Issue with execution of the Ribo-ODDR tool

fallerlab / Ribo-ODDR

Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

GNU General Public License v3.0

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Issue with execution of the Ribo-ODDR tool #2

Closed sammywinchester19 closed 4 years ago

sammywinchester19 commented 4 years ago

I am trying to design rRNA depletion probes and I tried to use the example data with mouse_rRNA.fa as -r input and then placed the output in the current directory

it gives this error

Traceback (most recent call last): File "src/Ribo-ODDR.py", line 495, in main() File "src/Ribo-ODDR.py", line 317, in main if len(args.samples)<1: TypeError: object of type 'NoneType' has no len()

Can you please explain whats going on ?

ferhatalkan commented 4 years ago

Hi there. Seems like there is a problem with how you pass your input files to the pipeline. Can you share your full command so that I can help?

sammywinchester19 commented 4 years ago

This is the command I placed in terminal

Ribo-ODDR-master/src/Ribo-ODDR.py -r DATA/Ribosomal_RNA -o /Results

ferhatalkan commented 4 years ago

Ribo-ODDR cannot design oligos without any pilot Ribo-seq data. It is made for designing oligos in an experiment-specific manner, with pilot data provided by the user for the specific experimental conditions. In your command line, you are not passing any pilot data to the pipeline, therefore it fails to execute. Please take a look at our README file to see how you can pass your pilot data to the pipeline.

sammywinchester19 commented 4 years ago

Yes, thank you