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egonozer / Spine

Identification of conserved nucleotide core genome of bacteria and other small genome organisms
http://vfsmspineagent.fsm.northwestern.edu
GNU General Public License v3.0
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Error when prepare comb (fasta+gff) #6

Open Fusika1203 opened 1 month ago

Fusika1203 commented 1 month ago

Hello, I want to run core gene analysis with Spine locally and also want to include gff file, I use -f for genome_files.txt which containing paths to fasta file and their coresponding gff files. It is like that: /path/to/sequece1.fasta,path/to/fasta1.gff NIH-001-1 comb /path/to/sequece2.fasta,path/to/fasta2.gff NIH-001-2 comb And get this error: Use of uninitialized value $fileid in substitution (s///) at spine.pl line 408. Use of uninitialized value $fileid in substitution (s///) at spine.pl line 408. ERROR: All files must be given an ID Or I try another format for genome_files.txt and get some errors I want to ask that if I want to intergrate both fasta and gff files of same sequences at the same time to get annotation for CDS, what format should I prepare for genome_files.txt? Thank you in advanced and sorry if my expression is confusing

egonozer commented 1 month ago

Hi, I think you may have extra blank lines in your genome_files.txt file. Make sure to delete any empty lines from the file and try again. Also, make sure that you have tabs and not just single spaces in between the three entries in each line, otherwise the program can't tell the three entries apart.

Ayushi-verma30 commented 1 month ago

Hello, I am using spine for core gene analysis using command perl spine.pl -f input -g 10 where input has two genome files in fasta sequence and gff file . But i am getting an error ERROR: Couldn't run nucmer_backbone.pl: Please enter a valid list for option -g I added -g option also still the same error persists. Thanks in advance