Could not read file (reference file) error

[george-githinji]

Hi @andrewjpage
I ran assembly improvement against a spades assembly and a virus reference sequence provided on the command line and I get this error. I decided to just run the order_contigs_with_abacus script and again it raises this error. Is this a known issue or something wrong with my setup? The reference file was provided in the arguments.

This is with improve_assembly
For some reason it is unable to locate the given files and arguments.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/assembly/spades/sample1/improved_no_ref_assembly/ucgdTSn1uJ/scaffolds.scaffolded.gapfilled.length_filtered.sorted.fa_KP317916_1.fasta.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:435
STACK: Bio::AssemblyImprovement::Abacas::DelimiterRole::_split_sequence_on_delimiter /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm:70
STACK: Bio::AssemblyImprovement::Abacas::Main::run /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/AssemblyImprovement/Abacas/Main.pm:73
STACK: Bio::AssemblyImprovement::Abacas::Iterative::_run_abacas /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/AssemblyImprovement/Abacas/Iterative.pm:74
STACK: Bio::AssemblyImprovement::Abacas::Iterative::run /apps/perl/5.24.0/lib/site_perl/5.24.0/Bio/AssemblyImprovement/Abacas/Iterative.pm:46
STACK: /apps/perl/5.24.0/bin/order_contigs_with_abacas:57
-----------------------------------------------------------

I had provided all the arguments with the correct paths to where these files are located.

[nysdan]

I'm running through the same issue. What does this mean? Did the software finish or I've got an intermediate file that's not worth to work with?

[yirui0214]

Four years later...I meet the same question. Do you find any way to solve it?