Qiime2-2019.1 issues on ubuntu 18.10

(Mrudhulaks) #1

Hi team,

I am trying to install qiime2-2019.1 on Ubuntu18.10 through Conda. I have already installed qiime2 before on this environment (which worked without any errors before). However, when I tried to install qiime 2 on conda environment, there are couple of issues. Please see the command and exact message (Copy and pasted).

(base) [email protected]:~$ conda activate qiime2-2019.1
(qiime2-2019.1) [email protected]:~$ qiime --help

Command 'qiime' not found, but can be installed with:

sudo apt install qiime

(qiime2-2019.1) [email protected]:~$

And when I tried to work the command sudo apt install qiime, the following error messages popped up.

Err:1 http://au.archive.ubuntu.com/ubuntu cosmic-updates/main amd64 linux-libc-dev amd64 4.18.0-12.13
  404  Not Found [IP: 202.158.214.106 80]
Err:2 http://au.archive.ubuntu.com/ubuntu cosmic-updates/main amd64 openjdk-11-jre-headless amd64 11.0.1+13-2ubuntu1
  404  Not Found [IP: 202.158.214.106 80]
Err:3 http://au.archive.ubuntu.com/ubuntu cosmic-updates/main amd64 openjdk-11-jre amd64 11.0.1+13-2ubuntu1
  404  Not Found [IP: 202.158.214.106 80]
E: Failed to fetch http://au.archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-libc-dev_4.18.0-12.13_amd64.deb  404  Not Found [IP: 202.158.214.106 80]
E: Failed to fetch http://au.archive.ubuntu.com/ubuntu/pool/main/o/openjdk-lts/openjdk-11-jre-headless_11.0.1+13-2ubuntu1_amd64.deb  404  Not Found [IP: 202.158.214.106 80]
E: Failed to fetch http://au.archive.ubuntu.com/ubuntu/pool/main/o/openjdk-lts/openjdk-11-jre_11.0.1+13-2ubuntu1_amd64.deb  404  Not Found [IP: 202.158.214.106 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

Could you please help me with this.

Thank you so much!

Regards,
Mrudhula

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(Matthew Ryan Dillon) #2

Hi @Mrudhulaks!

Can you please run the following and provide the results here?

conda activate qiime2-2019.1
conda list

Thanks!

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(Mrudhulaks) #3

Hi,

Please find the results

(qiime2-2019.1) [email protected]:~ conda activate qiime2-2019.1 (qiime2-2019.1) [email protected]:~ conda list
WARNING: The conda.compat module is deprecated and will be removed in a future release.

packages in environment at /home/ubuntu/miniconda3/envs/qiime2-2019.1:

Name Version Build Channel

_r-mutex 1.0.0 anacondar_1
arb-bio-tools 6.0.6 h5901010_6 bioconda
asn1crypto 0.24.0 py35_0
atk 2.25.90 hf2eb9ee_1001 conda-forge
atomicwrites 1.2.1 py_0 conda-forge
attrs 18.2.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
backports 1.0 py35_1
backports.shutil_get_terminal_size 1.0.0 py35_2
bcftools 1.9 h47928c2_2 bioconda
bibtexparser 1.1.0 py_0 conda-forge
bioconductor-biobase 2.38.0 r341h219a75b_1 bioconda
bioconductor-biocgenerics 0.24.0 r341_1 bioconda
bioconductor-biocparallel 1.12.0 r341h219a75b_1 bioconda
bioconductor-biostrings 2.46.0 r3.4.1_0 bioconda
bioconductor-dada2 1.6.0 r3.4.1_0 bioconda
bioconductor-delayedarray 0.4.1 r3.4.1_0 bioconda
bioconductor-genomeinfodb 1.14.0 r3.4.1_0 bioconda
bioconductor-genomeinfodbdata 1.0.0 r3.4.1_1 bioconda
bioconductor-genomicalignments 1.14.1 r3.4.1_0 bioconda
bioconductor-genomicranges 1.30.3 r3.4.1_0 bioconda
bioconductor-iranges 2.12.0 r3.4.1_0 bioconda
bioconductor-rsamtools 1.30.0 r3.4.1_0 bioconda
bioconductor-s4vectors 0.16.0 r3.4.1_0 bioconda
bioconductor-shortread 1.36.0 r3.4.1_0 bioconda
bioconductor-summarizedexperiment 1.8.0 r3.4.1_0 bioconda
bioconductor-xvector 0.18.0 r3.4.1_0 bioconda
bioconductor-zlibbioc 1.24.0 r3.4.1_0 bioconda
biom-format 2.1.6 py35_1 bioconda
biopython 1.72 py35h04863e7_0
blas 1.0 openblas
blast 2.7.1 h4422958_6 bioconda
bleach 3.1.0 py_0 conda-forge
bokeh 0.13.0 py35_0
boost 1.67.0 py35_4
boost-cpp 1.67.0 h3a22d5f_0 conda-forge
bowtie2 2.3.4.3 py35h2d50403_0 bioconda
bz2file 0.98 py_0 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
cachecontrol 0.12.5 py_0 conda-forge
cairo 1.14.12 h80bd089_1005 conda-forge
certifi 2018.8.24 py35_1
cffi 1.11.5 py35he75722e_1
chardet 3.0.4 py35_1
click 7.0 py_0 conda-forge
cryptography 2.3.1 py35hc365091_0
curl 7.61.0 h93b3f91_2 conda-forge
cutadapt 1.18 py35_0 bioconda
cycler 0.10.0 py_1 conda-forge
dbus 1.13.2 h714fa37_1
deblur 1.1.0 py35_0 bioconda
decorator 4.3.2 py_0 conda-forge
entrypoints 0.2.3 py35_2
expat 2.2.5 hf484d3e_1002 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.9.1 h94bbf69_1005 conda-forge
future 0.16.0 py35_2
gdk-pixbuf 2.36.12 h4f1c04b_1001 conda-forge
get_terminal_size 1.0.0 haa9412d_0
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.56.2 had28632_1001 conda-forge
gmp 6.1.2 hf484d3e_1000 conda-forge
gneiss 0.4.4 py_0 bioconda
gnutls 3.5.19 h2a4e5f8_1 conda-forge
gobject-introspection 1.56.1 py35hbc4ca2d_2
graphite2 1.3.13 hf484d3e_1000 conda-forge
gsl 2.2.1 h0c605f7_3
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
gtk2 2.24.31 h5baeb44_1000 conda-forge
h5py 2.8.0 py35h989c5e5_3
harfbuzz 1.9.0 he243708_1001 conda-forge
hdf5 1.10.2 hba1933b_1
hdmedians 0.13 py35h035aef0_0
htslib 1.9 h47928c2_5 bioconda
icu 58.2 hf484d3e_1000 conda-forge
idna 2.7 py35_0
ijson 2.3 py_1 conda-forge
intel-openmp 2019.1 144
ipykernel 4.10.0 py35_0
ipython 4.2.0 py35_0
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
iqtree 1.6.9 he860b03_1 bioconda
jinja2 2.10.1 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 2.6.0 py35h4395190_0
jupyter_client 5.2.4 py_3 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.0.1 py35hf484d3e_0
krb5 1.14.6 0 conda-forge
libarbdb 6.0.6 h5901010_6 bioconda
libboost 1.67.0 h46d08c1_4
libcurl 7.61.1 heec0ca6_0
libdeflate 1.0 h14c3975_1 bioconda
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.3.0 hdf63c60_0
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3
libiconv 1.15 h516909a_1005 conda-forge
libopenblas 0.2.20 h9ac9557_7
libpng 1.6.36 h84994c4_1000 conda-forge
libsodium 1.0.16 h14c3975_1001 conda-forge
libssh2 1.8.0 h1ad7b7a_1003 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0
libtiff 4.0.10 h9022e91_1002 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
lockfile 0.12.2 py_1 conda-forge
mafft 7.310 1 bioconda
markupsafe 1.0 py35h14c3975_1
matplotlib 3.0.0 py35h5429711_0
mistune 0.8.3 py35h14c3975_1
mkl 2019.1 144
more-itertools 4.3.0 py35_0
msgpack-python 0.5.6 py35h6bb024c_1
natsort 5.5.0 py_0 conda-forge
nbconvert 5.3.1 py35_0
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nettle 3.3 0 conda-forge
nose 1.3.7 py35_2
notebook 5.6.0 py35_0
numpy 1.13.3 py35_nomklh2b20989_4
olefile 0.46 py_0 conda-forge
openjdk 11.0.1 h516909a_1015 conda-forge
openssl 1.0.2p h14c3975_1002 conda-forge
packaging 19.0 py_0 conda-forge
pandas 0.23.4 py35h04863e7_0
pandoc 2.5 1 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.40.14 hf0c64fd_1003 conda-forge
parso 0.3.2 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.43 he6710b0_0
perl 5.26.2 h14c3975_1002 conda-forge
perl-archive-tar 2.32 pl526_0 bioconda
perl-carp 1.38 pl526_2 bioconda
perl-compress-raw-bzip2 2.084 pl526hfc679d8_0 bioconda
perl-compress-raw-zlib 2.084 pl526h2d50403_0 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.34 pl526_3 bioconda
perl-io-compress 2.084 pl526hfc679d8_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-pathtools 3.73 h470a237_2 bioconda
perl-scalar-list-utils 1.45 pl526h470a237_3 bioconda
perl-test-more 1.001002 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
pexpect 4.6.0 py35_0
pickleshare 0.7.4 py35hd57304d_0
pigz 2.3.4 0 conda-forge
pip 10.0.1 py35_0
pixman 0.34.0 h14c3975_1003 conda-forge
pluggy 0.8.1 py_0 conda-forge
prometheus_client 0.5.0 py_0 conda-forge
prompt_toolkit 2.0.8 py_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py35_0
py 1.7.0 py_0 conda-forge
py-boost 1.67.0 py35h04863e7_4
pycparser 2.19 py35_0
pygments 2.3.1 py_0 conda-forge
pyopenssl 18.0.0 py35_0
pyparsing 2.3.0 py_0 conda-forge
pyqt 5.9.2 py35h05f1152_2
pysam 0.15.2 py35h0380709_0 bioconda
pysocks 1.6.8 py35_0
python 3.5.6 hc3d631a_0
python-dateutil 2.7.5 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
pyyaml 3.13 py35h14c3975_0
pyzmq 17.1.2 py35h14c3975_0
q2-metaphlan2 1.0.4 py35h39e3cac_0 fasnicar
qt 5.9.6 h8703b6f_2
r-assertthat 0.2.0 r341h6115d3f_1 conda-forge
r-base 3.4.1 h4fe35fd_8 conda-forge
r-bh 1.66.0_1 r341_1001 conda-forge
r-bitops 1.0_6 r341hc070d10_2 conda-forge
r-cli 1.0.0 r341h6115d3f_1 conda-forge
r-cluster 2.0.7_1 r341h364d78e_0 conda-forge
r-colorspace 1.3_2 r341hc070d10_2 conda-forge
r-crayon 1.3.4 r341h6115d3f_1 conda-forge
r-data.table 1.11.4 r341hc070d10_2 conda-forge
r-digest 0.6.18 r341hc070d10_0 conda-forge
r-fansi 0.3.0 r341hc070d10_0 conda-forge
r-formatr 1.5 r341h6115d3f_1 conda-forge
r-futile.logger 1.4.3 r341h6115d3f_1 conda-forge
r-futile.options 1.0.1 r341h6115d3f_0 conda-forge
r-ggplot2 3.1.0 r341h6115d3f_0 conda-forge
r-glue 1.3.0 r341h470a237_2 conda-forge
r-gtable 0.2.0 r341h6115d3f_1 conda-forge
r-hwriter 1.3.2 r341h6115d3f_1 conda-forge
r-labeling 0.3 r341h6115d3f_1 conda-forge
r-lambda.r 1.2.3 r341h6115d3f_0 conda-forge
r-lattice 0.20_35 r341hc070d10_0 conda-forge
r-latticeextra 0.6_28 r341h6115d3f_1 conda-forge
r-lazyeval 0.2.1 r341hc070d10_2 conda-forge
r-magrittr 1.5 r341h6115d3f_1 conda-forge
r-mass 7.3_50 r341hc070d10_2 conda-forge
r-matrix 1.2_14 r341hc070d10_2 conda-forge
r-matrixstats 0.54.0 r341hc070d10_0 conda-forge
r-mgcv 1.8_24 r341hc070d10_2 conda-forge
r-munsell 0.5.0 r341h6115d3f_1 conda-forge
r-nlme 3.1_137 r341h364d78e_0 conda-forge
r-permute 0.9_4 r341_1002 conda-forge
r-pillar 1.3.0 r341h6115d3f_0 conda-forge
r-plyr 1.8.4 r341h9d2a408_2 conda-forge
r-r6 2.2.2 r341h6115d3f_1 conda-forge
r-rcolorbrewer 1.1_2 r341h6115d3f_1 conda-forge
r-rcpp 1.0.0 r341h9d2a408_0 conda-forge
r-rcppparallel 4.4.1 r341h9d2a408_0 conda-forge
r-rcurl 1.95_4.11 r341hc070d10_3 conda-forge
r-reshape2 1.4.3 r341h9d2a408_2 conda-forge
r-rlang 0.3.0.1 r341h470a237_0 conda-forge
r-scales 1.0.0 r341h9d2a408_1 conda-forge
r-snow 0.4_3 r341h6115d3f_0 conda-forge
r-stringi 1.2.4 r341h9d2a408_1 conda-forge
r-stringr 1.3.1 r341h6115d3f_1 conda-forge
r-tibble 1.4.2 r341hc070d10_2 conda-forge
r-utf8 1.1.4 r341hc070d10_0 conda-forge
r-vegan 2.5_3 r341h364d78e_0 conda-forge
r-viridislite 0.3.0 r341h6115d3f_1 conda-forge
r-withr 2.1.2 r341h6115d3f_0 conda-forge
raxml 8.2.12 h470a237_0 bioconda
readline 7.0 hf8c457e_1001 conda-forge
requests 2.14.2 py35_0
samtools 1.9 h57cc563_6 bioconda
scikit-bio 0.5.1 np113py35_0
scipy 1.1.0 py35_nomklh9d22d0a_0
seaborn 0.9.0 py_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 40.2.0 py35_0
simplegeneric 0.8.1 py35_2
sina 1.4.0 h4ef8376_0 bioconda
sip 4.19.8 py35hf484d3e_0
six 1.11.0 py35_1
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.26.0 h67949de_1001 conda-forge
statsmodels 0.9.0 py35h3010b51_0
tbb 2019.3 h6bb024c_1000 conda-forge
terminado 0.8.1 py35_1
testpath 0.4.2 py_1001 conda-forge
tk 8.6.9 h84994c4_1001 conda-forge
tornado 5.1.1 py35h7b6447c_0
traitlets 4.3.2 py35ha522a97_0
tzlocal 1.5.1 py_0 conda-forge
unifrac 0.9.3 py35h5a278d6_0 bioconda
vsearch 2.7.0 1 bioconda
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wget 1.19.5 h1ad7b7a_0
wheel 0.31.1 py35_0
widgetsnbextension 3.4.1 py35_0
xopen 0.4.1 py_0 bioconda
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h516909a_1004 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.6 h14c3975_1000 conda-forge
xorg-libxau 1.0.8 h14c3975_1006 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h516909a_1004 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.2.5 hf484d3e_1006 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
zstd 1.3.3 1 conda-forge
(qiime2-2019.1) [email protected]:~$

Thank you!

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(Matthew Ryan Dillon) #4

Thanks for sharing, @Mrudhulaks. You might have noticed that your environment does not have qiime2, or any of the q2-plugins installed, once you reviewed that list. I suggest you deactivate the environment, delete the environment, and then re-install.

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