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