blast error ?creating index

Question

[alhafidzhamdan]

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 DO10900T.fa.02.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 

cd $BLAST

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?

[lieven.sterck]

What is the file size of your input .fa file that you used in your makeblastdb cmd?

Can you also check that there is a file called <your blastdb name>.nal present.

[alhafidzhamdan]

It is 177G . And there is no .nal file. just lots of .nhr .nin .nsq and no .nog .nsd .nsi (as for hg38 when i tested this).

[GenoMax]

There may be a space between DATABASE= /gpfs/igmmfs01/eddie/Glioblastoma-WGS/blast/DO10900T.fa the equal to sign and the rest of the directory path. At least there is one in the command you pasted above. Can you check and remove that?

[alhafidzhamdan]

Sorry that was my bad- there wasn't any space in the actual run.

[alhafidzhamdan]

Thanks guys! It turned out i didn't have the .nal files as memory had run out. So I re-ran it with enough memory and it worked fine.

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Answer 1

[lieven.sterck]

then something probably went wrong with formatting your blastDBs , if the resulting blastDB is split in several sub parts , such as in your case, there should be a .nal file 'joining' them to be used as a single DB.

did you check the log file of your blastDB formatting?