LiorZ comments

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                                            LiorZ

setup_databases fails with "Error: indexdb died" when running mmseqs createindex step

It occurs because of a memory overflow. It worked for me when I ran the process on a machine with larger memory (>160Gb).

How to specify a control tag in the sample script?

@okaris Apparently this repo is for ProGen2. In ProGen2 the control tags were removed AFAIK. The Nature Biotechenology paper refers to ProGen1 and that's what made the confusion. Will be...

Add Singularity arguments for specific rules in Snakefile

I would also be happy to see this feature included in the next release :-)

CSV file is loading with just first row

I splitted the csv to one line per file .. it works find :)

[Youtube] Got server error HTTP Error 403: Forbidden(latest master version)

I'm also experiencing this error, but when i changed the user-agent to: "Mozilla/5.0 (Linux; Android 10; K) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/127.0.6533.103 Mobile Safari/537.36" (mobile user agent of the latest...

Initial support for 3D conformer loading

Hi, is there anything else I can do so that it would be merged with main?

NotImplementedError: Make sure that a `_reorder_cache` function is correctly implemented in transformers.models.llama.modeling_llama to enable beam search for <class 'transformers.models.llama.modeling_llama.LlamaForCausalLM'>

@yelboudouri - you didn't load the model with unsloth FastLanguageModel.from_pretrained(...) , though...

NotImplementedError: Make sure that a `_reorder_cache` function is correctly implemented in transformers.models.llama.modeling_llama to enable beam search for <class 'transformers.models.llama.modeling_llama.LlamaForCausalLM'>

Yes, sorry, thanks for the reply. I must have missed that. In case the model is small that may work, but not calling FastLanguageModel implies that you don't patch the...