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> 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
>
>
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