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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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misformatted lines in gff output #46

Closed charlottewright closed 1 year ago

charlottewright commented 1 year ago

Hi Toby!

I've been analysing the results from running the latest version of earlGrey and ran into an error when using bedtools coverage with the final gff made by Earl Grey (found in X_summaryFiles).

The error from running bedtools coverage -a species.seqlen.bed -b species.repeats.gff is:

Error: Invalid record in file species.repeats.gff. Record is LR990257.1 RepeatMasker Unknown 66015 65838 500 - . TSTART=2;TEND=63;ID=RND-1_FAMILY-358;SHORTTE=T

I believe this is because Bedtools expects gffs to be formatted to always have a start coordinate smaller than the end format, which is conventional for gffs. It would be great if this could be fixed so that gffs are consistent.

Best wishes,

Charlotte

TobyBaril commented 1 year ago

Hi Charlotte,

This definitely should not be the case! I've added some more failsafes to ensure some GFFs don't slip through - the updates have been committed to the main branch