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issue at Step 3 : No such file ... #6

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CedricMariac opened this issue Jan 31, 2018 · 0 comments
Open

issue at Step 3 : No such file ... #6

CedricMariac opened this issue Jan 31, 2018 · 0 comments

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@CedricMariac
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Hi,
I encounter a problem at the third step with the following error message:
the only file available in the outdir directory is named:
02_3_organelle_assembly01.fasta

============================================================
3) Running scaffolding (SSPACE) (mer. janv. 31 07:47:47 CET 2018)

3.1- Running SSPACE-Long

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'test1250reads/03_1_organelle_assembly.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /usr/local/perl-5.24.0/lib/site_perl/5.24.0/Bio/SeqIO.pm:435
STACK: main::get_seqstats /usr/local/Organelle-PBA-1.0/Organelle_PBA/OrganelleRef_PBA:2127
STACK: /usr/local/Organelle-PBA-1.0/Organelle_PBA/OrganelleRef_PBA:1041

an idea ?
Thank you for your help

Cédric

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