[Jalview-discuss] problem with fasta files

[Judith Cohn]

Hi,

I have been using Jalview 2.3 for some time now on an Mac Pro running  
Leopard and it has worked very well.  Recently I upgraded to Jalview  
2.4 and have experienced some strange behavior with fasta files of  
multiple sequence alignments produced by the Muscle alignment program.

With Jalview 2.3 (labelled May 2007, version 12.2.0), I have no  
trouble either opening these files via the menu or by calling a script  
which executes the jar file with the alignment fasta file plus an  
automatically generated features file as arguments.  When I upgraded  
to Jalview 2.4 (labelled Sept 16, 2008, version 12.2.0) and tried to  
run my script from the command line,  I get an error message stating:

Couldn't load xxxxx.fa.muscle
Formats currently supported are Fasta, MSF, Clustal, BLC, PIR, MSP and  
PFAM

If I tried to manually select this same file from the menu, Jalview  
just hangs on "loading...".

I then went back to Jalview 2.3 (I have both 2.3 and 2.4 installed).   
I could no longer view the files from my script, getting the Couldn't  
load error message.  But I could load them via the menu option.  I  
kept going back and forth between 2.4 and 2.3 to trouble shoot.  
Seemingly randomly,  2.3 would work again with the script.  I could  
never get 2.4 to work.

I should mentioned that I uninstalled 2.3 (using the uninstall  
option), installed 2.4 (using install.app).  When 2.4 didn't work, I  
used Time Machine to get 2.3 back and rename the 2.4 directory in the  
Applications folder.

I also have a clean version of 2.4 on my laptop which I installed a  
few months ago.  This version is labelled Aug 27 2008 rather than  
September.  It works fine on the same files - both via the script and  
by manually loading the files from the menu.  The laptop is a Macbook  
Air running the same version of Leopard (10.5.7).

A colleague did a clean install of 2.4 (I think the same version as on  
my laptop) and he also cannot use the script but he can manually load  
the files.

I am completely at a loss to explain this behavior.  Has anyone else  
suffered from similar problems?  Any solutions?

Judith Cohn

--------------------

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone:  505-665-0999
email:  jcohn at lanl.gov




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