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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Error while DB update #104

Closed ajkarloss closed 2 years ago

ajkarloss commented 3 years ago

"./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/mlst@2.16.1/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/__mlst@2.16.1/scripts/../db/blast/mlst.fa does not exist Created BLAST database for /opt/galaxy/server/database/dependencies/_conda/envs/mlst@2.16.1/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/__mlst@2.16.1/bin/../db/blast/mlst.fa] in search path [/opt/galaxy/server/database/jobs_directory/002/2212/working::]

Could you help me?

watsonar commented 2 years ago

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

watsonar commented 2 years ago

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. :)