I ran the test data of “biobakery_workflows wmgx” process, but I got the following mistake, I’m sure I installed trf software.
Run Finished
Task 0 failed
Name: kneaddata____LV16R4_subsample
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/Share/app/anaconda3-20211117/envs/biobakery3/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in _run_task_locally
action_func(task)
File “/Share/app/anaconda3-20211117/envs/biobakery3/lib/python3.7/site-packages/anadama2/helpers.py”, line 107, in actually_sh
ret = _sh(s, **kwargs)
File “/Share/app/anaconda3-20211117/envs/biobakery3/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode(‘utf-8’), ret[1].decode(‘utf-8’)))
anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /Share/home/lk/test-data/LV16R4_subsample.fastq.gz --output /Share/home/lk/out2/kneaddata/main --threads 1 --output-prefix LV16R4_subsample --cat-final-output --reference-db /Share/app/biobakery_workflows_database/kneaddata_db_human_genome --serial --run-trf && gzip -f /Share/home/lk/out2/kneaddata/main/LV16R4_subsample.fastq ’ failed.
Out:
Err: ERROR: Unable to find trf. Please provide the full path to trf with --trf.