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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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OSError: [Errno30] #150

Open davidjquispe opened 5 years ago

davidjquispe commented 5 years ago

Hello,

I have a problem with the dammit pipeline at the beginning. Thanks for the help you can give me.

-David

Here is my code: dammit annotate Trinity.fasta

This is the error message that I received:

dammit

a tool for easy de novo transcriptome annotation

by Camille Scott v1.0rc2, 2018 Traceback (most recent call last): File "/home/jgarcia/dquispe/miniconda3/envs/dammit/bin/dammit", line 9, in sys.exit(app.DammitApp(arg_src=sys.argv[1:]).run()) File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/app.py", line 45, in run return self.args.func() File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/app.py", line 289, in handle_annotate log.start_logging() File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/log.py", line 39, in run logging.basicConfig(level=logging.DEBUG, **config) File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/logging/init.py", line 1808, in basicConfig h = FileHandler(filename, mode) File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/logging/init.py", line 1032, in init StreamHandler.init(self, self._open()) File "/home/jgarcia/dquispe/miniconda3/envs/dammit/lib/python3.6/logging/init.py", line 1061, in _open return open(self.baseFilename, self.mode, encoding=self.encoding) OSError: [Errno 30] Read-only file system: '/home/jgarcia/dquispe/.dammit/log/dammit-all.log'

camillescott commented 4 years ago

Hi there, sorry for the long wait. It looks like you don't have write access to the log directory. Is this on a shared system?

Also, I recommend upgrading to 1.2, which is on biocionda.