Closed liamfriar closed 1 year ago
I used mmseqs databases NR which re-downloaded NR from NCBI and prepared everything as databases which are now working fine. So, not sure why the above didn't work, but the workflow is now moving again.
Download nr
wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz gunzip nr.gz
Make a blastdb and diamond db of nr
makeblastdb -in nr -dbtype prot
It's probably because there're no taxidmapping information the way you make blastdb without -taxid_map
.
Read this Building a BLAST database with your (local) sequences
or you could download preformatted nr (https://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz ~ https://ftp.ncbi.nlm.nih.gov/blast/db/nr.79.tar.gz the numbers may change by time) and try again. It works for me.
Expected Behavior
Starting from nr which was already downloaded, generate all of the required files to run mmseqs taxonomy to assign taxonomy to metagenome assembled genomes.
Current Behavior
nr.fnaDB_mapping is empty (ls -thor reveals it is 0 bytes and mmseqs easy-taxonomy displays "nr.fnaDB_mapping is empty. Rerun createtaxdb to recreate taxonomy mapping.")
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.
Download nr
wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz gunzip nr.gz
Make a blastdb and diamond db of nr
makeblastdb -in nr -dbtype prot diamond makedb --in nr -d nr.dmnd
Prepare taxonomy database for mmseqs2
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz mkdir taxonomy && tar -xxvf taxdump.tar.gz -C taxonomy rm taxdump.tar.gz blastdbcmd -db nr -entry all > nr.fna blastdbcmd -db nr -entry all -outfmt "%a %T" > nr.fna.taxidmapping mmseqs createdb nr.fna nr.fnaDB && \ mmseqs createtaxdb nr.fnaDB tmp --ncbi-tax-dump taxonomy/ --tax-mapping-file nr.fna.taxidmapping
MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Context
I want to use MMseqs2 to assign taxonomy to contig-level metagenome-assembled genomes. I had previously downloaded nr as above, so hopefully the way I downloaded it works for MMseqs? I could alternatively re-download nr entirely with the mmseqs workflows, but would prefer not to do that if possible for consistency with analyses that are already done and used the version of nr that I have downloaded. I don't think versioning is actually a problem as I downloaded nr within the past couple months.
Your Environment
Include as many relevant details about the environment you experienced the bug in. I am using a conda environment created using
conda install -c bioconda mmseqs2
on April 19, 2023. version: 14.7e284 (via conda list in activated environment)