Processing on unannotated vcf in new environment about bayescmg HOT 2 CLOSED

conda create -n bayescmg

conda activate bayescmg

bash ~/bin/VarBayes/run.sh -v 17-10-13_ARUP-Marth-Subependymal_Heterotopia_Final_1511985898.vcf.gz -p 17-10-13_ARUP-Marth-Subependymal_Heterotopia.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 -t 0.01 -j 0.6 -y 0.1 -o 350 -e 0.1 -f ./
wget: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/libuuid.so.1: no version information available (required by wget)
--2020-03-15 10:50:08--  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)... 130.14.250.10, 2607:f220:41e:250::11
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.10|: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 ... 25088270
==> PASV ... done.    ==> RETR clinvar.vcf.gz ... done.
Length: 25088270 (24M) (unauthoritative)

100%[=========================================================================================================================================================================>] 25,088,270  21.2MB/s   in 1.1s   

2020-03-15 10:50:12 (21.2 MB/s) - ‘data/clinvar.grc37.vcf.gz’ saved [25088270]

wget: /uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/miniconda3/lib/libuuid.so.1: no version information available (required by wget)
--2020-03-15 10:50:12--  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)... 130.14.250.10, 2607:f220:41e:250::11
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.10|: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 ... 283593
==> PASV ... done.    ==> RETR clinvar.vcf.gz.tbi ... done.
Length: 283593 (277K) (unauthoritative)

100%[=========================================================================================================================================================================>] 283,593     1.00MB/s   in 0.3s   

2020-03-15 10:50:13 (1.00 MB/s) - ‘data/clinvar.grc37.vcf.gz.tbi’ saved [283593]

/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 131: vep: command not found
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 152: bgzip: command not found
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 153: tabix: command not found
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 156: externals/slivar/slivar: No such file or directory
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 162: vep: command not found
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 183: bgzip: command not found
/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/VarBayes/run.sh: line 184: tabix: command not found
python VarBayes.py -v data/slivar.tmp.vep.vcf.gz -f 17-10-13_ARUP-Marth-Subependymal_Heterotopia.ped -d ./ -c data/clinvar.grc37.vep.vcf.gz -e 0.1 -o 350 -p 0.1 -a 0.01 -r 0.6
python: can't open file 'VarBayes.py': [Errno 2] No such file or directory