FEELnc_codpot.pl -i candidate_lncRNA.gtf -a stringtie_merged.gtf -g /mnt/data1/project/HYHjellyfish20230508/0_genome.nextpolish/genome.nextpolish.fasta --mode=intergenic
Possible precedence issue with control flow operator at /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
You do not have specified a maximum number mRNAs transcripts for the training. Use all the annotation, can be long...
You do not have specified a maximum number lncRNA transcripts for the training. Use all the annotation, can be long...
> Extract ORFs/cDNAs for mRNAs from a GTF file
Parsing file 'stringtie_merged.gtf'...
Parse input file: [----------------------------------------------------------------------------------------------------]
Your input GTF file 'stringtie_merged.gtf' contains *125672* transcripts
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the file must be less than 65,536 characters. Line 322 is 16157994 chars.
**STACK: Error::throw**
STACK: Bio::Root::Root::throw /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::DB::IndexedBase::_check_linelength /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757
STACK: Bio::DB::Fasta::_calculate_offsets /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/Fasta.pm:227
STACK: Bio::DB::IndexedBase::_index_files /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:659
STACK: Bio::DB::IndexedBase::index_file /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:487
STACK: Bio::DB::IndexedBase::new /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:364
STACK: ExtractFromFeature::feature2seq /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/ExtractFromFeature.pm:399
STACK: ExtractCdnaOrf::CreateORFcDNAFromGTF /mnt/data/software/miniconda3/envs/feelnc/lib/site_perl/5.26.2/ExtractCdnaOrf.pm:303
STACK: /mnt/data/software/miniconda3/envs/feelnc/bin/FEELnc_codpot.pl:298
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what's wrong? Could you help me? Thanks for your help!
my command line:
what's wrong? Could you help me? Thanks for your help!