Using PROmer as part of ABACAS (PAGIT)

[akjones]

Hi all,

I have recently installed PAGIT on Mac OSX and am working with ABACAS. So far I have gotten abacas to run using the default parameter settings and NUCmer. The command I entered was $PAGIT_HOME/ABACAS/abacas.pl -r Ddesulfuricans132.fasta -q Stringentcontigs_avg_cvg10orgreater.fa -p nucmer -m -b -o firstrun (where Ddesulfuricans132.fasta and Stringentcontigs_avg_cvg_10orgreater.fa are my reference and query, respectively), this worked fine and generated the expected result files. I wanted to try using PROmer instead of NUCmer and entered the same command as above, only this time using PROmer after the "-p" flag and changing the output prefix. It did not work and I got this error message: ERROR: Could not parse delta file, promer.delta
error no:400

I have no idea what that means, I tried Googling the error (high tech, I know) and couldn't find anything useful. Any thoughts or suggestions? I would greatly appreciate it. Also as an fyi, I am very much a beginner with bioinformatics in general and especially with running programs in Unix or Linux command line. Please keep that in mind with feedback.

Thanks,
~akjones

[ThomasDOtto]

Hi Akjones,

it is actually a bug in PAGIT, that will be fixed in the next version, sorry. The path in the promer file are not consistent with the installation.

Assuming you have sourced the configuration file of PAGIT, or working on the virtual machine, do
source nucmer
Looking into this file, like with less. Following should be seen:
use lib "$ENV{PAGIT_HOME}/lib";
use Foundation;
use File::Spec::Functions;
use strict;

my $AUX_BIN_DIR = "$ENV{PAGIT_HOME}/bin/aux_bin";
my $BIN_DIR = "$ENV{PAGIT_HOME}/bin";
my $SCRIPT_DIR = "$ENV{PAGIT_HOME}/bin/scripts";

If you do the same with promer, the variable are set absolutely, and not with
$ENV{PAGIT_HOME}/bin/

If you change promer to the same values than nucmer, it should work. Let me know if not, and I'll send you the fixed file, or put in on the pagit web page.

Cheers,
Thomas

[akjones]

Thanks very much, I will give that a shot!

[akjones]

Thomas,

I followed your suggestion and was able to view both the nucmer and promer files, I used the command "v" in "less" to allow me to edit. However, when I did this something very bizarre happened to my keyboard, I think it spontaneously changed it's format. My quote/double quotes key turned into the @ symbol and my hash/3 key turned into a pound symbol (as in currency). Any idea what that is about? Or how to fix it? I can't make the changes to promer if I cannot access my characters properly

Thanks again for your help,

~Ana

[akjones]

Alright, fixed keyboard problems and changed the discussed promer values to match the nucmer values, still got the same error. So if you could send the fixed file or put it on the pagit webpage that would be awesome!

[ThomasDOtto]

Hi,

it should be updated now:

http://www.sanger.ac.uk/resources/software/pagit/#Bugs

Basically, download the promer file and replace the old. I did test it here, but this means little...

Cheers,
Thomas