Closed mattbawn closed 4 years ago
Hi Mat,
thanks for reporting.
these errors seem like something that Python 3 would say if fed Python 2 code. It is likely to happen if your default python is 3, which really it should as it's the modern thing.
because I'm old-fashioned I used Python 2 extensively in Pantagruel and referred to it ambiguously as just python
.
I will try and disambiguate which interpreter to use in the whole pipeline so that it is avoided. I'll notify you of the fix.
in waiting you can try and declare your default python as being Python 2 before running the Pantagruel command; something like alias python=python2
should probably work.
commits 76858aa and 18f8df2 should have sorted this.
Also I just noticed that your initial call returns an error that does not come from pantagruel:
activate does not accept more than one argument:
['pantagruel', '-d', 'database', '-r', '.', '-f', 'PANTAGFAM', '-a', 'genomes/', 'init']
This seems to be coming from some environment wrapper (maybe conda?).
Given the followinv logs, it seems the arguments are passed on correctly to pantagruel so maybe nothing to worry about, but just in case I would give a look to the resulting configuration file environ_pantagruel_database.sh
to see if the variables are set correctly where you expect them to be.
I have recently installed pantagruel:
This is Pantagruel pipeline version 82ae5db4dea2c59df6019ed7f16babf442180cbf
on our cluster and am trying to run it on 134 custom assmeblies. I believe I have created the correct file structure and dat file:However, I get the following erroro when i try and run init:
Any help would be appreciated.
Thanks