Error in Analyze Step

[yzy990924]

When using your Pyro models of SARS-CoV-2 variants--pyro-cov，I have made some problems, and desperately hope this issue will be resolved.

make preprocess

My program is cloned by github website on July 4, 2022. When running this command, the program has an error, like this:

make analyze

Then, I changed 3e6 to 4e6, the program can run successfully. However, when I next analyze, run this program: make analyze, there were other errors that I couldn't solve, and I had to ask you for help.

[kjshan]

where and how do you change 3e6 to 4e6？

[yzy990924]

I just modified the code in line 283 of scripts/preprocess_usher.py

[yhldhit]

Hey, have you solved this problem? I encounter exactly the same one as yours.

[aaronnnnnChoi]

I encountered the same error as @yzy990924 in MAKE ANALYZE process when I used a very small batch of GISAID data for test input, as I failed to obtain a FEED from GISAID. And later when I included more instance (~1000 as GISAID limits a maximum instance for every download), the MAKE ANALYZE succeed and the error did not occur.

So my guess is with too much dropout in the previous steps, it failed to shape the T × P × C array (56 × 1560 × 3000)? I did not thoroughly read the code so hopefully @fritzo or anyone could provide some comment.

Anyway, although I did not fully figure out how this problem come up or what is the proper solution, I hope my trail & error could shared some common with your situation @yzy990924 .