Hey so for the past two days I have been trying to install and execute a stand alone blast named ncbi-blast-2.2.30+ on a centos os system. I managed to download a nr ref sequence from ncbi ftp using the command wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz and extracted the file using the command tar -xvpf nr.gz. I got an nr file of 33 gb size but when I try to format the file using the command
./makeblastdb -in /home/Desktop/ncbi-blast-2.2.30+/db/nr -dbtype 'nucl' -input_type 'fasta' -out /home/Desktop/ncbi-blast-2.2.30+/output
I get the error showing
BLAST Database creation error: FASTA-Reader: No residues given
Can anyone give any suggestions on the nature of the problem and how I can solve it?
•
written
by
vigneshprbh37 •
3 answers
Ok I think I found the problem. When making a blast db or using any masker algorithm like DUST Windowmasker etc, it raises an error if the program finds an empty record. This means a record in the form:
>gi|xxxx|
>gi|yyyyy|
AGACCGATGACT
I'm sure there are many ways of remove empty records from a fasta file. A simple and fast way is using awk. You could simply copy and paste this command in the terminal (obviously substituting the name of your file):
awk -v RS=">" -v FS="\n" -v ORS="" ' { if ($2) print ">"$0 } ' your_fasta_file.fna > output.fna
If you want the explanation of the code follow this thread:
2. yes it is a 33.6 gb file.
3. What's the difference with a prebuilt db, I don't know.
•
written
by
vigneshprbh37 •
EDITED: Now I realize it wasn't the same error so it maybe won't work for you. Tell us if this works for you or the way you solved this problem =)
Hi, I got the same error either making a blastDB from fasta files or using a masking algorithm like DUST.
For me the problem was that some of my sequences had a blank line between the last line of nucleotides from one sequence and the header of the next one like:
>gi|xxxx|
ATGACCGT...
[[:BLANK:]]
>gi|yyyy|
ACGATCGG...
An easy way of remove that blank lines in UNIX is with grep:
grep -v '^$' fasta_with_blanks.fna > fasta_without_blanks.fna
Saludos!
Log in to answer this question.
-
blast+ v2.10.1. error Error: mdb_env_open: Cannot allocate memory
written by MEITUO •
-
BLAST Database error: No alias or index file found for protein database [nr] in search path [D:\Tes…
written by Eric Wang •
-
BLAST Database creation error
written by sahilbioinf0 •
-
blastn errors following building of database
written by rbronste
-
creating a blast database
written by sukesh1411 •
-
Using nr database for BLAST search
written by cookm346 •
-
makeblastdb command not found
written by linhuixinnn •
-
restricting number of hits for blastn execution format
written by vigneshprbh37 •
-
blastn execution error, the correct command line format
written by vigneshprbh37 •
-
Opening A Fasta File In Windows
written by Vivek •
You need a
zin your tar command for gzip files. Use-xvzf. The file is probably not unzipped correctly. but also, the nr database is protein ("Non-Redundant peptides") so you will be creating a protein database. Think about whether that is what you want and why. I believe that if you ran the makeblastdb correctly it would tell you that you are mixing up protein and nucleotides. If you want the whole nucleotide database it is called 'nt ("Non-Translated nucleotides). I can't remember if they are the official acronyms or whether it's just what my brain uses to keep them the correct way around.