Augustus error

Question

[Shakunthala Natarajan]

I have obtained a protein hint file of a fungal genome using prothint in the .gff format. I am now using this as a hint file to run augustus. When I add the name of the extrinsic config file, and run augustus, the following error occurs:

./bin/augustus: ERROR
    FeatureCollection::readExtrinsicCFGFile: FeatureCollection::esource: invalid source key: #

Can someone please help me to resolve this issue for running augustus?

Thank you!

[Shakunthala Natarajan]

There was also another two lines of error along with the above error message. They are:

Unknown hint feature 'P'. Ignoring it. For a list of the 17 allowed features see the first column of the table in config/extrinsic/extrinsic.cfg.

unknown Feature Type: P

Answer 1

[Mensur Dlakic]

./bin/augustus: ERROR FeatureCollection::readExtrinsicCFGFile: FeatureCollection::esource: invalid source key: #

A literal interpretation of this error is that somewhere in your config or .gff file there is a # sign where it shouldn't be. Tough to say more without seeing what exact command you used, first several lines of the .gff file. You can save yourself some waiting time, and us the time it requires to write a follow-up question (basically, this message), by providing as much information about your problem as possible. For all the problems, providing the exact command is a basic minimum for troubleshooting, along with types of files and some file content.

[Shakunthala Natarajan]

Sure. I will add the exact commands I used clearly from now on. The command I used was:

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

[Mensur Dlakic]

Again,

that somewhere in your config or .gff file there is a # sign where it shouldn't be

How do we guess this without you showing us the contents of those files?

Three hours passed since you asked the original question and both of us wrote two messages apiece, yet I don't think we are any closer to answering your question.

For all the problems, providing the exact command is a basic minimum for troubleshooting, along with types of files and some file content.

Answer 2

[Shakunthala Natarajan]

Apologies. I missed that. I am new to these. Will do it properly henceforth. I searched my prothint_augustus.gff file for the character #. But the character # wasn't found in it. The extrinsic.cfg file had the following contents:

# 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
#