BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing

172 Views Asked by At

I am trying to create a blast database containing all plant sequences in Refseq release. I downloaded all the fasta files from the ftp site.

After discovering that some fasta files were larger than 1000000000 bytes, I split the overly large files into smaller fasta files using the following command:

awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=sprintf("chunk%d.fa",n);} print >> file; n++; next;} { print >> file; }' < multi.fa

Next, I proceeded to create the database using the command:

for i in *.f*a; do makeblastdb -in $i -dbtype nucl -taxid_map ../plant_refseq_genomic_taxidmap.txt -parse_seqids -title plantdb; done

Starting from over 1000 fasta files, I ended up with 1000 databases, each represented by 9 files (.ndb, .nhr, .nin, .nog, .nos, .not, .nsq, .ntf, .nto), that I want to group into a single alias.

I saved the list of all databases in a txt file:

plant.10.1.genomic.fna.1.fa
plant.10.1.genomic.fna.2.fa
plant.10.2.genomic.fna
plant.10.3.genomic.fna
plant.10.4.genomic.fna
etc.....

And I launched the following command:

blastdb_aliastool -dblist_file listdb.txt -dbtype nucl -out plantdb-refseq-release -title "plantdb-refseq-release"

But I am getting the following error:

BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing.

What could be the reason for this error and how can I resolve it?

thank you for your help

0

There are 0 best solutions below