Makeblastdb error: file does not exist.

Question

[adnan.sabar7865]

I just downloaded the blast command line applications and I would like to make a database of a MGEs nucleutides that i downloaded from ACLAME database site in fasta file. It is labeled as mydb.fasta and I have put the file into a bin folder of blast in the path C:\Program Files\NCBI\blast-2.12.0+\bin

Ive been typing this into the command line:

cd C:\Program Files\NCBI\blast-2.12.0+\bin to enter in directory

makeblastdb -in mydb.fasta -dbtype nucl -out DB

Building a new DB, current time: 09/23/2021 13:48:15 New DB name: C:\Program Files\NCBI\blast-2.12.0+\bin\DB New DB title: mydb.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B BLAST options error: File mydb.fasta does not exist

every time i got this error file does not exist. It is probably a simple problem to solve, but I cannot seem to get past it.

[vimalkvn]

Is mydb.fasta in the same directory, i.e., C:\Program Files\NCBI\blast-2.12.0+\bin?
If not, you will need to provide the complete path to that file in makeblastdb.

[adnan.sabar7865]

yes. its in same folder but still same error.

[vimalkvn]

That's strange. Would you be able to provide the output (or a screenshot) of the following commands?

pwd 
dir

Also, it is a better approach to call the command directly rather than copying your input files into the program installation directory. For example:

C:\Program Files\NCBI\blast-2.12.0+\bin\makeblastdb -in mydb.fasta -dbtype nucl -out DB

This would work anywhere in the filesystem. For convenience, you can also the bin directory to your PATH.