snipit error, not sure how to debug #149
Description
Running snipit pipeline.
MissingInputException in line 68 of /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/snipit_runner.smk:
Missing input files for rule gather_graphs:
/tmp/tmppiy9q6qf/snipit/.snipit.svg
[Mon Jan 17 16:46:59 2022]
Error in rule snipit:
jobid: 0
output: /tmp/tmppiy9q6qf/snipit/prompt.txt
RuleException:
CalledProcessError in line 247 of /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk:
Command 'set -euo pipefail; snakemake --nolock --snakefile /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/snipit_runner.smk --forceall --quiet --log-handler-script /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/utils/log_handler_handle.py --directory /tmp/tmppiy9q6qf --configfile /home/lab6/civet/civet/tests/file_test1_3/config.yaml --config fasta=/tmp/tmppiy9q6qf/hashed.aln.fasta csv=/home/lab6/civet/civet/tests/file_test1_3/master_metadata.csv --cores 1 && touch /tmp/tmppiy9q6qf/snipit/prompt.txt' returned non-zero exit status 1.
File "/home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk", line 247, in __rule_snipit
File "/home/lab6/anaconda3/envs/civet/lib/python3.9/concurrent/futures/thread.py", line 58, in run
Exiting because a job execution failed. Look above for error message
Exiting because a job execution failed. Look above for error message
achieved by running this code :
civet --input-metadata imr6_1/background_metadata.csv
--input-sequences imr6_1/background_sequences.aln.fasta
--timeline-dates sample_date
--datadir gisomi_1/
-bseq gisomi_1/background_sequences.aln.fasta
-bm gisomi_1/background_metadata.csv
-bicol sequence_header -icol sequence_header
-ta country --outdir file_test1
--snp-distance 100 -ds mode=normalise country -n 0.1