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Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Fix missing duplication rate in json report #169

Closed seallard closed 7 months ago

seallard commented 7 months ago

Description

The quality control implemented in cg fails for microsalt due to the duplication rate not being reported in the json output.

seallard commented 7 months ago

Deployed to production

θ64° [sebastian.allard@hasta:~] [P_base] 127 $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-prod.sh
on the host hasta.scilifelab.se, continue
This will install the latest version of microSALT on Production, are you sure? y/[n]y

/home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-prod.sh: line 21: microSALT: command not found
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  3052  100  3052    0     0   7992      0 --:--:-- --:--:-- --:--:--  8010
Welcome to the microSALT installation script. Q to exit
Name your microSALT environment ['microSALT']:
Would you like a 'release' or 'source' (development) environment ['release']?
Name the branch to install ['master']:
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 35149  100 35149    0     0  88477      0 --:--:-- --:--:-- --:--:-- 88314
Thank you, setting up environment P_microSALT!

Remove all packages in environment /home/proj/production/bin/miniconda3/envs/P_microSALT:

## Package Plan ##

  environment location: /home/proj/production/bin/miniconda3/envs/P_microSALT

The following packages will be REMOVED:

  _libgcc_mutex-0.1-conda_forge
  _openmp_mutex-4.5-2_gnu
  _r-mutex-1.0.1-anacondar_1
  alsa-lib-1.2.3.2-h166bdaf_0
  binutils_impl_linux-64-2.39-h6ceecb4_0
  binutils_linux-64-2.39-h5fc0e48_11
  blast-2.12.0-hf3cf87c_4
  bwa-0.7.17-h7132678_9
  bwidget-1.9.14-ha770c72_1
  bzip2-1.0.8-h7f98852_4
  c-ares-1.18.1-h7f98852_0
  ca-certificates-2022.9.24-ha878542_0
  cairo-1.16.0-h6cf1ce9_1008
  certifi-2021.5.30-py36h5fab9bb_0
  circos-0.69.8-hdfd78af_1
  curl-7.86.0-h7bff187_0
  cycler-0.11.0-pyhd8ed1ab_0
  entrez-direct-16.2-he881be0_1
  expat-2.5.0-h27087fc_0
  font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig-2.14.1-hc2a2eb6_0
  fonts-conda-ecosystem-1-0
  fonts-conda-forge-1-0
  freetype-2.12.1-hca18f0e_0
  fribidi-1.0.10-h36c2ea0_0
  gcc_impl_linux-64-9.5.0-h99780fb_19
  gcc_linux-64-9.5.0-h4258300_11
  gettext-0.21.1-h27087fc_0
  gfortran_impl_linux-64-9.5.0-hf1096a2_19
  gfortran_linux-64-9.5.0-hdb51d14_11
  giflib-5.2.1-h36c2ea0_2
  glimmerhmm-3.0.4-pl5321h87f3376_5
  graphite2-1.3.13-h58526e2_1001
  gsl-2.7-he838d99_0
  gxx_impl_linux-64-9.5.0-h99780fb_19
  gxx_linux-64-9.5.0-h43f449f_11
  harfbuzz-2.9.1-h83ec7ef_1
  htslib-1.13-h9093b5e_0
  icu-68.2-h9c3ff4c_0
  jbig-2.1-h7f98852_2003
  joblib-1.2.0-pyhd8ed1ab_0
  jpeg-9e-h166bdaf_2
  k8-0.2.5-hd03093a_2
  kernel-headers_linux-64-2.6.32-he073ed8_15
  keyutils-1.6.1-h166bdaf_0
  kiwisolver-1.3.1-py36h605e78d_1
  krb5-1.19.3-h3790be6_0
  lcms2-2.12-hddcbb42_0
  ld_impl_linux-64-2.39-hc81fddc_0
  lerc-2.2.1-h9c3ff4c_0
  libblas-3.9.0-16_linux64_openblas
  libcblas-3.9.0-16_linux64_openblas
  libcups-2.3.3-h3e49a29_2
  libcurl-7.86.0-h7bff187_0
  libdeflate-1.7-h7f98852_5
  libedit-3.1.20191231-he28a2e2_2
  libev-4.33-h516909a_1
  libffi-3.4.2-h7f98852_5
  libgcc-devel_linux-64-9.5.0-h0a57e50_19
  libgcc-ng-12.2.0-h65d4601_19
  libgd-2.3.3-h695aa2c_1
  libgfortran-ng-12.2.0-h69a702a_19
  libgfortran5-12.2.0-h337968e_19
  libglib-2.74.1-h7a41b64_0
  libgomp-12.2.0-h65d4601_19
  libiconv-1.17-h166bdaf_0
  libidn2-2.3.4-h166bdaf_0
  liblapack-3.9.0-16_linux64_openblas
  libnghttp2-1.47.0-hdcd2b5c_1
  libnsl-2.0.0-h7f98852_0
  libopenblas-0.3.21-pthreads_h78a6416_3
  libpng-1.6.38-h753d276_0
  libsanitizer-9.5.0-h2f262e1_19
  libsqlite-3.39.4-h753d276_0
  libssh2-1.10.0-haa6b8db_3
  libstdcxx-devel_linux-64-9.5.0-h0a57e50_19
  libstdcxx-ng-12.2.0-h46fd767_19
  libtiff-4.3.0-hf544144_1
  libunistring-0.9.10-h7f98852_0
  libuuid-2.32.1-h7f98852_1000
  libwebp-1.2.4-h11a3e52_0
  libwebp-base-1.2.4-h166bdaf_0
  libxcb-1.13-h7f98852_1004
  libxml2-2.9.12-h72842e0_0
  libzlib-1.2.13-h166bdaf_4
  llvm-openmp-8.0.1-hc9558a2_0
  make-4.3-hd18ef5c_1
  matplotlib-base-3.3.4-py36hd391965_0
  minimap2-2.24-h7132678_1
  ncurses-6.2-h58526e2_4
  numpy-1.19.5-py36hfc0c790_2
  olefile-0.46-pyh9f0ad1d_1
  openjdk-11.0.9.1-h5cc2fde_1
  openmp-8.0.1-0
  openssl-1.1.1q-h166bdaf_1
  pango-1.48.10-hb8ff022_1
  pcre-8.45-h9c3ff4c_0
  pcre2-10.37-hc3806b6_1
  perl-5.32.1-2_h7f98852_perl5
  perl-archive-tar-2.40-pl5321hdfd78af_0
  perl-b-cow-0.007-pl5321h166bdaf_0
  perl-carp-1.50-pl5321hd8ed1ab_0
  perl-clone-0.46-pl5321hec16e2b_0
  perl-common-sense-3.75-pl5321hd8ed1ab_0
  perl-compress-raw-bzip2-2.201-pl5321h166bdaf_0
  perl-compress-raw-zlib-2.202-pl5321h166bdaf_0
  perl-config-general-2.65-pl5321hdfd78af_0
  perl-digest-perl-md5-1.9-pl5321hdfd78af_2
  perl-encode-3.19-pl5321h166bdaf_0
  perl-exporter-5.74-pl5321hd8ed1ab_0
  perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0
  perl-extutils-makemaker-7.64-pl5321hd8ed1ab_0
  perl-font-ttf-1.06-pl5321hdfd78af_1
  perl-gd-2.76-pl5321h5b5514e_1
  perl-io-compress-2.201-pl5321h87f3376_0
  perl-io-string-1.08-pl5321hdfd78af_4
  perl-io-zlib-1.11-pl5321hdfd78af_0
  perl-json-4.10-pl5321hdfd78af_0
  perl-json-xs-2.34-pl5321h9f5acd7_5
  perl-list-moreutils-0.430-pl5321hdfd78af_0
  perl-list-moreutils-xs-0.430-pl5321hec16e2b_1
  perl-math-bezier-0.01-pl5321hdfd78af_2
  perl-math-round-0.07-pl5321hdfd78af_2
  perl-math-vecstat-0.08-pl5321hdfd78af_2
  perl-module-implementation-0.09-pl5321hdfd78af_3
  perl-module-runtime-0.016-pl5321hdfd78af_2
  perl-number-format-1.75-pl5321hdfd78af_4
  perl-params-validate-1.30-pl5321hec16e2b_1
  perl-parent-0.238-pl5321hd8ed1ab_0
  perl-pathtools-3.75-pl5321h166bdaf_0
  perl-readonly-2.05-pl5321hdfd78af_1
  perl-regexp-common-2017060201-pl5321hd8ed1ab_0
  perl-scalar-list-utils-1.63-pl5321h166bdaf_0
  perl-set-intspan-1.19-pl5321hdfd78af_2
  perl-statistics-basic-1.6611-pl5321hdfd78af_3
  perl-storable-3.15-pl5321h166bdaf_0
  perl-svg-2.87-pl5321hd8ed1ab_0
  perl-text-format-0.62-pl5321hdfd78af_0
  perl-time-hires-1.9764-pl5321hec16e2b_2
  perl-try-tiny-0.31-pl5321ha770c72_0
  perl-types-serialiser-1.01-pl5321hdfd78af_0
  perl-xml-parser-2.44_01-pl5321hc3e0081_1003
  picard-2.20.3-0
  pigz-2.4-h84994c4_0
  pillow-8.3.1-py36h5aabda8_0
  pip-21.2.4-pyhd8ed1ab_0
  pixman-0.40.0-h36c2ea0_0
  pthread-stubs-0.4-h36c2ea0_1001
  pyparsing-3.0.9-pyhd8ed1ab_0
  python-3.6.15-hb7a2778_0_cpython
  python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi-3.6-2_cp36m
  quast-5.0.2-py36pl5321hcac48a8_7
  r-base-4.1.1-hb93adac_1
  readline-8.1-h46c0cb4_0
  samtools-1.13-h8c37831_0
  sed-4.8-he412f7d_0
  setuptools-49.6.0-py36h5fab9bb_3
  simplejson-3.17.5-py36h8f6f2f9_0
  six-1.16.0-pyh6c4a22f_0
  spades-3.13.1-h2d02072_2
  sqlite-3.37.0-h9cd32fc_0
  sysroot_linux-64-2.12-he073ed8_15
  tk-8.6.12-h27826a3_0
  tktable-2.10-hb7b940f_3
  tornado-6.1-py36h8f6f2f9_1
  trimmomatic-0.39-hdfd78af_2
  wget-1.20.3-ha56f1ee_1
  wheel-0.37.1-pyhd8ed1ab_0
  xorg-fixesproto-5.0-h7f98852_1002
  xorg-inputproto-2.3.2-h7f98852_1002
  xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice-1.0.10-h7f98852_0
  xorg-libsm-1.2.3-hd9c2040_1000
  xorg-libx11-1.7.2-h7f98852_0
  xorg-libxau-1.0.9-h7f98852_0
  xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext-1.3.4-h7f98852_1
  xorg-libxfixes-5.0.3-h7f98852_1004
  xorg-libxi-1.7.10-h7f98852_0
  xorg-libxrender-0.9.10-h7f98852_1003
  xorg-libxt-1.2.1-h7f98852_2
  xorg-libxtst-1.2.3-h7f98852_1002
  xorg-recordproto-1.14.2-h7f98852_1002
  xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto-7.3.0-h7f98852_1002
  xorg-xproto-7.0.31-h7f98852_1007
  xz-5.2.6-h166bdaf_0
  zlib-1.2.13-h166bdaf_4
  zstd-1.5.2-h6239696_4

Preparing transaction: done
Verifying transaction: done
Executing transaction: \ Removing /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/silva
  Downloading BUSCO database...
Downloading bacteria database (file: bacteria.tar.gz)...

ERROR! Failed downloading bacteria database (url: https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco/bacteria.tar.gz and restart QUAST
WARNING: Failed to download bacteria database from https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz and unpack it into /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco
  Downloading BUSCO database...
Downloading eukaryota database (file: eukaryota.tar.gz)...

ERROR! Failed downloading eukaryota database (url: https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco/eukaryota.tar.gz and restart QUAST
WARNING: Failed to download eukaryota database from https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz and unpack it into /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco
  Downloading BUSCO database...
Downloading fungi database (file: fungi.tar.gz)...

ERROR! Failed downloading fungi database (url: https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco/fungi.tar.gz and restart QUAST
WARNING: Failed to download fungi database from https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz and unpack it into /home/proj/production/bin/miniconda3/envs/P_microSALT/lib/python3.6/site-packages/quast_libs/busco

done
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/proj/production/bin/miniconda3/envs/P_microSALT

  added / updated specs:
    - pip
    - python=3.6

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  ca-certificates    conda-forge/linux-64::ca-certificates-2023.11.17-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3 
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_3 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.44.2-h2797004_0 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5 
  ncurses            conda-forge/linux-64::ncurses-6.4-h59595ed_2 
  openssl            conda-forge/linux-64::openssl-1.1.1w-hd590300_0 
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0 
  python             conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython 
  python_abi         conda-forge/linux-64::python_abi-3.6-2_cp36m 
  readline           conda-forge/linux-64::readline-8.2-h8228510_1 
  setuptools         conda-forge/linux-64::setuptools-58.0.4-py36h5fab9bb_2 
  sqlite             conda-forge/linux-64::sqlite-3.44.2-h2c6b66d_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate P_microSALT
#
# To deactivate an active environment, use
#
#     $ conda deactivat