omarkr8
commented
2 years ago Turns out it helps to check the actual error logs. Had many independent issues with alignment fastas
Closed omarkr8 closed 2 years ago
omarkr8
commented
2 years ago Turns out it helps to check the actual error logs. Had many independent issues with alignment fastas
Hi, am slowly trying to figure out the inputs and commands to make civet work. currently getting this error:
Error in rule find_catchment: jobid: 0 output: /tmp/tmp7uuq8_p2/updown_ignore.txt, /tmp/tmp7uuq8_p2/catchments.csv log: /tmp/tmp7uuq8_p2/logs/updown_top_ranking.txt (check log file(s) for error message)
RuleException: CalledProcessError in line 120 of /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk: Command 'set -euo pipefail; gofasta updown topranking -q /tmp/tmp7uuq8_p2/hashed.aln.fasta -t '/media/lab6/7875-1CEE/civettest/civet_alignment.fasta' -o /tmp/tmp7uuq8_p2/catchments.csv --reference '/home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/data/reference.fasta' --dist-push --dist-up 2 --dist-down 2 --dist-side 2 --ignore /tmp/tmp7uuq8_p2/updown_ignore.txt &> /tmp/tmp7uuq8_p2/logs/updown_top_ranking.txt' returned non-zero exit status 1. File "/home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk", line 120, in __rule_find_catchment 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
running this command : civet -bm civet_test.csv -bseq civet_alignment.fasta -d /path/civettest -bicol name -fm Factor=A --query-table-content name -ta sample_date --catchment-table-content name -rc 1
am stuck figuring out if its a command/option or file input problem, perhaps a tutorial from an earlier version is available elsewhere for me to refer to?