Question: DISOPRED3 Blastpgp Failed 256
gravatar for euduca
14 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 14 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 13 months ago by fishgolden280

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 13 months ago • written 13 months ago by euduca0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1752 users visited in the last hour