Question: DISOPRED3 Blastpgp Failed 256
gravatar for euduca
4 months ago by
Brasil, Ilhéus, UESC
euduca0 wrote:

Hi, all =)

I'm trying to use de DISOPRED3 program, but this error appears:

$  ../ ../examples/example.fasta 
Running PSI-BLAST search ...

[../] ERROR: /home/eac16/local/ncbi/blast/legacy/2.2.26/bin/blastpgp -i /home/eac16/local/DISOPRED/3.16/examples/example.fasta -d /scratch/eac16/dbs/blast/legacy/uniprot/uniref90 -a 2 -b 0 -j 3 -h 0.001 -C /home/eac16/local/DISOPRED/3.16/examples/example_16870_8d0a0101.chk -o /home/eac16/local/DISOPRED/3.16/examples/example_16870_8d0a0101.blast 
 **failed: 256**

The DISOPRED3 uses the legacy blast, so I used the command "formatdb" (2.2.26 version ) to create the database.

$ formatdb -i uniref90.fasta -p T -o T

The paths are correct and the variables at the's script too:

my $NCBI_DIR = "/home/eac16/local/ncbi/blast/legacy/2.2.26/bin/";
my $SEQ_DB = "/scratch/eac16/dbs/blast/legacy/uniprot/uniref90";
my $PSIBLAST_PAR = "-a 1 -b 0 -j 3 -h 0.001";

I installed and used the DISOPRED3 in a HPC once and use to predict (proteins) an entire genome and it was done. But now I moved to another lab, and I don't know what is wrong with the software/instalation.

Can someone help me?

Thanks. Eduardo.

ADD COMMENTlink written 4 months ago by euduca0

Try blastpgp with the same command. Then blast pgp will give you more information.

/home/eac16/local/ncbi/blast/legacy/2.2.26/bin/blastpgp -i /home/eac16/local/DISOPRED/3.16/examples/example.fasta -d /scratch/eac16/dbs/blast/legacy/uniprot/uniref90 -a 2 -b 0 -j 3 -h 0.001 -C /home/eac16/local/DISOPRED/3.16/examples/example_16870_8d0a0101.chk -o /home/eac16/local/DISOPRED/3.16/examples/example_16870_8d0a0101.blast

However, I'm afraid that

my $SEQ_DB = "/scratch/eac16/dbs/blast/legacy/uniprot/uniref90";

should be

my $SEQ_DB = "/scratch/eac16/dbs/blast/legacy/uniprot/uniref90.fasta";

but not checked.

ADD REPLYlink written 4 months ago by yamule180

Hi Yamule. You're right about the variable $SEQ_DB. I fixed this.

But the error still persisted, so I figured out that variable $BLASTDB was pointed, by default, to the NR database in the HPC. So, before to run the script I set the variable $BLASTDB to:

export BLASTDB=/scratch/eac16/dbs/blast/legacy/uniprot/uniref90

After this the blastpgp worked properly.

I wrongly presumed that variable $SEQ_DB would be enough to set the database.

Thanks for your help.

ADD REPLYlink modified 4 months ago • written 4 months ago by euduca0
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