All the three test steps were done. But, error occurred when i use my transcripts in step 2. I have reference genome, so my command was:
FEELnc_codpot.pl -i step1_PtrLnc.gtf -a Ptr.cds.all.fa -l Ptr.lncrnas.gtf -g Populus_trichocarpa.JGI2.0.dna.toplevel.chr.nocaff.fa -o step2_out --outdir=./FEElnc
I also tried command: FEELnc_codpot.pl -i step1_PtrLnc.gtf -a Ptr.cds.all.fa -g Populus_trichocarpa.JGI2.0.dna.toplevel.chr.nocaff.fa --mode=intergenic -l Ptr.lncrnas.gtf
All get Error below:
Your input GTF file 'Populus_trichocarpa_lncrnas.gtf' contains 4322 transcripts
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 18835764 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::DB::IndexedBase::_check_linelength /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:744
STACK: Bio::DB::Fasta::_calculate_offsets /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/Fasta.pm:175
STACK: Bio::DB::IndexedBase::_index_files /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:648
STACK: Bio::DB::IndexedBase::index_file /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:484
STACK: Bio::DB::IndexedBase::new /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:364
STACK: ExtractFromFeature::feature2seq /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/ExtractFromFeature.pm:399
STACK: ExtractCdnaOrf::CreateORFcDNAFromGTF /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/ExtractCdnaOrf.pm:303
STACK: /Data/Yexx/feelnc/bin/FEELnc_codpot.pl:322
So tell me where did we go wrong?
Thanks for your help!
All the three test steps were done. But, error occurred when i use my transcripts in step 2. I have reference genome, so my command was: FEELnc_codpot.pl -i step1_PtrLnc.gtf -a Ptr.cds.all.fa -l Ptr.lncrnas.gtf -g Populus_trichocarpa.JGI2.0.dna.toplevel.chr.nocaff.fa -o step2_out --outdir=./FEElnc
I also tried command: FEELnc_codpot.pl -i step1_PtrLnc.gtf -a Ptr.cds.all.fa -g Populus_trichocarpa.JGI2.0.dna.toplevel.chr.nocaff.fa --mode=intergenic -l Ptr.lncrnas.gtf All get Error below: Your input GTF file 'Populus_trichocarpa_lncrnas.gtf' contains 4322 transcripts
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 18835764 chars. STACK: Error::throw STACK: Bio::Root::Root::throw /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::DB::IndexedBase::_check_linelength /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:744 STACK: Bio::DB::Fasta::_calculate_offsets /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/Fasta.pm:175 STACK: Bio::DB::IndexedBase::_index_files /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:648 STACK: Bio::DB::IndexedBase::index_file /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:484 STACK: Bio::DB::IndexedBase::new /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:364 STACK: ExtractFromFeature::feature2seq /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/ExtractFromFeature.pm:399 STACK: ExtractCdnaOrf::CreateORFcDNAFromGTF /Data/Yexx/feelnc/lib/perl5/site_perl/5.22.0/ExtractCdnaOrf.pm:303 STACK: /Data/Yexx/feelnc/bin/FEELnc_codpot.pl:322
So tell me where did we go wrong? Thanks for your help!