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.
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.