text: user1075: I am working on a GNU/Linux machine. I have installed BUSCO using conda. I have downloaded the nematode dataset nematoda_odb9.tar.gzhere. I downloaded the reference sequence of C. elegans from Ensembl. 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?
  
  user4552: 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. This image has all dependencies installed and properly configured.
  
original_text: 1075: <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>
   4552: <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>
  