BUSCO does not find buscos in reference sequence of C. elegans (technical problem) 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 &gt; busco.o 2&gt; 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?
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.