Hi,
I prepared the exon hint with cufflinks using my RNAseq data(convert cufflinks output .gtf file to .gff file with gtf2gff.pl in the scripts directory.).
Then I merged this exon hint with intron hint and repeat hint and ran augustus with this command:
Code: Select all
augustus --species=Myspecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W.cfg --alternatives-from-evidence=true --hintsfile=merged_hint.gff --allow_hinted_splicesites=atac genome.fa > output
Code: Select all
No source specified (e.g. by source=M in the last column)
Error in hint line: scaffoldXX_covXXX Cufflinks exon ddddddd ddddddd . . . gene_id "XXXX_dddddd"; transcript_id "XXXX_dddddd"; exon_number "d"; oId "CUFF.ddddd.d"; tss_id "TSSddddd";
…
Maybe you used spaces instead of tabulators?
I think this message means exon hint was not used for gene prediction.
What's wrong?