Title says it all biobakery_workflows vis fails when there is a dash (-) in path:
(Nov 09 16:24:30) [1/3 - 33.33%] **Skipped ** Task 0: humann_rename_table_ecs
(Nov 09 16:24:30) [1/3 - 33.33%] **Ready ** Task 2: document
(Nov 09 16:24:30) [1/3 - 33.33%] **Started ** Task 2: document
(Nov 09 16:25:12) [2/3 - 66.67%] **Failed ** Task 2: document
(Nov 09 16:25:12) [3/3 - 100.00%] **Failed ** Task 4: archive
Run Finished
Task 2 failed
Name: document
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in _run_task_locally
action_func(task)
File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.7/site-packages/anadama2/document.py”, line 321, in create
sh(pandoc_command.format(intermediate_template, temp_report),log_command=True)()
File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.7/site-packages/anadama2/helpers.py”, line 107, in actually_sh
ret = _sh(s, **kwargs)
File “/home/theoscilicium/miniconda3/envs/biobakery/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 `pandoc /home/theoscilicium/biobakery/biobakery-pipeline/report/tmpy2ctgtya/wmgx_report.md -o /home/theoscilicium/biobakery/biobakery-pipeline/report/tmpy2ctgtya/wmgx_report…pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone -V geometry:left=1in -V geometry:right=1in -V geometry:top=1in -V geometry:bottom=1in --toc’ failed.
Out:
Err: pandoc: /home/theoscilicium/biobakery/biobakery- pipeline/report/figures/qc_table_paired.png: openBinaryFile: does not exist (No such file or directory)
Notice how there is an added whitespace in the path after the -: biobakery- pipeline should be biobakery-pipeline.
Not sure if the problem comes from pandoc or biobakery_workflows.
Changing the path to avoid the - fixed the problem for me.