Predicting a complex with pair_mode="unpaired" fails

Expected Behavior

Runs fine

Current Behavior

The program fails, due to the lack of the paired_msa variable.

Steps to Reproduce (for bugs)

• Predict a complex using the AlphaFold2.ipynb notebook
• Choose parameter pair_mode="unpaired"

ColabFold Output (for bugs)

2022-04-02 08:51:28,698 Could not generate input features 3f5wcomplex_da929: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1141, in run
model_type,
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 839, in generate_input_feature
paired_msa[sequence_index]
TypeError: 'NoneType' object is not subscriptable
2022-04-02 08:51:28,700 Done

Context

Three relatively short chains that are not necessarily found as complexes in nature.

Your Environment

Current main branch (https://github.com/sokrypton/ColabFold/commit/b532e910b15434f707f0b7460abc25c70fcb9b26), running on Google Colab

Start with AlphaFold2.ipynb and reproduce the failure using pair_mode="unpaired". Then inspect colabfold/batch.py around generate_input_feature at line 839, where paired_msa is accessed; the work is done when complex prediction completes without the NoneType error.