updated the conda environment

conda-environment.yml

 name: strandseqnation
 channels:
   - bioconda
-  - conda-forge
-  - defaults
   - r
+  - defaults
+  - conda-forge
 dependencies:
-  - bcftools=1.9=h4da6232_0
-  - bioconductor-biobase=2.38.0=r341h219a75b_1
-  - bioconductor-biocgenerics=0.24.0=r341_1
-  - bioconductor-biocinstaller=1.28.0=r341_1
-  - bioconductor-biocparallel=1.12.0=r341h219a75b_1
-  - bioconductor-biostrings=2.46.0=r3.4.1_0
-  - bioconductor-bsgenome=1.46.0=r3.4.1_0
-  - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.1=r3.4.1_2
-  - bioconductor-complexheatmap=1.17.1=r3.4.1_0
-  - bioconductor-delayedarray=0.4.1=r3.4.1_0
-  - bioconductor-fastseg=1.24.0=r3.4.1_0
-  - bioconductor-genomeinfodb=1.14.0=r3.4.1_0
-  - bioconductor-genomeinfodbdata=1.1.0=r341_0
-  - bioconductor-genomicalignments=1.14.1=r3.4.1_0
-  - bioconductor-genomicranges=1.30.3=r3.4.1_0
-  - bioconductor-iranges=2.12.0=r3.4.1_0
-  - bioconductor-rsamtools=1.30.0=r3.4.1_0
-  - bioconductor-rtracklayer=1.38.3=r3.4.1_0
-  - bioconductor-s4vectors=0.16.0=r3.4.1_0
-  - bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
-  - bioconductor-xvector=0.18.0=r3.4.1_0
-  - bioconductor-zlibbioc=1.26.0=r341h470a237_0
-  - filechunkio=1.6=py36_0
-  - freebayes=1.2.0=py36h82df9c4_3
-  - ftputil=3.2=py36_0
-  - htslib=1.9=hc238db4_4
-  - libdeflate=1.0=h470a237_0
-  - parallel=20160622=1
-  - perl-threaded=5.22.0=13
-  - pyasn1-modules=0.0.5=py36_0
-  - pyfaidx=0.5.4.1=py_0
-  - pygraphviz=1.3.1=py36_0
-  - pysam=0.15.1=py36h0380709_0
-  - pysftp=0.2.9=py36_0
-  - pyvcf=0.6.8=py36_0
-  - r-data.table=1.11.6=r341hc070d10_0
-  - r-peer=1.3=r341h470a237_1
-  - rsa=3.1.4=py36_0
-  - samtools=1.9=h8ee4bcc_1
-  - snakemake=5.3.0=py36_1
-  - snakemake-minimal=5.3.0=py36_0
-  - urllib3=1.12=py36_0
-  - whatshap=0.17=py36h470a237_0
-  - xopen=0.3.2=py_1
-  - aioeasywebdav=2.2.0=py36_0
-  - aiohttp=3.4.3=py36h470a237_0
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_llvm
+  - _r-mutex=1.0.1=anacondar_1
+  - aioeasywebdav=2.4.0=py37_1000
+  - aiohttp=3.6.2=py37h516909a_0
   - appdirs=1.4.3=py_1
-  - asn1crypto=0.24.0=py36_1003
-  - async-timeout=3.0.0=py36_0
-  - attrs=18.2.0=py_0
-  - blas=1.1=openblas
-  - boost=1.68.0=py36h3e44d54_0
-  - boost-cpp=1.68.0=h3a22d5f_0
-  - boto3=1.7.84=py_0
-  - botocore=1.10.84=py_0
-  - bz2file=0.98=py_0
-  - bzip2=1.0.6=h470a237_2
-  - ca-certificates=2018.8.24=ha4d7672_0
-  - cachetools=2.1.0=py_0
-  - cairo=1.14.12=h276e583_5
-  - certifi=2018.8.24=py36_1001
-  - cffi=1.11.5=py36h5e8e0c9_1
-  - chardet=3.0.4=py36_1003
-  - cmake=3.12.3=h011004d_0
-  - configargparse=0.13.0=py_1
-  - cryptography=2.3.1=py36hdffb7b8_0
-  - cryptography-vectors=2.3.1=py36_1000
-  - curl=7.61.0=h93b3f91_2
-  - decorator=4.3.0=py_0
-  - docutils=0.14=py36_1001
-  - dropbox=7.3.1=py36_0
-  - expat=2.2.5=hfc679d8_2
-  - fontconfig=2.13.1=h65d0f4c_0
-  - freetype=2.9.1=h6debe1e_4
-  - gettext=0.19.8.1=h5e8e0c9_1
-  - glib=2.56.2=h464dc38_0
-  - google-auth=1.2.1=py_0
-  - google-auth-httplib2=0.0.2=py36_0
-  - google-cloud-core=0.24.1=py36_0
-  - google-cloud-storage=1.1.1=py36_0
-  - google-resumable-media=0.0.2=py36_0
-  - googleapis-common-protos=1.5.3=py_1
-  - graphite2=1.3.12=hfc679d8_1
-  - graphviz=2.38.0=h08bfae6_9
-  - gsl=2.2.1=blas_openblash47a8a8e_5
-  - harfbuzz=1.9.0=h04dbb29_1
-  - httplib2=0.11.3=py36_1001
-  - icu=58.2=hfc679d8_0
-  - idna=2.7=py36_1002
-  - idna_ssl=1.0.0=0
-  - jinja2=2.10=py_1
-  - jmespath=0.9.3=py_1
-  - jpeg=9c=h470a237_1
-  - jsonschema=2.6.0=py36_1002
-  - krb5=1.14.6=0
-  - libffi=3.2.1=hfc679d8_5
-  - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=7.2.0=hdf63c60_3
-  - libgfortran=3.0.0=1
-  - libiconv=1.15=h470a237_3
-  - libpng=1.6.35=ha92aebf_2
-  - libprotobuf=3.6.1=hd28b015_0
-  - libssh2=1.8.0=h5b517e9_2
-  - libstdcxx-ng=7.2.0=hdf63c60_3
-  - libtiff=4.0.9=he6b73bb_2
-  - libtool=2.4.6=h470a237_2
-  - libuuid=2.32.1=h470a237_2
-  - libuv=1.23.2=h470a237_0
-  - libxcb=1.13=h470a237_2
-  - libxml2=2.9.8=h422b904_5
-  - markupsafe=1.0=py36h470a237_1
-  - multidict=4.4.2=py36h470a237_0
-  - ncurses=6.1=hfc679d8_1
-  - networkx=2.2=py_1
-  - numpy=1.15.2=py36_blas_openblashd3ea46f_1
-  - openblas=0.2.20=8
-  - openssl=1.0.2p=h470a237_0
-  - pandas=0.23.4=py36hf8a1672_0
-  - pango=1.40.14=he752989_2
-  - paramiko=2.4.1=py36_0
-  - pcre=8.41=hfc679d8_3
-  - perl=5.26.2=h470a237_0
-  - pip=18.1=py36_1000
-  - pixman=0.34.0=h470a237_3
-  - prettytable=0.7.2=py_2
-  - protobuf=3.6.1=py36hfc679d8_1
-  - psutil=5.4.7=py36h470a237_1
-  - pthread-stubs=0.4=h470a237_1
-  - pyasn1=0.4.4=py_0
-  - pycparser=2.19=py_0
-  - pynacl=1.1.2=py36_0
-  - python=3.6.6=h5001a0f_0
-  - python-dateutil=2.7.3=py_0
-  - python-irodsclient=0.7.0=py_0
-  - pytz=2018.5=py_0
-  - pyyaml=3.13=py36h470a237_1
-  - r-assertthat=0.2.0=r341h6115d3f_1
-  - r-base=3.4.1=h4fe35fd_8
-  - r-bh=1.66.0_1=r341_1
-  - r-bindr=0.1.1=r341h6115d3f_1
-  - r-bindrcpp=0.2.2=r341h9d2a408_1
-  - r-bitops=1.0_6=r341hc070d10_2
-  - r-catools=1.17.1.1=r341h9d2a408_2
-  - r-circlize=0.4.4=r341_0
-  - r-cli=1.0.0=r341h6115d3f_1
-  - r-colorspace=1.3_2=r341hc070d10_2
-  - r-cowplot=0.9.3=r341h6115d3f_1
-  - r-crayon=1.3.4=r341h6115d3f_1
-  - r-curl=3.2=r341hc070d10_2
-  - r-devtools=1.13.6=r341h6115d3f_1
-  - r-dichromat=2.0_0=r3.4.1_0
-  - r-digest=0.6.16=r341hc070d10_1
-  - r-dplyr=0.7.6=r341h9d2a408_1
-  - r-fansi=0.3.0=r341hc070d10_0
-  - r-formatr=1.5=r341h6115d3f_1
-  - r-futile.logger=1.4.3=r341h6115d3f_1
-  - r-futile.options=1.0.1=r341h6115d3f_0
-  - r-gdata=2.18.0=r341h6115d3f_1
-  - r-getoptlong=0.1.7=r341_0
-  - r-ggplot2=2.2.1=r3.4.1_0
-  - r-git2r=0.23.0=r341h1b3b946_0
-  - r-globaloptions=0.1.0=r341_1
-  - r-glue=1.3.0=r341h470a237_2
-  - r-gplots=3.0.1=r341h6115d3f_1
-  - r-gridextra=2.3=r341h6115d3f_1
-  - r-gtable=0.2.0=r341h6115d3f_1
-  - r-gtools=3.8.1=r341hc070d10_2
-  - r-hexbin=1.27.2=r341h364d78e_2
-  - r-httr=1.3.1=r341h6115d3f_1
-  - r-jsonlite=1.5=r341hc070d10_2
-  - r-kernsmooth=2.23_15=r341h364d78e_2
-  - r-labeling=0.3=r341h6115d3f_1
-  - r-lambda.r=1.2.3=r341h6115d3f_0
-  - r-lattice=0.20_35=r341hc070d10_0
-  - r-lazyeval=0.2.1=r341hc070d10_2
-  - r-magrittr=1.5=r341h6115d3f_1
-  - r-mass=7.3_50=r341hc070d10_2
-  - r-matrix=1.2_14=r341hc070d10_2
-  - r-matrixstats=0.54.0=r341hc070d10_0
-  - r-mc2d=0.1_18=r3.4.1_0
-  - r-memoise=1.1.0=r341h6115d3f_1
-  - r-mime=0.5=r341hc070d10_2
-  - r-munsell=0.5.0=r341h6115d3f_1
-  - r-mvtnorm=1.0_8=r341h364d78e_0
-  - r-openssl=1.0.2=r341h9f97512_0
-  - r-pheatmap=1.0.10=r341h6115d3f_1
-  - r-pillar=1.3.0=r341h6115d3f_0
-  - r-pkgconfig=2.0.2=r341h6115d3f_1
-  - r-plogr=0.2.0=r341h6115d3f_1
-  - r-plyr=1.8.4=r341h9d2a408_2
-  - r-purrr=0.2.5=r341hc070d10_1
-  - r-r6=2.2.2=r341h6115d3f_1
-  - r-rcolorbrewer=1.1_2=r341h6115d3f_1
-  - r-rcpp=0.12.17=r341h9d2a408_2
-  - r-rcurl=1.95_4.11=r341h86b9717_2
-  - r-reshape2=1.4.3=r341h9d2a408_2
-  - r-rjson=0.2.20=r341h9d2a408_0
-  - r-rlang=0.2.2=r341h470a237_0
-  - r-rstudioapi=0.7=r341h6115d3f_1
-  - r-scales=1.0.0=r341h9d2a408_1
-  - r-shape=1.4.4=r341_1
-  - r-snow=0.4_3=r341h6115d3f_0
-  - r-stringi=1.2.4=r341h9d2a408_1
-  - r-stringr=1.3.1=r341h6115d3f_1
-  - r-tibble=1.4.2=r341hc070d10_2
-  - r-tidyselect=0.2.4=r341h9d2a408_2
-  - r-utf8=1.1.4=r341hc070d10_0
-  - r-viridislite=0.3.0=r341h6115d3f_1
-  - r-whisker=0.3_2=r341h6115d3f_1
-  - r-withr=2.1.2=r341h6115d3f_0
-  - r-xml=3.98_1.16=r341hc070d10_0
-  - ratelimiter=1.2.0=py36_1000
-  - readline=7.0=haf1bffa_1
-  - requests=2.13.0=py36_0
-  - rhash=1.3.6=h470a237_1
-  - s3transfer=0.1.13=py36_1001
-  - scipy=1.1.0=py36_blas_openblash7943236_201
-  - setuptools=40.4.3=py36_0
-  - six=1.11.0=py36_1001
-  - sqlite=3.25.2=hb1c47c0_0
-  - tk=8.6.8=ha92aebf_0
-  - wheel=0.32.1=py36_0
-  - wrapt=1.10.11=py36h470a237_1
+  - async-timeout=3.0.1=py_1000
+  - attrs=19.3.0=py_0
+  - bcftools=1.10.2=hd2cd319_0
+  - bcrypt=3.1.7=py37h516909a_0
+  - binutils_impl_linux-64=2.33.1=h53a641e_8
+  - binutils_linux-64=2.33.1=h9595d00_17
+  - bioconductor-biobase=2.42.0=r351h14c3975_1
+  - bioconductor-biocgenerics=0.28.0=r351_1
+  - bioconductor-biocinstaller=1.32.1=r351_0
+  - bioconductor-biocparallel=1.16.6=r351h1c2f66e_0
+  - bioconductor-biostrings=2.50.2=r351h14c3975_0
+  - bioconductor-bsgenome=1.50.0=r351_0
+  - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.1=r351_5
+  - bioconductor-complexheatmap=2.0.0=r351_0
+  - bioconductor-delayedarray=0.8.0=r351h14c3975_0
+  - bioconductor-fastseg=1.28.0=r351hf484d3e_1
+  - bioconductor-genomeinfodb=1.18.1=r351_0
+  - bioconductor-genomeinfodbdata=1.2.1=r351_0
+  - bioconductor-genomicalignments=1.18.1=r351h14c3975_0
+  - bioconductor-genomicranges=1.34.0=r351h14c3975_0
+  - bioconductor-iranges=2.16.0=r351h14c3975_0
+  - bioconductor-rsamtools=1.34.0=r351hf484d3e_0
+  - bioconductor-rtracklayer=1.42.1=r351h9d9f1b6_1
+  - bioconductor-s4vectors=0.20.1=r351h14c3975_0
+  - bioconductor-summarizedexperiment=1.12.0=r351_0
+  - bioconductor-xvector=0.22.0=r351h14c3975_0
+  - bioconductor-zlibbioc=1.28.0=r351h14c3975_0
+  - biopython=1.76=py37h516909a_0
+  - boost=1.72.0=py37h9de70de_0
+  - boost-cpp=1.72.0=h8e57a91_0
+  - boto3=1.12.17=py_0
+  - botocore=1.15.17=py_0
+  - bwidget=1.9.14=0
+  - bzip2=1.0.8=h516909a_2
+  - ca-certificates=2020.1.1=0
+  - cachetools=3.1.1=py_0
+  - cairo=1.16.0=hfb77d84_1002
+  - certifi=2019.11.28=py37_0
+  - cffi=1.14.0=py37hd463f26_0
+  - chardet=3.0.4=py37_1003
+  - cmake=3.16.4=h28c56e5_0
+  - configargparse=1.0=py_0
+  - cryptography=2.8=py37h72c5cf5_1
+  - curl=7.68.0=hf8cf82a_0
+  - datrie=0.8=py37h516909a_0
+  - decorator=4.4.2=py_0
+  - docutils=0.15.2=py37_0
+  - dropbox=9.4.0=py_0
+  - expat=2.2.9=he1b5a44_2
+  - fftw=3.3.8=nompi_h7f3a6c3_1110
+  - filechunkio=1.8=py_2
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=2.001=hab24e00_0
+  - font-ttf-source-code-pro=2.030=hab24e00_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.13.1=h86ecdb6_1001
+  - fonts-conda-forge=1=0
+  - freebayes=1.3.2=py37hc088bd4_0
+  - freetype=2.10.0=he983fc9_1
+  - fribidi=1.0.5=h516909a_1002
+  - ftputil=3.4=py_0
+  - gcc_impl_linux-64=7.3.0=hd420e75_5
+  - gcc_linux-64=7.3.0=h553295d_17
+  - gdk-pixbuf=2.38.2=h3f25603_0
+  - gettext=0.19.8.1=hc5be6a0_1002
+  - gfortran_impl_linux-64=7.3.0=hdf63c60_5
+  - gfortran_linux-64=7.3.0=h553295d_17
+  - ghostscript=9.22=hf484d3e_1001
+  - giflib=5.2.1=h516909a_2
+  - gitdb=4.0.2=py_0
+  - gitpython=3.1.0=py_0
+  - glib=2.58.3=py37h6f030ca_1002
+  - gobject-introspection=1.58.2=py37h5503ade_1002
+  - google-api-core=1.16.0=py37_1
+  - google-auth=1.11.2=py_0
+  - google-cloud-core=1.3.0=py_0
+  - google-cloud-storage=1.26.0=py_0
+  - google-resumable-media=0.5.0=py_1
+  - googleapis-common-protos=1.51.0=py37_1
+  - graphite2=1.3.13=hf484d3e_1000
+  - graphviz=2.42.3=h0511662_0
+  - gsl=2.5=h294904e_1
+  - gxx_impl_linux-64=7.3.0=hdf63c60_5
+  - gxx_linux-64=7.3.0=h553295d_17
+  - harfbuzz=2.4.0=h9f30f68_3
+  - htslib=1.10.2=h78d89cc_0
+  - icu=64.2=he1b5a44_1
+  - idna=2.9=py_1
+  - imagemagick=7.0.10_0=pl526ha9fe49d_0
+  - importlib_metadata=1.5.0=py37_0
+  - ipython_genutils=0.2.0=py_1
+  - jbig=2.1=h14c3975_2001
+  - jinja2=2.11.1=py_0
+  - jmespath=0.9.5=py_0
+  - jpeg=9c=h14c3975_1001
+  - jsonschema=3.2.0=py37_0
+  - jupyter_core=4.6.3=py37_0
+  - krb5=1.16.4=h2fd8d38_0
+  - ld_impl_linux-64=2.33.1=h53a641e_8
+  - libblas=3.8.0=15_openblas
+  - libcblas=3.8.0=15_openblas
+  - libcroco=0.6.13=h8d621e5_0
+  - libcurl=7.68.0=hda55be3_0
+  - libdeflate=1.3=h516909a_0
+  - libedit=3.1.20170329=hf8c457e_1001
+  - libffi=3.2.1=he1b5a44_1006
+  - libgcc-ng=9.2.0=h24d8f2e_2
+  - libgfortran-ng=7.3.0=hdf63c60_5
+  - libgomp=9.2.0=h24d8f2e_2
+  - libiconv=1.15=h516909a_1005
+  - libidn2=2.3.0=h516909a_0
+  - liblapack=3.8.0=15_openblas
+  - libopenblas=0.3.8=h5ec1e0e_0
+  - libpng=1.6.37=hed695b0_0
+  - libprotobuf=3.11.4=h8b12597_0
+  - librsvg=2.46.4=h33a7fed_0
+  - libssh2=1.8.2=h22169c7_2
+  - libstdcxx-ng=9.2.0=hdf63c60_2
+  - libtiff=4.1.0=hc3755c2_3
+  - libtool=2.4.6=h14c3975_1002
+  - libunistring=0.9.10=h14c3975_0
+  - libuuid=2.32.1=h14c3975_1000
+  - libuv=1.34.0=h516909a_0
+  - libwebp=1.0.2=h56121f0_5
+  - libxcb=1.13=h14c3975_1002
+  - libxml2=2.9.10=hee79883_0
+  - llvm-openmp=9.0.1=hc9558a2_2
+  - lz4-c=1.8.3=he1b5a44_1001
+  - make=4.3=h516909a_0
+  - markupsafe=1.1.1=py37h516909a_0
+  - multidict=4.7.5=py37h516909a_0
+  - nbformat=5.0.4=py_0
+  - ncurses=6.1=hf484d3e_1002
+  - networkx=2.4=py_1
+  - numpy=1.18.1=py37h95a1406_0
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+prefix: /MMCI/TM/scratch/maryam/anaconda3/envs/strandseqnation-2020-03-09
+