SilasK
commented
2 years ago I think atlas_analyze is no longer needed I implemented most of the steps in atlas v 2.8.1 together with the tutorial scripts in R and jupyter
Closed paleome closed 2 years ago
SilasK
commented
2 years ago I think atlas_analyze is no longer needed I implemented most of the steps in atlas v 2.8.1 together with the tutorial scripts in R and jupyter
Hi team, i am facing the error pasted below. This is a run that successfully completed in Atlas. Do you know what the problem is?
Traceback (most recent call last): File "/home/marco/miniconda3/atlas-testing/.snakemake/scripts/tmpgsvxn6_u.get_taxonomy.py", line 11, in
from utils.mag_scripts import tax2table
ModuleNotFoundError: No module named 'utils'
[Wed Sep 29 18:02:47 2021]
Error in rule get_taxonomy:
jobid: 3
output: Results/taxonomy.tsv
Traceback (most recent call last): File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/executors/init.py", line 593, in _callback raise ex File "/home/marco/miniconda3/envs/analyze/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, *self.kwargs) File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/executors/init.py", line 579, in cached_or_run run_func(args) File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/executors/init.py", line 2460, in run_wrapper raise ex File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/executors/init.py", line 2441, in run_wrapper runtime_sourcecache_path, File "/home/marco/miniconda3/atlas_analyze/Snakefile", line 97, in rule_get_taxonomy "Results/mapping_rate.tsv" File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/script.py", line 1365, in script executor.evaluate() File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/script.py", line 377, in evaluate self.execute_script(fd.name, edit=edit) File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/script.py", line 578, in execute_script self._execute_cmd("{py_exec} {fname:q}", py_exec=py_exec, fname=fname) File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/script.py", line 421, in _execute_cmd **kwargs File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/shell.py", line 265, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'set -euo pipefail; /home/marco/miniconda3/envs/analyze/bin/python3.7 /home/marco/miniconda3/atlas-testing/.snakemake/scripts/tmpgsvxn6_u.get_taxonomy.py' returned non-zero exit status 1. Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/marco/miniconda3/atlas-testing/.snakemake/log/2021-09-29T180246.949895.snakemake.log Traceback (most recent call last): File "./analyze.py", line 21, in
"snakemake "
File "/home/marco/miniconda3/envs/analyze/lib/python3.7/site-packages/snakemake/shell.py", line 265, in new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail; snakemake -d /home/marco/miniconda3/atlas-testing/ -j 1 -s ./Snakefile' returned non-zero exit status 1.