Makeblastdb error: file does not exist.
0
0
Entering edit mode
4 weeks ago

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.

blastdb blast • 245 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

yes. its in same folder but still same error.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1988 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6