Intermediate file not found?

[joanmarticarreras]

Dear @andrewjpage

I've been trying, for a couple of days already, to properly install and run your assembly improvment pipeline.

After installing all dependencies highlighted by cpanm -f Bio::AssemblyImprovement and test with dzil test runs smoothly within the github cloned folder.

However, when I run as follows (and only if I decide to include a reference with -c):

$ improve_assembly -a denovo_assembly/complete/KB10_trim_contigs.fasta -f clinic1/raw_reads/KB10_R1.fastq.gz -r clinic1/raw_reads/KB10_R2.fastq.gz -s bin/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -g bin/GapFiller_v1-10_linux-x86_64/GapFiller.pl  -o improve_assembly_KB10/   -c references/polyoma_dunlop_reference.fasta

Reports back the following error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/jmarti/polyoma/7wWtvgPPJ7/KB10_trim_contigs.scaffolded.fasta_polyoma_dunlop_reference.fasta.fasta': Bestand of map bestaat niet
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/jmarti/perl5/lib/perl5/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io /home/jmarti/perl5/lib/perl5/Bio/Root/IO.pm:272
STACK: Bio::SeqIO::_initialize /home/jmarti/perl5/lib/perl5/Bio/SeqIO.pm:508
STACK: Bio::SeqIO::fasta::_initialize /home/jmarti/perl5/lib/perl5/Bio/SeqIO/fasta.pm:88
STACK: Bio::SeqIO::new /home/jmarti/perl5/lib/perl5/Bio/SeqIO.pm:384
STACK: Bio::SeqIO::new /home/jmarti/perl5/lib/perl5/Bio/SeqIO.pm:430
STACK: Bio::AssemblyImprovement::Abacas::DelimiterRole::_split_sequence_on_delimiter /home/jmarti/perl5/lib/perl5/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm:70
STACK: Bio::AssemblyImprovement::Abacas::Main::run /home/jmarti/perl5/lib/perl5/Bio/AssemblyImprovement/Abacas/Main.pm:73
STACK: Bio::AssemblyImprovement::Abacas::Iterative::_run_abacas /home/jmarti/perl5/lib/perl5/Bio/AssemblyImprovement/Abacas/Iterative.pm:74
STACK: Bio::AssemblyImprovement::Abacas::Iterative::run /home/jmarti/perl5/lib/perl5/Bio/AssemblyImprovement/Abacas/Iterative.pm:46
STACK: /home/jmarti/perl5/bin/improve_assembly:142
-----------------------------------------------------------

I have the impression that /home/jmarti/polyoma/7wWtvgPPJ7/KB10_trim_contigs.scaffolded.fasta_polyoma_dunlop_reference.fasta.fasta merges names of both my assembly file and reference. Is it a bug? Is it supposed to have an intermediate file like this? Is there an error with the requirements?

Excited to make this pipeline to work. Thank you very much!

~ Joan ~

[shankar2318]

Is there a solution to this issue? Have been trying to solve it but to no avail. Would love to have this pipeline work.