Using Prothint output in augustus

Question

[Shakunthala Natarajan]

I have obtained the prothint_augustus.gff file from prothint. I used it for gene prediction with augustus. But an error shows up as:

Unknown hint feature 'P'. Ignoring it. For a list of 17 allowed features see, /config/extrinsic.cfg. The command I used to run augustus was:

augustus --hintsfile=prothint_augustus.gff --extrinsicCfgfile=extrinsic.cfg --species=species_name genome.fasta > output.gff

Is augustus ignoring my protein hints? Should I call this feature type in any other manner? Please help!

PS: Contents in my extrinsic config file were as follows:

extrinsic information configuration file for AUGUSTUS

protein hints

include with --extrinsicCfgFile=filename

date: 16.10.2007

Mario Stanke ([e-mail])

source of extrinsic information:

M manual anchor (required)

P protein database hit

E est database hit

C combined est/protein database hit

D Dialign

R retroposed genes

T transMapped refSeqs

[SOURCES] M RM P stop tts dss tss ass exon exonpart intron CDSpart intronpart CDS UTRpart UTR irpart nonexonpart genicpart

individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set

and the whole hint group is disregarded when one hint in it is unsatisfiable.

1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for

hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.

# [SOURCE-PARAMETERS]

feature bonus malus gradelevelcolumns

# 1 1

#

the gradelevel colums have the following format for each source

sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot

[GENERAL] start 1 0.3 M 1 1e+100 P 1 1000 stop 1 0.3 M 1 1e+100 P 1 1000 tss 1 1 M 1 1e+100 P 1 1 tts 1 1 M 1 1e+100 P 1 1 ass 1 0.8 M 1 1e+100 P 1 300 dss 1 0.8 M 1 1e+100 P 1 300 exonpart 1 1 M 1 1e+100 P 1 1 exon 1 1 M 1 1e+100 P 1 1 intronpart 1 1 M 1 1e+100 P 1 1 intron 1 1 M 1 1e+100 P 1 1 CDSpart 1 .995 M 1 1e+100 P 1 100
CDS 1 0.3 M 1 1e+100 P 1 1e4 UTRpart 1 1 M 1 1e+100 P 1 1 UTR 1 1 M 1 1e+100 P 1 1 irpart 1 1 M 1 1e+100 P 1 1 nonexonpart 1 1 M 1 1e+100 P 1 1 genicpart 1 1 M 1 1e+100 P 1 1

#

Explanation: see original extrinsic.cfg file

#