Hello cricket,

For the memory issue, can you try higher max heap sizes e.g. 2000m?


For the contig/fasta issue, is it possible to email one example file (by 
personal email if you prefer) so I can be sure I am understanding the issue 
correctly?


Thanks,


Mungo


Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>
________________________________
From: jalview-discuss-boun...@jalview.org <jalview-discuss-boun...@jalview.org> 
on behalf of cricket <work.er...@gmail.com>
Sent: 20 September 2016 12:24:16
To: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Input Files and Multiple Alignment

Greetings.

I am attempting to use Jalview for the first time. I have watched some of the 
Jalview videos and read some of the Jalview manual. I would like to do multiple 
sequence alignment for the sole purpose of making trees and performing some PCA 
(PCoA) analysis.

...But I am having some issues getting started. I have 26 E. coli genomes that 
I would like to align to a reference genome (EDL933) -- however the 26 E. coli 
genomes are not complete. The 26 genomes are draft assemblies that are in fasta 
(nucleotide) format, and have many contigs in each fasta file.

I have tried to drag and drop the fasta files in one of the windows. Assuming I 
do not try to drag too many files, I am able to look at each file in its own 
separate window. However, each contig is listed as what looks like a new 
sequence that can be aligned rather than as a single fasta file (containing 
multiple contigs). I did do a multi-fasta file alignment (to the reference) 
using Mauve, but when I try to look at the alignment file in Jalview, I get the 
memory error, and all of the contigs are still there.

How should I address the contig/fasta file issue?

I am using the desktop version of Jalview on a CentOS computer.

Any assistance is greatly appreciated. - cer

On Mon, Sep 19, 2016 at 4:01 PM, cricket 
<errcric...@gmail.com<mailto:errcric...@gmail.com>> wrote:
Greetings.

I am attempting to use Jalview for the first time. I have watched some of the 
Jalview videos and read some of the Jalview manual. I would like to do multiple 
sequence alignment for the sole purpose of making trees and performing some PCA 
(PCoA) analysis.

...But I am having some issues getting started. I have 26 E. coli genomes that 
I would like to align to a reference genome -- however the 26 E. coli genomes 
are not complete. The 26 genomes are draft assemblies that are in fasta 
(nucleotide) format, and have many contigs in each fasta file.

ISSUES:


  1.  I generally run out of memory when trying to use more than one file (Out 
of memory when calculating consensus!!!).
     *   I have opened the Jalview.lax file and put the following as the last 
two lines (but I am still getting the memory error):
     *   lax.nl.java.option.java.heap.size.max=1000m
     *   lax.nl.java.option.java.heap.size.initial=900m
  2.  I have tried to drag and drop the fasta files in one of the windows. 
Assuming I do not try to drag too many files, I am able to look at each file in 
its own separate window. However, each contig is listed as what looks like a 
new sequences that can be aligned rather than as a single fasta file with 
multiple contigs. I did do a multi-fasta file alignment (to the reference) 
using Mauve, but when I try to look at the alignment, I get the memory error, 
and all of the contigs are still there.

QUESTIONS:

  1.  Each fasta file (n=26) is around 5MB. How much should I increase my 
memory so that it is an appropriate amount?
  2.  How should I address the contig/fasta file issue?

I am using the desktop version of Jalview on a CentOS computer.

[root@c588 jalview]# free -mh
             total       used       free     shared    buffers     cached
Mem:          126G       124G       1.3G        18M       468M       114G
-/+ buffers/cache:       9.4G       116G
Swap:          63G        62M        63G


Any assistance is greatly appreciated. - cer



The University of Dundee is a registered Scottish Charity, No: SC015096
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