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PombertLab / SYNY

The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
MIT License
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gff3_to_gbff.pl fails #8

Open jacob-israel opened 2 hours ago

jacob-israel commented 2 hours ago

operating system : Ubuntu Server 24.04 LTS all dependencies for SYNY are already installed shell command:

ka@prot:~$ /data2TB/apps/SYNY/Utils/gff3_to_gbff.pl -f $HOME/Documents/Tricho/syri/Tatroviridev3_lessctgs.fasta -g $HOME/Documents/Tricho/syri/Tatroviride_lessctgs.gff3

when I run the script gff3_to_gbff.pl with the fasta file and the gff3 file as parameters, the script fails and the following error appears

Use of uninitialized value $gff3 in pattern match (m//) at /data2TB/apps/SYNY/Utils/gff3_to_gbff.pl line 168, line 451890. Use of uninitialized value $gff3 in open at /data2TB/apps/SYNY/Utils/gff3_to_gbff.pl line 171, line 451890. Use of uninitialized value $gff3 in concatenation (.) or string at /data2TB/apps/SYNY/Utils/gff3_to_gbff.pl line 171, line 451890. Can't read: No such file or directory

what could be the problem?

thank you so much

Jacob

Pombert-JF commented 2 hours ago

gff3_to_gbff.pl was tested with GFF3 files from NCBI. If the format of your GFF3 file differs, that would cause parsing issues. Can you paste a small section from it so that I can look at it?