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pachterlab / sircel

Identify cell barcodes from single-cell genomics sequencing experiments
MIT License
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running kallisto failed #9

Closed doublehelixlf closed 7 years ago

doublehelixlf commented 7 years ago

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

ahy1221 commented 7 years ago

Yes, I also meet this problem right now. Another question is that can we just only run the kallisto step after fixing this bug ?

doublehelixlf commented 7 years ago

BTW, there was no problem running kallisto with an earlier version of Sircel. Hope the author could add an option of running kallisto only.

axtambe commented 7 years ago

Sorry everyone. Problem is now fixed