hint groups never obeyed
Posted: Thu Nov 19, 2015 5:09 pm
Originally posted in the old forum by EJ Blom on 10.10.2014 - 14:00
Dear Augustus developers,
I noticed something strange. I am performing a de novo gene prediction analysis on a plant genome. Since another genome was already published in the public domain, I mapped the predicted proteins from that analysis on my own genome using exonerate. Next I created hints from the exonerate out. The resulting file looks like this:
Scaffold0000001 xnt2h CDSpart 3836352 3836419 . + . src=P;grp=prot86786_cds;pri=4
Scaffold0000001 xnt2h intron 3836435 3842304 . + . src=P;grp=prot86786_cds;pri=4
For the config file, I used: extrinsic.MP.cfg
Although I have many 100% mappings (according to exonerate), my hints never get incorporated into my prediction.
First all matching hints get thrown out:
Delete group HintGroup prot64455_cds, 56065-6653123, mult= 1, priority= 4 75 features
Delete group HintGroup prot125425_cds, 57671-6319842, mult= 1, priority= 4 6 features
Delete group HintGroup prot125424_cds, 57671-6319842, mult= 1, priority= 4 6 features
which is reflected by later messages:
incompatible hint groups: 1
P: 1 (prot106446_cds)
and
hint groups fully obeyed: 0
This is how I run Augustus
$AUGUSTUS --species=plant --protein=on --codingseq=on --progress=true --gff3=on --alternatives-from-evidence=false --hintsfile=$ HINTS --alternatives-from-sampling=false --extrinsicCfgFile=$EXCFFILE $GENOME_PART > $PREDICTED_GENES;
Perhaps the option --alternatives-from-evidence=false disables the integration of hints? I've used this option in order to obtain only the longest predicted gene.
Thanks in advance,
Best
EJ Blom
Dear Augustus developers,
I noticed something strange. I am performing a de novo gene prediction analysis on a plant genome. Since another genome was already published in the public domain, I mapped the predicted proteins from that analysis on my own genome using exonerate. Next I created hints from the exonerate out. The resulting file looks like this:
Scaffold0000001 xnt2h CDSpart 3836352 3836419 . + . src=P;grp=prot86786_cds;pri=4
Scaffold0000001 xnt2h intron 3836435 3842304 . + . src=P;grp=prot86786_cds;pri=4
For the config file, I used: extrinsic.MP.cfg
Although I have many 100% mappings (according to exonerate), my hints never get incorporated into my prediction.
First all matching hints get thrown out:
Delete group HintGroup prot64455_cds, 56065-6653123, mult= 1, priority= 4 75 features
Delete group HintGroup prot125425_cds, 57671-6319842, mult= 1, priority= 4 6 features
Delete group HintGroup prot125424_cds, 57671-6319842, mult= 1, priority= 4 6 features
which is reflected by later messages:
incompatible hint groups: 1
P: 1 (prot106446_cds)
and
hint groups fully obeyed: 0
This is how I run Augustus
$AUGUSTUS --species=plant --protein=on --codingseq=on --progress=true --gff3=on --alternatives-from-evidence=false --hintsfile=$ HINTS --alternatives-from-sampling=false --extrinsicCfgFile=$EXCFFILE $GENOME_PART > $PREDICTED_GENES;
Perhaps the option --alternatives-from-evidence=false disables the integration of hints? I've used this option in order to obtain only the longest predicted gene.
Thanks in advance,
Best
EJ Blom