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

snakemake download not successful #4

Open
Frank-LIU-520 opened this issue Dec 3, 2024 · 0 comments
Open

snakemake download not successful #4

Frank-LIU-520 opened this issue Dec 3, 2024 · 0 comments

Comments

@Frank-LIU-520
Copy link

[Tue Dec 3 08:51:42 2024]
localrule download:
output: sequences/ERR3664756_Heavy_IGHG.list
jobid: 169
reason: Missing output files: sequences/ERR3664756_Heavy_IGHG.list
wildcards: filename=ERR3664756_Heavy_IGHG
resources: tmpdir=/tmp

gzip: stdin: unexpected end of file
[Tue Dec 3 08:51:44 2024]
Error in rule download:
jobid: 169
output: sequences/ERR3664756_Heavy_IGHG.list
shell:
wget -qO- http://opig.stats.ox.ac.uk/webapps/ngsdb/unpaired/Bender_2020/csv/ERR3664756_Heavy_IGHG.csv.gz | gunzip -c | tail -n+3 | cut -d, -f1 > sequences/ERR3664756_Heavy_IGHG.list
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job download since they might be corrupted:
sequences/ERR3664756_Heavy_IGHG.list
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-12-03T085136.348937.snakemake.log
WorkflowError:
At least one job did not complete successfully.

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