Error: (803.7) [makeblastdb] Blast-def-line-set.E.title

[William-chen777]

Dear developer:
RoseTTAFold2NA is a wonderful tool for predicting protein and nuclear interaction, but I have a problem when I running the code, like this:

Error: (803.7) [makeblastdb] Blast-def-line-set.E.title
Bad char [0x81] in string at byte 44
Oculatella neakameniensis str. KOVÁČIK 1990/54 bacterial LSU rRNA
Error: (803.7) [makeblastdb] Blast-def-line-set.E.title
Bad char [0xCC] in string at byte 46
Oculatella neakameniensis str. KOVÁČIK 1990/54 bacterial LSU rRNA
Error: (803.7) [makeblastdb] Blast-def-line-set.E.title
Bad char [0x8C] in string at byte 47
Oculatella neakameniensis str. KOVÁČIK 1990/54 bacterial LSU rRNA
FASTA-Reader: Ignoring invalid residues at position(s): On line 105003909: 10
FASTA-Reader: Ignoring invalid residues at position(s): On line 105004664: 1
FASTA-Reader: Ignoring invalid residues at position(s): On line 105005148: 1
FASTA-Reader: Ignoring invalid residues at position(s): On line 105005321: 6
FASTA-Reader: Ignoring invalid residues at position(s): On line 105005559: 8, 13
FASTA-Reader: Ignoring invalid residues at position(s): On line 105005654: 17
FASTA-Reader: Ignoring invalid residues at position(s): On line 105006513: 24

And how can I solve the problem? Could you help me?
Best wishes

[anar-rzayev]

Same issue here ...

[iammarcol]

Hi! Same issue now, have you been able to solve it?

[iammarcol]

Hello,

I've managed to solve this.

Download the db file

wget ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz

gunzip and save it to fasta

gunzip -c rnacentral_species_specific_ids.fasta.gz > rnacentral_species_specific_ids.fasta

modify the file to get rid of bad characters

cat rnacentral_species_specific_ids.fasta | perl -ne 's/[^\x00-\x7F]+/ /g; print;' > rnacentral_species_specific_ids_cleaned.fasta

make a db

makeblastdb -in rnacentral_species_specific_ids_cleaned.fasta -dbtype nucl -parse_seqids -out rnacentral.fasta -title "RNACentral"

Bad-char error is solved, but FASTA-Reader will still give this warning. However, I managed to run the RNA-prot example w/ any issues.

Best,
M