MAVID

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MAVID Multiple alignment of large genomic sequences.

[edit] Email

-------- Original Message --------
Subject: 	mavid.pl problems
Date: 	Sun, 18 Feb 2007 19:01:40 -0600
From: 	Jay Hannah <jay@jays.net>
To: 	Jay Hannah <jay@jays.net>

Hi Kiran --

Can you forward this question to the MAVID folks? I think this is  
where something is going wrong...

=======


Hello,

I'm trying to use mavid.pl and I'm hitting errors right away. I'm  
hoping you can help.

---
$ /usr/local/mavid/mavid/mavid.pl NC_006570.fasta
/usr/local/mavid/mavid/randtree NC_006570.fasta
/usr/local/mavid/mavid/mavid ./mavid.ph NC_006570.fasta

*******************************************************
*                                                     *
*                  Welcome to MAVID.                  *
*                  (version 2.0, build 4)             *
*                                                     *
*******************************************************


Error: The masking file could not be found.

WARNING: non-zero return from mavid.  Call was:
/usr/local/mavid/mavid/mavid ./mavid.ph NC_006570.fasta
/usr/local/clustalw/clustalw ./mavid.mfa -tree
---

I used the Perl debugger to try to understand what might be going  
wrong. It appears that on line 80 of mavid.pl a call to randtree is  
executed

/usr/local/mavid/mavid/randtree NC_006570.fasta

and then on line 81 mavid.pl tries to move "treefile" to "mavid.ph".
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