| Subject: | Bug when running with reference genome |
| Date: | Sat, 5 Oct 2013 18:49:19 +0000 |
| To: | "bug-Bio_AssemblyImprovement [...] rt.cpan.org" <bug-Bio_AssemblyImprovement [...] rt.cpan.org> |
| From: | Kaisa Thorell <kaisa.thorell [...] gu.se> |
Hi!
I sent this a couple of weeks ago but I don't know if you came to any conclusion so I send it again.
I have been running
perl ~/perl5/bin/improve_assembly -a contigs.fasta -f R1.fastq -r R2.fastq -i $insert -c reference_complete.fasta
However, I get the following error message:
Can't locate object method "final_output_filename" via package "Bio::AssemblyImprovement::Abacas::Iterative" at /c3se/users/thorellk/Glenn/perl5/bin/improve_assembly line 123.
In the equivalent Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative there is a sub defining final_output_filename but in Bio::AssemblyImprovement::Abacas::Iterative there isn't, could that be the problem? That's at least the conclusion I draw with my very limited perl knowledge but that could also be entirely incorrect... Despite of this warning it outputs a .scaffolded.filtered and a .scaffolded.scaffolded.filtered file.
Running without the -c option generates no complaints.
Best wishes
Kaisa