SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Command line Blast.. not as good as it was? susanklein Bioinformatics 1 02-20-2018 05:43 PM
Question: Running PSI-BLAST Against Multiple Queries Morgis89 Bioinformatics 0 11-16-2015 03:41 AM
Creating a Command Line BLAST+ Database GSviral Bioinformatics 3 01-29-2015 05:22 AM
Running out of disk space with BWA, wrong CMD line? sindrle RNA Sequencing 3 11-26-2013 07:14 AM
Command line blast with remote option nupurgupta Bioinformatics 2 05-18-2012 07:47 AM

Reply
 
Thread Tools
Old 08-26-2019, 07:57 PM   #1
Katerys
Junior Member
 
Location: San Diego, California

Join Date: Aug 2019
Posts: 2
Exclamation 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!
Katerys is offline   Reply With Quote
Old 08-30-2019, 09:37 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

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?
maubp is offline   Reply With Quote
Old 08-30-2019, 10:00 PM   #3
Katerys
Junior Member
 
Location: San Diego, California

Join Date: Aug 2019
Posts: 2
Default

Quote:
Originally Posted by maubp View Post
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
Katerys is offline   Reply With Quote
Old 09-02-2019, 01:41 AM   #4
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

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).
maubp is offline   Reply With Quote
Reply

Tags
cmd, psiblast

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:35 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO