.2         > logs/count_kmers/kmc/B00HOQU/kmc_canon.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant