running kallisto failed
Closed this issue · 3 comments
Reads_split worked well. But kallisto failed to execute. Error message is below.
Flushing assignments index
Split reads. Time elapsed 230.84725165367126 seconds
Running kallisto
Traceback (most recent call last):
File "/home/feng/anaconda3/lib/python3.5/runpy.py", line 170, in _run_module_as_main
"main", mod_spec)
File "/home/feng/anaconda3/lib/python3.5/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/feng/anaconda3/lib/python3.5/site-packages/sircel-0.1-py3.5.egg/sircel/main.py", line 4, in
output_files = run_all(args)
File "/home/feng/anaconda3/lib/python3.5/site-packages/sircel-0.1-py3.5.egg/sircel/Sircel_master.py", line 101, in run_all
output_files)
File "/home/feng/anaconda3/lib/python3.5/site-packages/sircel-0.1-py3.5.egg/sircel/Sircel_master.py", line 129, in run_kallisto
'-i', args['kallisto_idx'],
NameError: name 'args' is not defined
Yes, I also meet this problem right now. Another question is that can we just only run the kallisto step after fixing this bug ?
BTW, there was no problem running kallisto with an earlier version of Sircel. Hope the author could add an option of running kallisto only.
Sorry everyone. Problem is now fixed