I would strongly recommend to use Bioconda instead of compiling. It is one of the channels ("distributors of packages") in Anaconda Cloud which is basically a package source for conda.
In short - conda allows you to create virtual environments isolated from system and to install various precompiled software packages with one command (so, by the way, you can ...
The manual says fields in a tabular output file are space-delimited. It should be fairly straightforward to load a space-delimited file in pandas.
From the manual:
--tblout <f> Save a simple tabular (space-delimited) file summarizing the per-target output, with one data line per homologous target model found.
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.
I don't have time to give you a polished fully functional version but this will get you started. The next step will be a bit harder as you will need to capture the start of the first CDS in the chunk and end of the last CDS instead of just hardcoding as I have here.
fout = open('/path/first3.gbk','w')
for record in SeqIO.parse('/path/NC_000962.3.final.gbk','...
This time conda uninstall hmmer in the root environment did the job. The sequence of commands that led me there is shown below. Thanks Devon Ryan.
conda list | grep hmmer
hmmer 3.1b2 3 bioconda
conda uninstall hmmer
Solving environment: done
## Package Plan ##
environment location: /Users/user/anaconda