Manta SV caller: I can't find a file in the path specified by the user guide
The --config file option for Manta can be used to override the defaults in the global config file. If you type configManta.py -h, you'll see where the global config file has been installed. For me, it's here:
/home/steve/miniconda3/envs/manta/share/manta-1.6.0-1/bin/configManta.py.ini

So the command in your log file takes a specific config file installed into:
/opt/illumina/Isis/2.6.25.18/...

I suspect 'Isis' is a reference to Illumina's analysis tool 'IsisRNA'. Papers that mention Illumina's 'RnaReadCounter' tool, say that it is part of the internal analysis tool 'IsisRNA'. Because it's one of Illumina's in-house tools, I think you'd need to contact Illumina support to get a copy. I would only do this though if you need to reproduce exactly as per the command in your log file. If you only need to roughly reproduce the output, the defaults in the global config file are probably fine.