Doug Senalik's Blog — Things that aren't on the internet yet

I am posting this in case it happens a THIRD time and google will then lead me here (hopefully).

A new gbrowse database I was setting up shows only a big red "Not Found" error. Not helpful.

Apache log shows lines like:

[Mon Mar 14 10:00:09 2011] [error] [client 128.128.128.128] indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/dbnamehere/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053., referer: http://cranberry.vcru.wisc.edu:7280/cgi-gb/gbrowse/mynewdbnamehere/

Still not so helpful.
I made a short Perl program with just this essential part:

use Bio::DB::Fasta;
  my $db      = Bio::DB::Fasta->new('/var/www/html/gbrowse2/databases/mynewdbnamehere');

This gave useful error messages!

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #1682 '
..' is 19 != 52 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets /usr/local/share/perl5/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_dir /usr/local/share/perl5/Bio/DB/Fasta.pm:593
STACK: Bio::DB::Fasta::new /usr/local/share/perl5/Bio/DB/Fasta.pm:488
STACK: ./test.pl:11
-----------------------------------------------------------
indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/cucumbermito/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053.

So, the actual problem was that the FASTA file had lines of different lengths! Fixed that and the problem is gone.