DB dump PostgreSQL version

[odethier-ulb]

Hello,

I'm trying to execute the database initialization step of the installation,

poetry run fantasia initialize

using the following data source in the config file:

embeddings_url: "https://zenodo.org/records/17795871/files/BioData_Dec25_esm2_prott5_prostt5_ankh3_large_esm3c_Layer0.backup?download=1"

But I have the following error just after the download:

pg_restore failed (exit 1).
pg_restore: error: unsupported version (1.16) in file header

My pg_restore version (16) seems correct (pg_restore (PostgreSQL) 16.13 (Ubuntu 16.13-0ubuntu0.24.04.1)), however I see a version 18 in the first lines of the downloaded dump file:

PGDMP
BioData
18.1 (Ubuntu 18.1-1.pgdg24.04+2)
18.1 (Ubuntu 18.1-1.pgdg24.04+2)

Is there a version 16 of the dump somewhere (if it's the cause of the error)?

Regards,

[estolle]

any update on how to fix this? I have the exact same problem

[estolle]

Still not able to fix, but updating to postgresql-client v18 avoid that error but comes up later with another error:

sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
curl -fsSL https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo gpg --dearmor -o /etc/apt/trusted.gpg.d/postgresql.gpg
sudo apt update
sudo apt-get install postgresql-client-18

2026-06-03 13:32:37,968 - FANTASIA - INFO - PostgreSQL connection OK.
2026-06-03 13:32:37,972 - FANTASIA - INFO - RabbitMQ connection OK.
2026-06-03 13:32:37,972 - FANTASIA - INFO - Starting initialization...
2026-06-03 13:32:37,972 - FANTASIA - INFO - Downloading reference embeddings to /scratch/fantasia/embeddings/BioData_Dec25_esm2_prott5_prostt5_ankh3_large_esm3c_Layer0.backup...
2026-06-03 13:32:37,972 - FANTASIA - INFO - Loading embeddings into the database...
pg_restore failed (exit 1).
pg_restore: connecting to database for restore
pg_restore: executing SELECT pg_catalog.set_config('search_path', '', false);
pg_restore: while INITIALIZING:
pg_restore: error: could not execute query: ERROR:  unrecognized configuration parameter "transaction_timeout"
Command was: SET transaction_timeout = 0;
pg_restore: creating SCHEMA "public"
pg_restore: creating COMMENT "SCHEMA public"
pg_restore: creating EXTENSION "vector"
pg_restore: creating COMMENT "EXTENSION vector"
pg_restore: creating TABLE "public.accession"
pg_restore: creating TABLE "public.chain"
pg_restore: creating SEQUENCE "public.chain_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.chain_id_seq"
pg_restore: creating TABLE "public.go_terms"
pg_restore: creating TABLE "public.protein"
pg_restore: creating TABLE "public.protein_go_term_annotation"
pg_restore: creating SEQUENCE "public.protein_go_term_annotation_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.protein_go_term_annotation_id_seq"
pg_restore: creating TABLE "public.sequence"
pg_restore: creating TABLE "public.sequence_embedding_type"
pg_restore: creating SEQUENCE "public.sequence_embedding_type_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.sequence_embedding_type_id_seq"
pg_restore: creating TABLE "public.sequence_embeddings"
pg_restore: creating SEQUENCE "public.sequence_embeddings_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.sequence_embeddings_id_seq"
pg_restore: creating SEQUENCE "public.sequence_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.sequence_id_seq"
pg_restore: creating TABLE "public.state"
pg_restore: creating SEQUENCE "public.state_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.state_id_seq"
pg_restore: creating TABLE "public.structural_alignment_types"
pg_restore: creating SEQUENCE "public.structural_alignment_types_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.structural_alignment_types_id_seq"
pg_restore: creating TABLE "public.structure"
pg_restore: creating TABLE "public.structure_3di"
pg_restore: creating SEQUENCE "public.structure_3di_id_seq"
pg_restore: creating SEQUENCE OWNED BY "public.structure_3di_id_seq"
pg_restore: creating DEFAULT "public.chain id"
pg_restore: creating DEFAULT "public.protein_go_term_annotation id"
pg_restore: creating DEFAULT "public.sequence id"
pg_restore: creating DEFAULT "public.sequence_embedding_type id"
pg_restore: creating DEFAULT "public.sequence_embeddings id"
pg_restore: creating DEFAULT "public.state id"
pg_restore: creating DEFAULT "public.structural_alignment_types id"
pg_restore: creating DEFAULT "public.structure_3di id"
pg_restore: processing data for table "public.accession"
pg_restore: processing data for table "public.chain"
pg_restore: processing data for table "public.go_terms"
pg_restore: processing data for table "public.protein"
pg_restore: processing data for table "public.protein_go_term_annotation"
pg_restore: processing data for table "public.sequence"
pg_restore: processing data for table "public.sequence_embedding_type"
pg_restore: processing data for table "public.sequence_embeddings"
pg_restore: processing data for table "public.state"
pg_restore: processing data for table "public.structural_alignment_types"
pg_restore: processing data for table "public.structure"
pg_restore: processing data for table "public.structure_3di"
pg_restore: executing SEQUENCE SET chain_id_seq
pg_restore: executing SEQUENCE SET protein_go_term_annotation_id_seq
pg_restore: executing SEQUENCE SET sequence_embedding_type_id_seq
pg_restore: executing SEQUENCE SET sequence_embeddings_id_seq
pg_restore: executing SEQUENCE SET sequence_id_seq
pg_restore: executing SEQUENCE SET state_id_seq
pg_restore: executing SEQUENCE SET structural_alignment_types_id_seq
pg_restore: executing SEQUENCE SET structure_3di_id_seq
pg_restore: creating CONSTRAINT "public.accession accession_pkey"
pg_restore: creating CONSTRAINT "public.chain chain_pkey"
pg_restore: creating CONSTRAINT "public.go_terms go_terms_pkey"
pg_restore: creating CONSTRAINT "public.protein_go_term_annotation protein_go_term_annotation_pkey"
pg_restore: creating CONSTRAINT "public.protein protein_pkey"
pg_restore: creating CONSTRAINT "public.sequence_embedding_type sequence_embedding_type_name_key"
pg_restore: creating CONSTRAINT "public.sequence_embedding_type sequence_embedding_type_pkey"
pg_restore: creating CONSTRAINT "public.sequence_embeddings sequence_embeddings_pkey"
pg_restore: creating CONSTRAINT "public.sequence sequence_pkey"
pg_restore: creating CONSTRAINT "public.state state_pkey"
pg_restore: creating CONSTRAINT "public.structural_alignment_types structural_alignment_types_pkey"
pg_restore: creating CONSTRAINT "public.structure_3di structure_3di_pkey"
pg_restore: creating CONSTRAINT "public.structure structure_file_path_key"
pg_restore: creating CONSTRAINT "public.structure structure_pkey"
pg_restore: creating CONSTRAINT "public.protein_go_term_annotation uq_pga_protein_go"
pg_restore: creating CONSTRAINT "public.sequence_embeddings uq_seqemb_seq_type_layer"
pg_restore: creating INDEX "public.idx_sequence_hash"
pg_restore: creating INDEX "public.ix_seqemb_seq"
pg_restore: creating INDEX "public.ix_seqemb_type"
pg_restore: creating INDEX "public.ix_sequence_sequence_hash"
pg_restore: creating FK CONSTRAINT "public.accession accession_protein_id_fkey"
pg_restore: creating FK CONSTRAINT "public.chain chain_accession_code_fkey"
pg_restore: creating FK CONSTRAINT "public.chain chain_sequence_id_fkey"
pg_restore: creating FK CONSTRAINT "public.chain chain_structure_id_fkey"
pg_restore: creating FK CONSTRAINT "public.protein_go_term_annotation protein_go_term_annotation_go_id_fkey"
pg_restore: creating FK CONSTRAINT "public.protein_go_term_annotation protein_go_term_annotation_protein_id_fkey"
pg_restore: creating FK CONSTRAINT "public.protein protein_sequence_id_fkey"
pg_restore: creating FK CONSTRAINT "public.sequence_embeddings sequence_embeddings_embedding_type_id_fkey"
pg_restore: creating FK CONSTRAINT "public.sequence_embeddings sequence_embeddings_sequence_id_fkey"
pg_restore: creating FK CONSTRAINT "public.state state_chain_id_fkey"
pg_restore: creating FK CONSTRAINT "public.structure_3di structure_3di_state_id_fkey"
pg_restore: creating FK CONSTRAINT "public.structure structure_protein_id_fkey"
pg_restore: creating ACL "SCHEMA public"
pg_restore: warning: errors ignored on restore: 1

[estolle]

i installed on my Ubuntu24 now the postgresql-client version to match the one in the DB dump

sudo apt-get install postgresql-client-18=18.1-1.pgdg24.04+2
sudo apt-get install postgresql-18 postgresql-client-18 postgresql-server-dev-18
psql --version
# psql (PostgreSQL) 18.1 (Ubuntu 18.1-1.pgdg24.04+2

now postgre and clinet version should match (the transaction_timeout error was suggested to come from mismatches)

poetry run fantasia initialize

still fails

i am out of options now. the way the setup is described here and inthe Documentation (postgresql 16) is not compatible with the initialization code and v4.1 Database on my freshly installed ubuntu 24.04.