Batch input_dir result_dir

[MarkusZweckstetter]

Expected Behavior

I have successfully mounted my google drive and the batch ColaFold states using the Alphafold2 batch notebook at https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/batch/AlphaFold2_batch.ipynb

@title Mount google drive

from google.colab import drive drive.mount('/content/drive') Mounted at /content/drive

Subsequently I tried to specify the input_dir and results_dir through input_dir: /content/drive/MyDrive/input_fasta result_dir: /content/drive/MyDrive/result

Followed by successful "Install dependencies" and "Run Prediction"

Current Behavior

For "Run Prediction" I get an error message

OSError Traceback (most recent call last) in () 13 14 setup_logging(Path(result_dir).joinpath("log.txt")) ---> 15 queries, is_complex = get_queries(input_dir) 16 run( 17 queries=queries,

/usr/local/lib/python3.7/dist-packages/colabfold/batch.py in get_queries(input_path, sort_queries_by) 389 input_path = Path(input_path) 390 if not input_path.exists(): --> 391 raise OSError(f"{input_path} could not be found") 392 393 if input_path.is_file():

OSError: /content/drive/MyDrive/input_fasta could not be found

I am using a Mac book and my Google drive is mounted at /Users/name/Google Drive/My Drive This directory contains the two directories "input_fasta" and "result".

Steps to Reproduce (for bugs)

I am using https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/batch/AlphaFold2_batch.ipynb

ColabFold Output (for bugs)

See above

Context

So I guess I have to specify the input_dir and result_dir in a different manner. Any help would be appreciated.

Your Environment

macOS High Sierra Version 10.13.6 MacBook Pro

[martin-steinegger]

It seems that the input path could not be resolved. One way to get the correct path is to navigate to your input_fasta folder using the file navigator in Colab (see screenshot). Once you found your input_fasta folder use the right click on it and select "Copy path". Now the correct path should be in your clipboard, just past it in the input_dir form-field.

[MarkusZweckstetter]

Thanks! Now it seems to be running. Best Markus

From: Martin Steinegger @.> Reply-To: sokrypton/ColabFold @.> Date: Monday, 7. March 2022 at 15:49 To: sokrypton/ColabFold @.> Cc: "Zweckstetter, Markus" @.>, Author @.***> Subject: Re: [sokrypton/ColabFold] Batch input_dir result_dir (Issue #173)

It seems that the input path could not be resolved. One way to get the correct path is to navigate to your input_fasta folder using the file navigator in Colab (see screenshot). Once you found your input_fasta folder use the right click on it and select "Copy path". Now the correct path should be in your clipboard, just past it in the input_dir form-field.

[Screenshot 2022-03-07 at 23 45 35]https://user-images.githubusercontent.com/1413571/157056388-cd452b36-fff2-4432-be7f-555079f60eab.png

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