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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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mosdepth not found due to dependency issue #7

Open ashrosewood opened 4 years ago

ashrosewood commented 4 years ago

I recently tried your workflow, and found mosdepth was crashing due to a dependency issue. I was able to fix it by providing the versions that you have listed on the Structural variation analysis page on the Nanopore Community page:

channels:
    - bioconda
    - conda-forge
    - r
dependencies:
    - snakemake-minimal
    - minimap2=2.17
    - sniffles=1.0.11
    - samtools=1.9
    - nanofilt
    - nanoplot
    - pybedtools=0.8.0
    - bedtools=2.29.0
    - bcftools=1.9
    - pysam
    - scipy
    - tqdm
    - vcftools=0.1.16
    - vcflib
    - make
    - mosdepth=0.2.5
    - pyfaidx
    - pyvcf=0.6.8
    - progressbar2
    - python-Levenshtein
    - intervaltree=2.1.0
    - rtg-tools
    - r
    - r-nanopore
    - imagemagick
    - graphviz
    - pandoc
    - igv
    - bioconductor-rsamtools=2.0.0

And exported my environment for exact packages and dependancies. You may want to add the above versions to insure the environment does not have any dependency issues. It is quite a hefty amount of packages to install for this workflow.

Thanks, Ashley 

name: ont_tutorial_sv
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=0_gnu
  - _r-mutex=1.0.1=anacondar_1
  - alsa-lib=1.1.5=h516909a_1002
  - appdirs=1.4.3=py_1
  - attrs=19.3.0=py_0
  - bcftools=1.10.2=hd2cd319_0
  - bedtools=2.29.2=hc088bd4_0
  - binutils_impl_linux-64=2.33.1=he1b5a44_7
  - binutils_linux-64=2.33.1=h9595d00_16
  - bioconductor-annotationdbi=1.48.0=r36_0
  - bioconductor-annotationfilter=1.10.0=r36_0
  - bioconductor-biobase=2.46.0=r36h516909a_0
  - bioconductor-biocfilecache=1.10.0=r36_0
  - bioconductor-biocgenerics=0.32.0=r36_0
  - bioconductor-biocparallel=1.20.0=r36he1b5a44_0
  - bioconductor-biomart=2.42.0=r36_0
  - bioconductor-biostrings=2.54.0=r36h516909a_0
  - bioconductor-biovizbase=1.34.0=r36h516909a_0
  - bioconductor-bsgenome=1.54.0=r36_0
  - bioconductor-delayedarray=0.12.0=r36h516909a_0
  - bioconductor-ensembldb=2.10.0=r36_0
  - bioconductor-genomeinfodb=1.22.0=r36_0
  - bioconductor-genomeinfodbdata=1.2.2=r36_0
  - bioconductor-genomicalignments=1.22.0=r36h516909a_0
  - bioconductor-genomicfeatures=1.38.0=r36_0
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  - bioconductor-ggbio=1.34.0=r36_0
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  - bioconductor-shortread=1.44.0=r36he1b5a44_0
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  - gettext=0.19.8.1=hc5be6a0_1002
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  - ghostscript=9.18=1
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  - lcms2=2.9=hbd6801e_1
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  - libcblas=3.8.0=14_openblas
  - libclang=9.0.1=default_hde54327_0
  - libcroco=0.6.13=h8d621e5_0
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  - libiconv=1.15=h516909a_1005
  - liblapack=3.8.0=14_openblas
  - libllvm9=9.0.1=hc9558a2_0
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  - libpng=1.6.37=hed695b0_0
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  - 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
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  - libxml2=2.9.10=hee79883_0
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  - matplotlib=3.1.2=py36_1
  - matplotlib-base=3.1.2=py36h250f245_1
  - minimap2=2.17=h8b12597_1
  - more-itertools=8.1.0=py_0
  - mosdepth=0.2.7=hbeb723e_0
  - nanofilt=2.6.0=py_0
  - nanoget=1.12.0=py_0
  - nanomath=0.23.1=py_1
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  - pytest-runner=5.2=py_0
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  - python-levenshtein=0.12.0=py36_1
  - python-utils=2.3.0=py_1
  - pytz=2019.3=py_0
  - pyvcf=0.6.8=py36_0
  - pyyaml=5.3=py36h516909a_0
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  - tk=8.6.10=hed695b0_0
  - tktable=2.10=h555a92e_3
  - tornado=6.0.3=py36h516909a_0
  - tqdm=4.7.2=py36_0
  - urllib3=1.25.7=py36_0
  - vcflib=1.0.0_rc2=h56106d0_2
  - vcftools=0.1.16=he860b03_3
  - wcwidth=0.1.8=py_0
  - wheel=0.33.6=py36_0
  - wrapt=1.11.2=py36h516909a_0
  - xorg-fixesproto=5.0=h14c3975_1002
  - xorg-inputproto=2.3.2=h14c3975_1002
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.9=h516909a_0
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxfixes=5.0.3=h516909a_1004
  - xorg-libxi=1.7.10=h516909a_0
  - xorg-libxpm=3.5.13=h516909a_0
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxt=1.1.5=h516909a_1003
  - xorg-libxtst=1.2.3=h516909a_1002
  - xorg-recordproto=1.14.2=h516909a_1002
  - xorg-renderproto=0.11.1=h14c3975_1002
  - xorg-xextproto=7.3.0=h14c3975_1002
  - xorg-xproto=7.0.31=h14c3975_1007
  - xz=5.2.4=h14c3975_1001
  - yaml=0.2.2=h516909a_1
  - zipp=1.0.0=py_0
  - zlib=1.2.11=h516909a_1006
  - zstd=1.4.4=h3b9ef0a_1
philres commented 4 years ago

Thanks a lot, will do that.