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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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Prodigal v2.6.3 no stop_type output #91

Open Jemimacat opened 2 years ago

Jemimacat commented 2 years ago

Hi, I'm testing prodigal (v2.6.3 with Ubuntu) to find ORF in MAG files. Accroding to the documentation I should have got not only "start_type" but also "stop_type" information. But no such things. I don't know why? Could somebody give me some advice?

I also try to install by apt command or source code, but still not work for the "stop_type".

ID=1_1;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.382;conf=100.00;score=172.64;cscore=164.73;sscore=7.91;rscore=5.75;uscore=0.29;tscore=1.88;

althonos commented 1 year ago

Hi @Jemimacat

The stop_type is not recorded because it's always either a STOP codon, or the gene running off the contig edge, which can be checked with the partial flag (00: gene with a START and STOP codon, 01 or 10: gene running off the edge).