Question: Problem Using Hhsearch
1
gravatar for Gonzalo Parra
7.4 years ago by
Argentina
Gonzalo Parra40 wrote:

Hi everyone I am trying to use HHSearch an d HHRepID.

But I am having problems in running the buildali.pl script.

I filled with the paths in the lines:

-----------
my $dbbase="/home/gonzalo/blast-2.2.16/db/nr"; # will use PSI-BLAST dbs $dbbase."90" and $dbbase."70"  
my $hh=".";
my $perl=$hh;
my $ncbidir="/home/gonzalo/blast-2.2.16/bin"; # directory with ncbi BLAST binaries
my $blastpgp="$ncbidir/blastpgp -I T -s T"; # blastpgp executable
our $blastpgp.= " -I T -s T"; # show gi's in defline; use Smith-Waterman
-----------

But I got th following error when I run it: Building alignment for query with PSI-BLAST ...

$  -I T -s T -b 20000 -v 1 -e 0.001 -d /home/gonzalo/blast-2.2.16/db/nr90 -i /tmp/gonzalo/21668/P25963.seq &> /tmp/gonzalo/21668/P25963.bla
sh: Illegal option -

It is like the variable our $blastpgp is empty. I never used variables declared with our, and I'm not getting it. Why there are two variables called the same declared with my and our in the same script?

I tried to modify the line:

our $blastpgp.= " -I T -s T"; # show gi's in defline; use Smith-Waterman

with

our $blastpgp.= "blastpgp -I T -s T"; # show gi's in defline; use Smith-Waterman

But it give me the following error


$ ./reformat.pl -M first -noss a3m a3m P25963.seq /tmp/gonzalo/23720/P25963.in.a3m -> 1 $ ./reformat.pl -r a3m psi /tmp/gonzalo/23720/P25963.in.a3m /tmp/gonzalo/23720/P25963.psi -> 1

Building alignment for /tmp/gonzalo/23720/P25963 (sp|P25963|IKBA_HUMAN)

Building alignment for query with PSI-BLAST ... $ blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /home/gonzalo/blast-2.2.16/db/nr90 -i /tmp/gonzalo/23720/P25963.seq &> /tmp/gonzalo/23720/P25963.bla $ ./alignhits.pl -cov 80 -e 0.001 -bl 0.33 -bs 0.67 -best -psi -q /tmp/gonzalo/23720/P25963.seq /tmp/gonzalo/23720/P25963.bla /tmp/gonzalo/23720/P25963.core.psiError in alignhits.pl: blast output file /tmp/gonzalo/23720/P25963.bla truncated:

Error in buildali.pl: could not parse the result of ./alignhits.pl -cov 80 -e 0.001 -bl 0.33 -bs 0.67 -best -psi -q /tmp/gonzalo/23720/P25963.seq /tmp/gonzalo/23720/P25963.bla /tmp/gonzalo/23720/P25963.core.psi: regex=^(\d+) sequences extracted gonzalo@malbec:~/Desktop/HHrepID/hh_1.5.0.linux64$ BLASTP 2.2.16 [Mar-25-2007]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference for composition-based statistics: Schaffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005.

Query= sp|P25963|IKBA_HUMAN NF-kappa-B inhibitor alpha OS=Homo sapiens GN=NFKBIA PE=1 SV=1 (317 letters)

Database: nr90 3,820,465 sequences; 1,326,381,835 total letters

Searching.................................................

The blast ends working but is like the script does not wait it for ending and says that the report is truncated because it wants to read it before is done.

I don't know what is going on.

Thanks in advance

perl • 1.8k views
ADD COMMENTlink modified 7.0 years ago by Johannes Soeding40 • written 7.4 years ago by Gonzalo Parra40
1
gravatar for Pierre Lindenbaum
7.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

The error is in the following line:

$  -I T -s T -b 20000 -v 1 -e 0.001 -d ...

you just gave the options, but the shell needs first, the name of a program

$  myprogram -I T -s T -b 20000 -v 1 -e 0.001 -d ...
ADD COMMENTlink written 7.4 years ago by Pierre Lindenbaum118k
1
gravatar for Johannes Soeding
7.1 years ago by
Johannes Soeding40 wrote:

Please see the answer at http://biostar.stackexchange.com/questions/14132/problem-with-buildali-pl-from-hhsearch/18238#18238

Best regards, Johannes Soeding

ADD COMMENTlink written 7.1 years ago by Johannes Soeding40
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