Intron not within scaffold warnings

[francicco]

Hi,

I'm getting a lot of these warnings:

Warning: intron not within scaffold ([824483-824773], 0)
Warning: intron not within scaffold ([824484-824774], 1970381097)
Warning: intron not within scaffold ([824906-826922], -1519660128)
Warning: intron not within scaffold ([824907-826923], 1970381097)
Warning: intron not within scaffold ([827068-854449], 0)
Warning: intron not within scaffold ([854602-856488], 1970381097)

This is the commad line:

cufflinks -o $STRINGTIELABEL.cufflinks.out -p $THREADS -g augustus.Ref.$AUGREFSPECIES.ValidBraker.stringtie.gff -L $STRINGTIELABEL \
                                --library-type fr-firststrand --verbose --no-update-check $SPECIES.RNAonAnn.${ALIGNER}.$lib.Aligned.sortedByCoord.out.bam

Why do I get those?
Thanks a lot
Francesco

[ari7cr]

Hi Francesco, I currently have the same issue. Did you ever manage to find out why?