SequenceServer tries to format impossible FASTA files

[yannickwurm]

Sequence detection type failed (because its part AA part NT in this file - which should never exist in reality) and it returned false, but Seqserv tried to format the db anyways.

mixed_sequence_types.fasta.gz

Yannicks-MacBook-Pro ➜ a sequenceserver -v 2.0.0

Yannicks-MacBook-Pro ➜ a sequenceserver -d . -m
[2022-04-04 15:15:03] INFO Reading configuration file: /Users/yannickwurm/.sequenceserver.conf.

SequenceServer has scanned your databases directory and will now offer to convert FASTA files into BLAST databases. It will also offer to reformat any old-format BLAST databases and those created without the -parse_seqids option of makeblastdb (-parse_seqids option is required for sequence retrieval to correctly work).

Note that reformatting process can be slow large BLAST databases and fail if sequence identifiers are longer than 50 characters. While we exepect the reformatting process to work in most other cases, things can inevitably go wrong. Thus, please back up your databases before reformatting and post any issues to our Google Group/GitHub so that we can all learn from it.

Proceed? [y/n] (Default: y).

FASTA file to format: /Users/yannickwurm/tmp/a/invalid_residues.fasta FASTA type: false Proceed? [y/n] (Default: y): Enter a database title or will use 'invalid residues': Enter taxid (optional): Could not create BLAST database for: /Users/yannickwurm/tmp/a/invalid_residues.fasta Tried: makeblastdb -parse_seqids -hash_index -in '/Users/yannickwurm/tmp/a/invalid_residues.fasta' -dbtype fals -title 'invalid residues' -taxid 0 stdout: stderr: USAGE makeblastdb [-h] [-help] [-in input_file] [-input_type type] -dbtype molecule_type [-title database_title] [-parse_seqids] [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids] [-mask_desc mask_algo_descriptions] [-gi_mask] [-gi_mask_name gi_based_mask_names] [-out database_name] [-blastdb_version version] [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION Application to create BLAST databases, version 2.12.0+

Use '-help' to print detailed descriptions of command line arguments

Error: Argument "dbtype". Illegal value, expected nucl', prot': fals' Error: (CArgException::eConstraint) Argument "dbtype". Illegal value, expected nucl', prot': fals'