search

dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
Other
163 stars 32 forks source link

Error from running paga method #54

Closed DHGK closed 5 years ago

DHGK commented 5 years ago

Hi dyno community,

I was trying to run slingshot and paga methods on my data. Since paga method required a prior, I set "start_id" based on some assumptions. Using the dataset, I could get slingshot trajectory without any issue, but for the paga method I got following issue and not so sure how to interpret this error report. Has anyone got the same error before and what would be a way to resolve this? Thanks!!

R[write to console]: Error in parse_args(parser, args = args) :

Error in getopt(spec = spec, opt = args) : long flag "use_priors" is invalid Calls: -> -> -> parse_args

Traceback (most recent call last): File "/code/run.py", line 22, in task = dynclipy.main() File "/usr/local/lib/python3.7/site-packages/dynclipy/read.py", line 123, in main """) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/init.py", line 389, in call res = self.eval(p) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 192, in call .call(*args, kwargs)) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 121, in call res = super(Function, self).call(*new_args, *new_kwargs) File "/usr/local/lib/python3.7/site-packages/rpy2/rinterfacelib/conversion.py", line 28, in cdata = function(args, kwargs) File "/usr/local/lib/python3.7/site-packages/rpy2/rinterface.py", line 773, in call raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error in parse_args(parser, args = args) : Error in getopt(spec = spec, opt = args) : long flag "use_priors" is invalid Calls: -> -> -> parse_args

Error: Error during trajectory inference R[write to console]: Error in parse_args(parser, args = args) : Error in getopt(spec = spec, opt = args) : long flag "use_priors" is invalid Calls: -> -> -> parse_args

Traceback (most recent call last): File "/code/run.py", line 22, in task = dynclipy.main() File "/usr/local/lib/python3.7/site-packages/dynclipy/read.py", line 123, in main """) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/init.py", line 389, in call res = self.eval(p) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 192, in call .call(*args, kwargs)) File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 121, in call res = super(Function, self).call(*new_args, *new_kwargs) File "/usr/local/lib/python3.7/site-packages/rpy2/rinterfacelib/conversion.py", line 28, in cdata = function(args, kw

rcannood commented 5 years ago

Hello DHGK!

This problem occurs because the ti_paga container is outdated. Could you update dynmethods (devtools::install_github("dynverse/dynmethods"))? This should update the ti_paga container next time you try to use it.

Let us know whether this solved your problem. Robrecht

ryandhindsa commented 5 years ago

Hi, I was having the same problem. I ran devtools::install_github("dynverse/dynmethods"), but when I tried inferring the trajectory, I got a new error:

Error response from daemon: manifest for dynverse/ti_paga_tree:v0.9.9.04 not found

rcannood commented 5 years ago

Hey @ryandhindsa,

This is because ti_paga and ti_paga_tree currently cannot build anymore due to a problem with scanpy (theislab/scanpy#688).

I was able to perform some magic tricks and managed to create an updated ti_paga_tree:v0.9.9.04 for you to enjoy ;)

Can you confirm this is working for you?

Robrecht

rcannood commented 5 years ago

This problem should have been fixed, closing this issue.