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  • Combining BLAST nt and local database

    Hi all,

    I've made a custom local BLAST database and I'm trying to 'combine' it with the BLAST nt database using ncbi-blast-2.9.0+ blastdb_aliastool but I'm getting the error:

    "BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing"

    Here's what I've done:

    In the directory nt, on our LINUX computing cluster, I've downloaded the most recent version of the BLAST nt database and unpacked it

    $wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz"

    $for f in *.tar.gz; do tar -zxvf $f; rm $f; done

    This completes with no errors and produces what seems to be the correct number of files (10 files for each nt.* part of the database, plus nt.nal, and taxdb.btd and taxdb.bti). All parts of the nt database are present (nt.00 to nt.85) and all these parts are listed in the nt.nal file.

    Next, I make my local database:

    I scp my fasta file and my taxid file to the nt folder, so everything is in the same folder.

    $makeblastdb -in CocoaPESTLocal.fasta -parse_seqids -taxid_map CocoaPESTLocal_TaxonomyIDs.txt -blastdb_version 5 -title "Local database" -dbtype nucl -out loc

    Output:
    Building a new DB, current time: 12/24/2019 11:54:52
    New DB name: /ddn/data/mdzm87/BLASTdatabases/nt
    New DB title: Local database
    Sequence type: Nucleotide
    Keep MBits: T
    Maximum file size: 1000000000B
    Adding sequences from FASTA; added 44 sequences in 0.0142331 seconds.

    And nine files are created.

    Next, I try to 'combine' the databases using the blastdb_aliastool:

    $blastdb_aliastool -dblist "loc nt" -dbtype nucl -out comb -title "Combined database"

    BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing


    I also tried different variants of the command:

    $blastdb_aliastool -dblist "loc nt.00 nt.01 nt.02 nt.03 nt.04 nt.05 nt.06 nt.07 nt.08 nt.09 nt.10 nt.11 nt.12 nt.13 nt.14 nt.15 nt.16 nt.17 nt.18 nt.19 nt.20 nt.21 nt.22 nt.23 nt.24 nt.25 nt.26 nt.27 nt.28 nt.29 nt.30 nt.31 nt.32 nt.33 nt.34 nt.35 nt.36 nt.37 nt.38 nt.39 nt.40 nt.41 nt.42 nt.43 nt.44 nt.45 nt.46 nt.47 nt.48 nt.49 nt.50 nt.51 nt.52 nt.53 nt.54 nt.55 nt.56 nt.57 nt.58 nt.59 nt.60 nt.61 nt.62 nt.63 nt.64 nt.65 nt.66 nt.67 nt.68 nt.69 nt.70 nt.71 nt.72 nt.73 nt.74 nt.75 nt.76 nt.77 nt.78 nt.79 nt.80 nt.81 nt.82 nt.83 nt.84 nt.85" -dbtype nucl -out comb -title "Combined database"

    and

    $blastdb_aliastool -dblist "loc nt.nal" -dbtype nucl -out comb -title "Combined database"

    And get the same error.

    However, if I make two copies of my local reference database (with different names loc and local)

    $blastdb_aliastool -dblist "local loc" -dbtype nucl -out comb -title "Combined database"

    Created nucleotide BLAST (alias) database comb with 88 sequences

    So it seems to be something wrong specifically with trying to 'combine' the BLAST nt database specifically with my local database.

    The only thing I notice is that the BLAST nt database has different names for some parts than my local database:

    nt.00.nhd
    nt.00.nhi
    nt.00.nhr
    nt.00.nin
    nt.00.nnd
    nt.00.nni
    nt.00.nog
    nt.00.nsd
    nt.00.nsi
    nt.00.nsq
    ....

    loc.ndb
    loc.nhr
    loc.nin
    loc.nog
    loc.nos
    loc.not
    loc.nsq
    loc.ntf
    loc.nto


    I've consulted the Blast+ manual and done lots of Googling but I can't seem to figure it out. Does anyone have any ideas?

    Thanks,
    Andreanna

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