ck7/esom

esom's Issues

Bio::Root::Exception; Bad end parameter

Hello! I'm trying to use prepare_esom_files.pl to prepare input for ABAWACA. I'm getting an error when I attempt to run prepare_esom_files, though, and I'm not well-versed enough in perl to figure out what's going on.

I have a fasta file of contigs (concat.fa) and a .sam file (mapped_concat.sam). I attempt to run the script using the command

perl prepare_esom_files.pl -k 4 --raw_abundances -sa mapped_concat.sam esom_output/ concat.fa,

and when I do I receive the following output, then error:

prepare_esom_files.pl V1.07
15:26:12 11/12/2017
Command line: prepare_esom_files.pl -k 4 --raw_abundances -sa mapped_concat.sam esom_output/ concat.fa
Determining segments ... ok, 117887 segments assigned
Computing DNA signature for k=4 ... 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bad end parameter (57646). End must be less than the total length of sequence (total=56257)
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/jwestrob/perl5/lib/perl5/Bio/Root/Root.pm:447
STACK: Bio::PrimarySeq::subseq /home/jwestrob/perl5/lib/perl5/Bio/PrimarySeq.pm:452
STACK: Bio::Seq::subseq /home/jwestrob/perl5/lib/perl5/Bio/Seq.pm:630
STACK: prepare_esom_files.pl:396
-----------------------------------------------------------

Any advice you have for me would be appreciated. I notice there is also an option to include an annotation file (-a); is this necessary? I can go and annotate my contigs and try again if so.

Also, I want to thank you for making this software- this is really cool and I'm excited to see what I can do with it once I get going!

Best,

Jacob