run.sh crashes even with all necessary components in PATH about bayescmg HOT 3 CLOSED

$ bash ~/bin/bAyesCMG/run.sh -v 18-08-03_VAR-Marth-PND_Final_1533364009.vcf.gz -p 18-08-03_VAR-Marth-PND.ped -r /scratch/ucgd/lustre/work/u0691312/reference/ucgd_reference/GRCh37/human_g1k_v37_decoy_phix.fasta -c -g /scratch/ucgd/lustre/work/u0691312/reference/slivar.gnomad.hg37.zip -d /scratch/ucgd/lustre/work/u0691312/reference/ensembl/ -u /scratch/ucgd/lustre/work/u0691312/reference/ensembl/Plugins/ -l /scratch/ucgd/lustre/work/u0691312/reference/ensembl/Plugins/revel_all_chromosomes_vep.tsv.gz -f 18-08-03_VAR-Marth-PND_Final_1533364009.vcf.gz_runme.vcf.gz

wget: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/libuuid.so.1: no version information available (required by wget)
--2020-04-20 11:41:21--  ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz
           => ‘data/clinvar.grc37.vcf.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::7
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/clinvar/vcf_GRCh37 ... done.
==> SIZE clinvar.vcf.gz ... 26624885
==> PASV ... done.    ==> RETR clinvar.vcf.gz ... done.
Length: 26624885 (25M) (unauthoritative)

100%[=====================================================================================================================================================================>] 26,624,885  22.9MB/s   in 1.1s   

2020-04-20 11:41:23 (22.9 MB/s) - ‘data/clinvar.grc37.vcf.gz’ saved [26624885]

wget: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/libuuid.so.1: no version information available (required by wget)
--2020-04-20 11:41:23--  ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz.tbi
           => ‘data/clinvar.grc37.vcf.gz.tbi’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::7
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/clinvar/vcf_GRCh37 ... done.
==> SIZE clinvar.vcf.gz.tbi ... 285247
==> PASV ... done.    ==> RETR clinvar.vcf.gz.tbi ... done.
Length: 285247 (279K) (unauthoritative)

100%[=====================================================================================================================================================================>] 285,247     1.24MB/s   in 0.2s   

2020-04-20 11:41:24 (1.24 MB/s) - ‘data/clinvar.grc37.vcf.gz.tbi’ saved [285247]

Possible precedence issue with control flow operator at /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

gzip: stdout: Broken pipe
[bgzip] No such file or directory: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/clinvar.grc37.vep.vcf
open: No such file or directory
[tabix] was bgzip used to compress this file? /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/clinvar.grc37.vep.vcf.gz
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/run.sh: line 162: externals/slivar/slivar: No such file or directory
Possible precedence issue with control flow operator at /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

-------------------- EXCEPTION --------------------
MSG: ERROR: File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/slivar.tmp" does not exist

STACK Bio::EnsEMBL::VEP::Parser::file /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Parser.pm:231
STACK Bio::EnsEMBL::VEP::Parser::new /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Parser.pm:125
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:791
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:818
STACK Bio::EnsEMBL::VEP::Runner::init /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:131
STACK Bio::EnsEMBL::VEP::Runner::run /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/share/ensembl-vep-99.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/bin/vep:224
Date (localtime)    = Mon Apr 20 11:54:06 2020
Ensembl API version = 99
---------------------------------------------------
[bgzip] No such file or directory: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/slivar.tmp.vep.vcf
open: No such file or directory
[tabix] was bgzip used to compress this file? /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/slivar.tmp.vep.vcf.gz
python /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/bAyesCMG.py -v /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/slivar.tmp.vep.vcf.gz -f 18-08-03_VAR-Marth-PND.ped -d 18-08-03_VAR-Marth-PND_Final_1533364009.vcf.gz_runme.vcf.gz -c /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/data/clinvar.grc37.vep.vcf.gz -e 2.0 -o 350 -p 0.1 -a 0.01 -r 0.6
Traceback (most recent call last):
  File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/bAyesCMG/bAyesCMG.py", line 13, in <module>
    import urllib.request
ImportError: No module named request