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BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Error during bracer summarize #42

Closed tiagobrc closed 4 years ago

tiagobrc commented 4 years ago

During summarization, an error is shown. It does not have a lot of information so I can't figure it out.

Do any of you have an idea of what I could possibly be doing wrong?

EDITED: Now no error message is shown but summarized files are empty, no BCR reconstruction is shown.


Traceback (most recent call last):
  File "/ru-auth/local/home/trezende/anaconda3/envs/py37/bin/bracer", line 11, in <module>
    load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
  File "/ru-auth/local/home/trezende/anaconda3/envs/py37/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/ru-auth/local/home/trezende/anaconda3/envs/py37/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/tasks.py", line 736, in run
    subdirectories = next(os.walk(self.root_dir))[1]
StopIteration
mstubb commented 4 years ago

Hi,

Please can you let us know the command that you ran that led to you getting this error?

Thanks,

Mike

On 19 Dec 2019, at 22:06, Tiago Bruno Rezende de Castro notifications@github.com wrote:

During summarization, an error is shown. It does not have a lot of information so I can't figure it out.

Do any of you have an idea of what I could possibly be doing wrong?

Traceback (most recent call last): File "/ru-auth/local/home/trezende/anaconda3/envs/py37/bin/bracer", line 11, in load_entry_point('bracer==0.1', 'console_scripts', 'bracer')() File "/ru-auth/local/home/trezende/anaconda3/envs/py37/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/launcher.py", line 43, in launch Task().run() File "/ru-auth/local/home/trezende/anaconda3/envs/py37/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/tasks.py", line 736, in run subdirectories = next(os.walk(self.root_dir))[1] StopIteration

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idalind commented 4 years ago

Hello, apologies for not seeing this post before today. Did you successfully run bracer assemble for all the cells prior to running summarise? It seems to me like you are not providing the correct path to the directory containing all the assembled cells you would like to summarise. Could this be the case?

tiagobrc commented 4 years ago

I fixed the problem by just reinstalling anaconda and all requirements. Thanks!