Hi All,
Has anyone encountered this error when using the vis workflow of biobakery:
2023-12-28 13:22:26,152 LoggerReporter task_failed ERROR: task 2, document : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery_vis/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in _run_task_locally
action_func(task)
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery_vis/lib/python3.7/site-packages/anadama2/document.py”, line 321, in create
sh(pandoc_command.format(intermediate_template, temp_report),log_command=True)()
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery_vis/lib/python3.7/site-packages/anadama2/helpers.py”, line 107, in actually_sh
ret = _sh(s, **kwargs)
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery_vis/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 43] Command pandoc /panfs/accrepfs.vampire/data/zhu_group/10272023_Danyvid/Adapter_trimmed/Quality_trimmed/filter/clean_reads/Danyvid_vis1/tmpc10u64yp/wmgx_report.md -o /panfs/accrepfs.vampire/data/zhu_group/10272023_Danyvid/Adapter_trimmed/Quality_trimmed/filter/clean_reads/Danyvid_vis1/tmpc10u64yp/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: Error producing PDF. ! LaTeX Error: File iftex.sty’ not found.
Type X to quit or to proceed,
or enter new name. (Default extension: sty)
Enter file name:
! Emergency stop.
<read *>
l.10 \ifPDFTeX
2023-12-28 13:22:26,152 LoggerReporter task_failed ERROR: task 4, archive : Failed! Error message : Task failed because parent task `2’ failed
Can you advise what is going on?
Thanks!
Best,
Wenhan