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jaleezyy / covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
MIT License
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KeyError phylo_include_seqs for ncov-tools integration #62

Closed raphenya closed 4 years ago

raphenya commented 4 years ago

Activating conda environment: /workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/conda/afb830cb Writing config for ncov to ncov-tools/config.yaml Traceback (most recent call last): File "/workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/scripts/tmptora1qx_.ncov-tools.py", line 59, in setup() File "/workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/scripts/tmptora1qx.ncov-tools.py", line 24, in set_up 'tree_include_consensus': f"'{os.path.abspath(snakemake.config['phylo_include_seqs'])}'", KeyError: 'phylo_include_seqs' [Tue May 26 22:37:32 2020] Error in rule ncov_tools: jobid: 0 conda-env: /workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/conda/afb830cb

RuleException: CalledProcessError in line 120 of /workspace/raphenar/sars-cov-2/covid-19-sequencing/Snakefile: Command 'source /home/raphenar/miniconda3/bin/activate '/workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/conda/afb830cb'; set -euo pipefail; python /workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/scripts/tmptora1qx_.ncov-tools.py' returned non-zero exit status 1. File "/workspace/raphenar/sars-cov-2/covid-19-sequencing/Snakefile", line 120, in __rule_ncov_tools File "/home/raphenar/miniconda3/envs/snakemake/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /workspace/raphenar/sars-cov-2/covid-19-sequencing/.snakemake/log/2020-05-26T223716.884897.snakemake.log

raphenya commented 4 years ago

updating main config.yaml with fasta similar to this fixed it:

phylo_include_seqs: '/workspace/raphenar/sars-cov-2/data/2020-02-13-GISAID-genomes.fasta'