Error while DB update

[ajkarloss]

"./mlst-download_pub_mlst | bash" Downloads "pubmlst/dbases.xml"

"./mlst-make_blast_db"
Building a new DB, current time: 08/24/2021 11:07:22
New DB name: /opt/galaxy/server/database/dependencies/_conda/envs/[email protected]/db/blast/mlst.fa
New DB title: PubMLST
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: File /opt/galaxy/server/database/dependencies/_conda/envs/[email protected]/scripts/../db/blast/mlst.fa does not exist
Created BLAST database for /opt/galaxy/server/database/dependencies/_conda/envs/[email protected]/scripts/../db/blast/mlst.fa

when I run MLST I am getting,

BLAST Database error: No alias or index file found for nucleotide database [/opt/galaxy/server/database/dependencies/_conda/envs/[email protected]/bin/../db/blast/mlst.fa] in search path [/opt/galaxy/server/database/jobs_directory/002/2212/working::]

Could you help me?

[watsonar]

I am having the same issue as above. I will update if I can find a solution.

[watsonar]

Hi @ajkarloss, I found that if I replace the contents of mlst/scripts/mlst-download_pub_mlst with the script from this comment and then re-do the database update, it works. :)