MSA Server error with RNA sequence

[yx0516]

Hi, when i run the prediction with RNA sequence by using MSA server（use_msa_server=True）. The error happens:

Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.

The input fasta is :

rna|A
GGGUCUCGCGGAACCGGUGAGUACACCGGAAUCCAGGAAACUGGAUUUGGGCGUGCCCCCGCGAGACC

Can the MSA server skip the RNA or DNA sequence?

[wukevin]

I'm not able to reproduce this error; I ran chai fold --use-msa-server rna_example.fasta outdir using the following contents of rna_example.fasta:

>rna|6U8D_1
GGGUCUCGCGGAACCGGUGAGUACACCGGAAUCCAGGAAACUGGAUUUGGGCGUGCCCCCGCGAGACC
>protein|6U8D_2
EISEVQLVESGGGLVQPGGSLRLSCAASGFYISSYSIHWVRQAPGKGLEWVASIYPSYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRYRSYYSRYGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
>protein|6U8D_3
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYYPSTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Perhaps you are missing a the leading carrot > in your input so the parsing doesn't happen correctly? The logic is already skipping MSA generation for inputs that are not proteins:

chai-lab/chai_lab/chai1.py

Lines 316 to 330 in 2d2646b

	protein_sequences = [
	chain.entity_data.sequence
	for chain in chains
	if chain.entity_data.entity_type == EntityType.PROTEIN
	]
	msa_dir = output_dir / "msas"
	msa_dir.mkdir(parents=True, exist_ok=False)
	generate_colabfold_msas(
	protein_seqs=protein_sequences,
	msa_dir=msa_dir,
	msa_server_url=msa_server_url,
	)
	msa_context, msa_profile_context = get_msa_contexts(
	chains, msa_directory=msa_dir
	)

I did realize though, when testing this, that some of the errors we log are overly verbose and do not apply to RNAs and other non-protein entities; see #209

[yx0516]

@wukevin The above error happens when there is only RNA sequences without proteins.

[wukevin]

Thanks for helping us narrow down this issue; we've resolved this issue in the mentioned PR. Please let us know if any other issues persist.