tried to add the hints.gff to the db:
~/p/drosophila/D_mel$ /home/TU/tuf29449/iw/Augustus/bin/load2sqlitedb --species=D_melanogaster --dbaccess=drosophila_anno.db dmel_main_chrs.hints.gff
I received this error:
Trying to open database drosophila_anno.db
Looks like dmel_main_chrs.hints.gff is in gff format.
Error in hint line: NC_004353.4 FlyBase start_codon 930 932 . + 0 gene_id "FBgn0267363"; gene_symbol "JYalpha"; transcript_id "FBtr0346692"; transcript_symbol "JYalpha-RB";
No source specified (e.g. by source=M in the last column)
Unknown hint feature 'start_codon'. Ignoring it. For a list of the 17 allowed features see the first column of the table in config/extrinsic/extrinsic.cfg.
insert failed on
NC_004353.4 FlyBase start_codon 930 932 0 + 0 src=? "1;1;0:0"
CHECK constraint failed: hints
jodyhey
commented
3 years ago
on linux 20.04, working on a set of drosophila genomes, following instructions pretty closely: https://bioinf.uni-greifswald.de/augustus/binaries/tutorial-cgp/de_novo.html#loadFa https://bioinf.uni-greifswald.de/augustus/binaries/tutorial-cgp/liftover.html
tried to add the hints.gff to the db: ~/p/drosophila/D_mel$ /home/TU/tuf29449/iw/Augustus/bin/load2sqlitedb --species=D_melanogaster --dbaccess=drosophila_anno.db dmel_main_chrs.hints.gff
I received this error: Trying to open database drosophila_anno.db Looks like dmel_main_chrs.hints.gff is in gff format. Error in hint line: NC_004353.4 FlyBase start_codon 930 932 . + 0 gene_id "FBgn0267363"; gene_symbol "JYalpha"; transcript_id "FBtr0346692"; transcript_symbol "JYalpha-RB"; No source specified (e.g. by source=M in the last column) Unknown hint feature 'start_codon'. Ignoring it. For a list of the 17 allowed features see the first column of the table in config/extrinsic/extrinsic.cfg. insert failed on NC_004353.4 FlyBase start_codon 930 932 0 + 0 src=? "1;1;0:0" CHECK constraint failed: hints
thanks for help