Blastn error, database creation problem, BLAST

Question

[biomagician]

Hi,

I am trying to blast contigs to the C. elegans reference genome sequence with the following 2 commands:

makeblastdb -in celegans.fa -input_type fasta -dbtype nucl -title celRef -out celegans.db -taxid 6239

blastn -subject celegans.db -query celegans.contigs.fasta -out bristol.txt -outfmt 6 -html -num_threads 8

More details here:

 makeblastdb -in output/genome/celegans/ref/seq/celegans.fa -input_type fasta -dbtype nucl -title celRef -out output/genome/celegans/ref/database/celegans.db -taxid 6239

    Building a new DB, current time: 08/30/2017 16:35:01
    New DB name:   /Users/cr517/Documents/phd/project/output/genome/celegans/ref/database/celegans.db
    New DB title:  celRef
    Sequence type: Nucleotide
    Deleted existing Nucleotide BLAST database named /Users/cr517/Documents/phd/project/output/genome/celegans/ref/database/celegans.db
    Keep MBits: T
    Maximum file size: 1000000000B
    Adding sequences from FASTA; added 7 sequences in 1.03467 seconds.

  blastn -subject output/genome/celegans/ref/database/celegans.db -query output/assembly/celegans/canu/bristol/celegans.contigs.fasta -out output/alignment/celegans/ref/pacbio/contigs/canu/blastn/bristol.txt -outfmt 6 -html -num_threads 8
    Command line argument error: Argument "subject". File is not accessible:  `output/genome/celegans/ref/database/celegans.db'

But when I check with ls, I do have database files in my directory:

ls output/genome/celegans/ref/database 
        celegans.db.nhr celegans.db.nin celegans.db.nsq

I do not understand why the database is not accessible. Your help would be appreciated.

Thanks.

Best, C.

Answer 1

[h.mon]

You want to use -db /path/to/celegans.db. -subject is used for blasting two sequences against each other - I think both in fasta format.

Answer 2

[st.ph.n]

Try providing the full path here:

output/genome/celegans/ref/database/celegans.db

What version of blast are you running? Change -subject to -db:

blastn -db celegans.db -query celegans.contigs.fasta -out bristol.txt -outfmt 6 -html -num_threads 8

[biomagician]

Hi,

I've changed it to -db and it is running now.

Thanks.

C.