Answers.Body: <p>Most likely your Augustus installation is not functioning properly. Did you install Augustus from source or using conda? I believe the conda version of Augustus is known to have some issues. </p>
  
  <p>Something worth trying: <a href="https://busco.ezlab.org/files/BUSCO_3_Ubuntu_Gnome_16.04.ova" rel="nofollow noreferrer">Running a complete busco install in a VM</a>. This image has all dependencies installed and properly configured.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-10T13:32:29.427Z
Answers.Text: It was installed via conda, the log output clearly shows the Anaconda being accessed for busco installation. Personally I'm surprised because Anaconda programs are very reliable, but that might just be the core installation (at least for  Mac OSX). Anyway its good advice to try a direct installation.
  
  Could you please point out what "some issues" might be?
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-10T20:57:52.887Z
Answers.Text: BUSCO worked with this Docker image: https://hub.docker.com/r/comics/busco I'll try again using the conda installation and point towards some issues but for the moment, I am happy I could run it in a Docker container.
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-11T17:00:02.097Z
Answers.Text: @MichaelG. you are right that is quite reliable in general. Augustus however, is quite tedious in it's installation (e.g. the location of the config file and the location of it's species training-sets). For example, the manual of [BRAKER](https://github.com/Gaius-Augustus/BRAKER#g2)(the automated gene annotation program) states: "Problems have been reported from users that tried to run BRAKER with AUGUSTUS releases maintained by third parties, i.e. Bioconda". They therefore recommend to install Augustus as distributed by the original developers
Answers.UserDisplayName: Jvstonebridge
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-11T17:00:36.880Z
Answers.Text: @charlesdarwin That's good to hear! Most likely the person that build that docker container did a correct installation of Augustus for you :)
Answers.UserDisplayName: Jvstonebridge
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-10T07:16:53.697Z
Answers.LastActivityDate: 2019-05-10T07:16:53.697Z
Answers.UserDisplayName: Jvstonebridge
Body: <p>I am working on a GNU/Linux machine. I have installed <a href="https://busco.ezlab.org/" rel="nofollow noreferrer">BUSCO</a> using conda. I have downloaded the nematode dataset <code>nematoda_odb9.tar.gz</code><a href="https://busco.ezlab.org/" rel="nofollow noreferrer">here</a>. I downloaded the reference sequence of <em>C. elegans</em> from <a href="https://www.ensembl.org/index.html" rel="nofollow noreferrer">Ensembl</a>. I then ran busco using the following command:</p>
  
  <p><code>run_busco --in Caenorhabditis_elegans.WBcel235.dna.toplevel.fa --cpu 1 --out busco --lineage_path ./nematoda_odb9/ --mode genome --force &gt; busco.o 2&gt; busco.e</code></p>
  
  <p>tblastn seems to have run properly. <code>run_busco/blast_output/tblastn_busco.tsv</code> contains lots of hits for many of the buscos.</p>
  
  <p>However, I have 982 "Missing BUSCOs".</p>
  
  <p>The file that contains logs and errors related to augustus (run_busco/augustus_output/augustus.log) contains:</p>
  
  <pre><code>Will create parameters for a EUKARYOTIC species!
  creating directory ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/ ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_parameters.cfg ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_weightmatrix.txt ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_metapars.cfg ...
  The necessary files for training BUSCO_busco_1395218643 have been created.
  Now, either run etraining or optimize_parameters.pl with --species=BUSCO_busco_1395218643.
  etraining quickly estimates the parameters from a file with training genes.
  optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.
  </code></pre>
  
  <p>It does not seem to contain any errors.</p>
  
  <p>I have the following error:</p>
  
  <p><code>Failed to open sequence file run_busco/augustus_output/extracted_proteins/EOG091H07ZC.faa.1</code> In fact, the folder <code>run_busco/augustus_output/extracted_proteins/</code> is empty.</p>
  
  <p>Anyone would know why I have no extracted proteins?</p>
  
Tags: <software-usage><hmmer><busco>
Title: BUSCO does not find buscos in reference sequence of C. elegans (technical problem)
ThreadText: # BUSCO does not find buscos in reference sequence of C. elegans (technical problem)
  
  (Asked by: username_0 on 2019-04-05)
  
  I am working on a GNU/Linux machine. I have installed [BUSCO](https://busco.ezlab.org/) using conda. I have downloaded the nematode dataset `nematoda_odb9.tar.gz`[here](https://busco.ezlab.org/). I downloaded the reference sequence of *C. elegans* from [Ensembl](https://www.ensembl.org/index.html). I then ran busco using the following command:
  
  `run_busco --in Caenorhabditis_elegans.WBcel235.dna.toplevel.fa --cpu 1 --out busco --lineage_path ./nematoda_odb9/ --mode genome --force > busco.o 2> busco.e`
  
  tblastn seems to have run properly. `run_busco/blast_output/tblastn_busco.tsv` contains lots of hits for many of the buscos.
  
  However, I have 982 "Missing BUSCOs".
  
  The file that contains logs and errors related to augustus (run\_busco/augustus\_output/augustus.log) contains:
  
  ```
  Will create parameters for a EUKARYOTIC species!
  creating directory ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/ ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_parameters.cfg ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_weightmatrix.txt ...
  creating ...anaconda/envs/busco3_0_2/config/species/BUSCO_busco_1395218643/BUSCO_busco_1395218643_metapars.cfg ...
  The necessary files for training BUSCO_busco_1395218643 have been created.
  Now, either run etraining or optimize_parameters.pl with --species=BUSCO_busco_1395218643.
  etraining quickly estimates the parameters from a file with training genes.
  optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.
  
  ```
  
  It does not seem to contain any errors.
  
  I have the following error:
  
  `Failed to open sequence file run_busco/augustus_output/extracted_proteins/EOG091H07ZC.faa.1` In fact, the folder `run_busco/augustus_output/extracted_proteins/` is empty.
  
  Anyone would know why I have no extracted proteins?
  
  **Tags:** software-usage, hmmer, busco
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-05-10. Score: 2
  
  Most likely your Augustus installation is not functioning properly. Did you install Augustus from source or using conda? I believe the conda version of Augustus is known to have some issues.
  
  Something worth trying: [Running a complete busco install in a VM](https://busco.ezlab.org/files/BUSCO_3_Ubuntu_Gnome_16.04.ova). This image has all dependencies installed and properly configured.
  
  > **Comments:**
  > **username_2**: It was installed via conda, the log output clearly shows the Anaconda being accessed for busco installation. Personally I'm surprised because Anaconda programs are very reliable, but that might just be the core installation (at least for  Mac OSX). Anyway its good advice to try a direct installation.  Could you please point out what "some issues" might be?  
  > **username_0**: BUSCO worked with this Docker image: https://hub.docker.com/r/comics/busco I'll try again using the conda installation and point towards some issues but for the moment, I am happy I could run it in a Docker container.  
  > **username_1**: @MichaelG. you are right that is quite reliable in general. Augustus however, is quite tedious in it's installation (e.g. the location of the config file and the location of it's species training-sets). For example, the manual of [BRAKER](https://github.com/Gaius-Augustus/BRAKER#g2)(the automated gene annotation program) states: "Problems have been reported from users that tried to run BRAKER with AUGUSTUS releases maintained by third parties, i.e. Bioconda". They therefore recommend to install Augustus as distributed by the original developers  
  > **username_1**: @charlesdarwin That's good to hear! Most likely the person that build that docker container did a correct installation of Augustus for you :)  
  
  ---
  
  