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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')\n"` #16

Closed Mavlarn closed 3 years ago

Mavlarn commented 3 years ago

Workflow error to run "biobakery_workflows wmgx". Error message is as below. It looks like humann3 should use "uniref90_rxn" but in the shotgun.py code, it use uniref90_level4ec.

Task 29 failed Name: humann_renorm_ecs_relab____HD42R4_subsample Original error: Task failed because parent task20' failed Task 19 failed Name: humann_regroup_UniRef2EC__HD32R1_subsample Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/usr/local/lib/python3.6/dist-packages/anadama2/util/init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 2] Command humann_regroup_table --input /data/result_wmgs_1/humann/main/HD32R1_subsample_genefamilies.tsv --output /data/result_wmgs_1/humann/regrouped/HD32R1_subsample_ecs.tsv --groups uniref90_level4ec' failed. Out: b'' Err: b"usage: humann_regroup_table [-h] [-i INPUT] [-g {uniref90_rxn,uniref50_rxn}]\n [-c CUSTOM] [-r] [-f {sum,mean}] [-e PRECISION]\n [-u {Y,N}] [-p {Y,N}] [-o OUTPUT]\nhumann_regroup_table: error: argument -g/--groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')\n"

github-actions[bot] commented 3 years ago

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