Cmd line psi-blast help

Katerys · 08-26-2019, 08:57 PM

Hello, I am needing some help with a dilemma I am having with cmd line psi-blast.

I set it to run ten iterations but it core dumps on me, the query sequence is correct and I have all the correct pathways as well as nr databases into my drive. It was suggested to tighten the search settings to increase the stringency. Is there a way to do this?
Also, how do you advise that I access any core dumped files?

Last but certainly not least, is there a cmd line syntax to run a PSI-BLAST using a PSSM generated from the first five iterations of a PSI-BLAST from an initial query sequence?

I'm new at this and could really use the help, thank you!

maubp · 08-30-2019, 10:37 AM

A core dump is bad - either a bug the NCBI BLAST team would want to fix, or a problem in how it was compiled and installed. Did you use the NCBI provided pre-compiled binaries? Did you use conda? Did you use a Linux distribution's packages? Did you compile it yourself?

Another key question, which version of BLAST are you using; and what operating system?

Katerys · 08-30-2019, 11:00 PM

Quote:

Originally Posted by maubp

A core dump is bad - either a bug the NCBI BLAST team would want to fix, or a problem in how it was compiled and installed. Did you use the NCBI provided pre-compiled binaries? Did you use conda? Did you use a Linux distribution's packages? Did you compile it yourself?

Another key question, which version of BLAST are you using; and what operating system?

I am using BLAST v 2.9.0 on windows64

maubp · 09-02-2019, 02:41 AM

OK. That is the latest release, good.

How did you install BLAST 2.9.0 on Windows 64? Was it using ncbi-blast-2.9.0+-win64.exe or ncbi-blast-2.9.0+-x64-win64.tar.gz (which one) from the NCBI FTP site?

If so, I suggest you email the BLAST help team with your reproducible example.

In the meantime, do you have access to a Mac or Linux machine to try the same example there? Or, if not any you are in a hurry, you could try an older BLAST release (in case this is a recent problem - this would also help in identifying the underlying problem for the NCBI to fix it).

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08-26-2019, 08:57 PM	#1
Katerys Junior Member Location: San Diego, California Join Date: Aug 2019 Posts: 2	Cmd line psi-blast help Hello, I am needing some help with a dilemma I am having with cmd line psi-blast. I set it to run ten iterations but it core dumps on me, the query sequence is correct and I have all the correct pathways as well as nr databases into my drive. It was suggested to tighten the search settings to increase the stringency. Is there a way to do this? Also, how do you advise that I access any core dumped files? Last but certainly not least, is there a cmd line syntax to run a PSI-BLAST using a PSSM generated from the first five iterations of a PSI-BLAST from an initial query sequence? I'm new at this and could really use the help, thank you!

08-30-2019, 10:37 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	A core dump is bad - either a bug the NCBI BLAST team would want to fix, or a problem in how it was compiled and installed. Did you use the NCBI provided pre-compiled binaries? Did you use conda? Did you use a Linux distribution's packages? Did you compile it yourself? Another key question, which version of BLAST are you using; and what operating system?

09-02-2019, 02:41 AM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	OK. That is the latest release, good. How did you install BLAST 2.9.0 on Windows 64? Was it using ncbi-blast-2.9.0+-win64.exe or ncbi-blast-2.9.0+-x64-win64.tar.gz (which one) from the NCBI FTP site? If so, I suggest you email the BLAST help team with your reproducible example. In the meantime, do you have access to a Mac or Linux machine to try the same example there? Or, if not any you are in a hurry, you could try an older BLAST release (in case this is a recent problem - this would also help in identifying the underlying problem for the NCBI to fix it).