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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Error during FEELnc_codpot.pl running #19

Closed wyim-pgl closed 6 years ago

wyim-pgl commented 6 years ago

Dear FEELnc,

During my running I've got an errors. It generated same error in Shuffle and intergenic mode. Do you have any idea? Thanks!

FEELnc_codpot.pl -i candidate_lncRNA.gtf -a ../../55_pasa/pasa_all2.assemblies.fasta.transdecoder.genome.complete.mrna.fasta -g ../../1_fasta/7_final_chr/iceplant_chr.fasta_sorted --mode=shuffle

FEELnc_codpot.pl -i candidate_lncRNA.gtf -a ../../55_pasa/pasa_all2.pasa_assemblies.gtf -g ../../1_fasta/7_final_chr/iceplant_chr.fasta_sorted --mode=intergenic

Your input GTF file 'pasa_all2.pasa_assemblies.gtf' contains 44844 transcripts

------------- EXCEPTION ------------- MSG: Each line of the qual file must be less than 65,536 characters. Line 18 is 35722859 chars. STACK Bio::DB::IndexedBase::_check_linelength /home/wyim/scratch/bin/FEELnc/lib/Bio/DB/IndexedBase.pm:744 STACK Bio::DB::Fasta::_calculate_offsets /home/wyim/scratch/bin/perl5/perlbrew/perls/perl-5.18.2/lib/site_perl/5.18.2/Bio/DB/Fasta.pm:227 STACK Bio::DB::IndexedBase::_index_files /home/wyim/scratch/bin/FEELnc/lib/Bio/DB/IndexedBase.pm:648 STACK Bio::DB::IndexedBase::index_file /home/wyim/scratch/bin/FEELnc/lib/Bio/DB/IndexedBase.pm:484 STACK Bio::DB::IndexedBase::new /home/wyim/scratch/bin/FEELnc/lib/Bio/DB/IndexedBase.pm:364 STACK ExtractFromFeature::feature2seq /home/wyim/scratch/bin/FEELnc/lib/ExtractFromFeature.pm:399 STACK ExtractCdnaOrf::CreateORFcDNAFromGTF /home/wyim/scratch/bin/FEELnc/lib/ExtractCdnaOrf.pm:303 STACK toplevel /home/wyim/scratch/bin/FEELnc/scripts/FEELnc_codpot.pl:298

wyim-pgl commented 6 years ago

Reference fasta window size was the problem.