gravatar for alhafidzhamdan

3 hours ago by

Hi all,

I have a sequence in fasta format that I want to blast against a tumour genome fasta file.
I have attempted to create a database of the tumour genome using this:

I am in /gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast

SAMPLE_ID=DO10900T makeblastdb -in ${SAMPLE_ID}.fa -title "TCGA1"
-dbtype nucl

This is the log:

Building a new DB, current time: 03/20/2020 12:33:54
New DB name: /gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast/DO10900T.fa
New DB title: TCGA1
Sequence type: Nucleotide
Keep MBits: T Maximum file size: 1000000000B

These are some of the output files:

DO10900T.fa.00.nhr DO10900T.fa.12.nsq DO10900T.fa.25.nin DO10900T.fa.38.nhr DO10900T.fa.50.nsq DO10900T.fa.63.nin
DO10900T.fa.00.nin DO10900T.fa.13.nhr DO10900T.fa.25.nsq DO10900T.fa.38.nin DO10900T.fa.51.nhr DO10900T.fa.63.nsq
DO10900T.fa.00.nsq DO10900T.fa.13.nin DO10900T.fa.26.nhr DO10900T.fa.38.nsq DO10900T.fa.51.nin DO10900T.fa.64.nhr
DO10900T.fa.01.nhr DO10900T.fa.13.nsq DO10900T.fa.26.nin DO10900T.fa.39.nhr DO10900T.fa.51.nsq DO10900T.fa.64.nin
DO10900T.fa.01.nin DO10900T.fa.14.nhr DO10900T.fa.26.nsq DO10900T.fa.39.nin DO10900T.fa.52.nhr DO10900T.fa.64.nsq
DO10900T.fa.01.nsq DO10900T.fa.14.nin DO10900T.fa.27.nhr DO10900T.fa.39.nsq DO10900T.fa.52.nin DO10900T.fa.65.nhr

And then I want to blast the sequence (CSE) file against the databse:

PATIENT_ID=head -n $SGE_TASK_ID $IDS | tail -n 1
DATABASE= /gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast/DO10900T.fa


blastn -db $DATABASE -query ${CSE} -out ${CSE}_${PATIENT_ID}${TYPE}.out

But I received the classic error of no index and alias found etc..

BLAST Database error: No alias or index file found for nucleotide
database [/gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast/DO10900T.fa] in
search path [/gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast::]

Any clues?

Source link