Medaka: unrecognized command 'tools' and samtools not found

Question

When trying to run medaka_consensus in ubuntu, I am getting the following error. I installed into a virtualenv to run on ubuntu.

(medaka) ubuntu:~/medaka$ medaka_consensus -i combined.fastq -d curated.fasta -t -o ~/medaka 10 -m r941_sup_plant_g610
TF_CPP_MIN_LOG_LEVEL is set to ‘3’
[main] unrecognized command ‘tools’
Attempting to automatically select model version.
WARNING: Failed to detect a model version, will use default: ‘’
Checking program versions
This is samtools 1.13
Using htslib 1.13+ds
Copyright (C) 2021 Genome Research Ltd.
Samtools compilation details:
    Features:       build=configure curses=yes
    CC:             gcc
    CPPFLAGS:       -frelease  -Wdate-time -D_FORTIFY_SOURCE=2
    CFLAGS:         -g -O2 -ffile-prefix-map=�BUILDPATH�=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
    LDFLAGS:        -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now
    HTSDIR:
    LIBS:
    CURSES_LIB:     -lcurses
HTSlib compilation details:
    Features:       build=configure plugins=yes, plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:: libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.1.1
    CC:             gcc
    CPPFLAGS:       -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2
    CFLAGS:         -g -O2 -ffile-prefix-map=/build/htslib-TQtOKr/htslib-1.13+ds=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden
    LDFLAGS:        -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden
HTSlib URL scheme handlers present:
    built-in:    preload, data, file
    crypt4gh-needed:     crypt4gh
    mem:         mem
Cannot import pyabpoa, some features may not be available.
Program    Version    Required   Pass
bcftools   1.13       1.11       True
bgzip      1.13+ds    1.11       True
minimap2   2.13       2.11       True
samtools   Not found  1.11       False
tabix      1.13+ds    1.11       True

I had been getting the error that samtools was not found, similar to above, but then I realized I had it in the wrong PATH. After that I wasn't getting the error until I tried to install tensorflow. I checked that the PATH for all files and other softwares are correct and that all softwares required are the correct version. I don't understand why it is not using the model I am feeding it and is instead saying "Failed to detect a model version, will use default" or why it is running samtools and then later saying it was not found. What could be causing these errors?