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filip-husnik / pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.
GNU General Public License v3.0
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refseq blastdb #53

Closed schmittel closed 1 year ago

schmittel commented 1 year ago

Good morning - Pseudofinder is a great program.

I'm trying to run Pseudofinder using the refseq_protein BLAST database that was downloaded using:

update_blastdb.pl --decompress --num_threads 40 refseq_protein

However I am getting the following error:

2023-03-13 09:19:37     CDS extracted from:                     /input_files/NC_012785.gb
                        Written to file:                        NC_012785_cds.fasta.
2023-03-13 09:19:37     Intergenic regions extracted from:      /input_files/NC_012785.gb
                        Written to file:                        NC_012785_intergenic.fasta.
2023-03-13 09:19:37     21 pseudogenes found in genbank file:   /input_files/NC_012785.gb
                        Written to file:                        NC_012785_input_pseudos.fasta.
2023-03-13 09:19:37     BLAST database indexes not found for /pseudofinder/blastdb/refseq_protein/refseq_protein
2023-03-13 09:19:37     Please run 'makeblastdb -dbtype prot -in /pseudofinder/blastdb/refseq_protein/refseq_protein -out /pseudofinder/blastdb/refseq_protein/refseq_protein

The refseq_protein database as downloaded using update_blastdb.pl is divided into multiple files:

refseq_protein.pto
refseq_protein.ptf
refseq_protein.pot
refseq_protein.pos
refseq_protein.pdb
refseq_protein.pal
refseq_protein.31.psq
refseq_protein.31.ppi
refseq_protein.31.ppd
refseq_protein.31.pog
refseq_protein.31.pin
refseq_protein.31.phr
refseq_protein.30.psq
refseq_protein.30.ppi
refseq_protein.30.ppd
refseq_protein.30.pog
refseq_protein.30.pin
refseq_protein.30.phr
etc

and I'm not aware of any additional ways to index the database.

Are you able to help?

Many thanks

mitchso commented 1 year ago

Hi,

I would first try to run classic command line blast using your database. Pseudofinder makes direct command line style calls to blast and if blast throws an error, then pseudofinder will show that error to the user. So, if you can make blast work on its own, you should be good to go when pseudofinder makes the calls as well.

(And be sure to the troubleshooting within the pseudofinder environment)

Best, Mitch