Qiime2 installation error

User Support
1

I have been pounding my head trying to get this installation and need someone with more knowledge of Python to point me in the right direction.

I am using two sources as references:

https://conda.io/miniconda.html which includes installation scripts for Miniconda2 and Miniconda3
and
https://docs.qiime2.org/2017.10/install/native/#install-miniconda which recommends installing qiime2 via miniconda

Problem #1) While the documentation indicates either Miniconda2 or Miniconda3 work, in reality the Miniconda2 installation hangs up after downloading pygments-2.2.0.

But the installation of Miniconda3, seems to work fine:

seq-bcm:tmp 972 $ mkdir /opt/apps/Miniconda3/
seq-bcm:tmp 973 $ date
Mon Nov 27 11:29:37 MST 2017
seq-bcm:tmp 974 $ ./Miniconda3-latest-Linux-x86_64.sh -f -p /opt/apps/Miniconda3/

Welcome to Miniconda3 4.3.30

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
. . . .
Do you accept the license terms? [yes|no]
[no] >>> yes

Miniconda3 will now be installed into this location:
/opt/apps/Miniconda3/
PREFIX=/opt/apps/Miniconda3
installing: python-3.6.3-hc9025b9_1 ...
Python 3.6.3 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 ...
. . . . .
installing: conda-4.3.30-py36h5d9f9f4_0 ...
installation finished.

$ module load Miniconda/3

$ which conda
/opt/apps/Miniconda3/bin/conda

And it seems complete:
$ conda update conda
Fetching package metadata .................
Solving package specifications: .

# All requested packages already installed.
# packages in environment at /opt/apps/Miniconda3:
#
conda 4.3.30 py36h5d9f9f4_0

$ conda create -n qiime2-2017.10 --file https://data.qiime2.org/distro/core/qiime2-2017.10-conda-linux-64.txt
qiime2-2017.10 100% |#############################################################################################|ETime:-0:00:00 811.96 kB/s
. . . . .
zlib-1.2.8-3.t 100% |#############################################################################################|ETime:-0:00:00 11.55 MB/s

Problem #2) Maybe it is OK but the installation script stopped after the zlib download/install

The command to “Activate the conda environment” seems to work:

$ source activate qiime2-2017.10

And new links are made:

(qiime2-2017.10) seq-bcm:chhtmp 1074 $ which3 conda
------------
Definitions of "conda":

conda is an executable in $PATH
/opt/apps/Miniconda3/envs/qiime2-2017.10/bin/conda -> /opt/apps/Miniconda3/bin/conda
Link resolves to /panfs/biopan01/apps/Miniconda3/bin/conda
type: Python script, ASCII text executable
/opt/apps/Miniconda3/bin/conda
type: Python script, ASCII text executable

Problem #3) The “qiime --help” command to test the installation fails:

$ qiime --help
bash: qiime: command not found

And I find no qiime executable the /opt/apps/Miniconda3/ directory tree:

$ find /opt/apps/Miniconda3/ -name '*qiime*'
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0.tar.bz2
/opt/apps/Miniconda3/pkgs/emperor-1.0.0beta11-py35_2/lib/python3.5/site-packages/emperor/qiime_backports
/opt/apps/Miniconda3/pkgs/q2-types-2017.10.0-py35_0/lib/python3.5/site-packages/q2_types/per_sample_sequences/tests/data/qiime1-demux-format
/opt/apps/Miniconda3/pkgs/q2cli-2017.10.0-py35_0/lib/python3.5/site-packages/q2cli-2017.10.0-py3.5.egg-info/scripts/tab-qiime
/opt/apps/Miniconda3/pkgs/q2cli-2017.10.0-py35_0/bin/qiime
/opt/apps/Miniconda3/pkgs/q2cli-2017.10.0-py35_0/bin/tab-qiime
/opt/apps/Miniconda3/pkgs/q2templates-2017.10.0-py35_0/lib/python3.5/site-packages/q2templates/templates/assets/img/qiime2-rect-200.png
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0/lib/python3.5/site-packages/qiime2-2017.10.0-py3.5.egg-info
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0/lib/python3.5/site-packages/qiime2
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0/lib/python3.5/site-packages/qiime2/tests/data/metadata/qiime1-empty.tsv
/opt/apps/Miniconda3/pkgs/qiime2-2017.10.0-py35_0/lib/python3.5/site-packages/qiime2/tests/data/metadata/qiime1.tsv
/opt/apps/Miniconda3/pkgs/scikit-bio-0.5.1-np113py35_0/lib/python3.5/site-packages/skbio/diversity/alpha/tests/data/qiime-191-tt
/opt/apps/Miniconda3/pkgs/scikit-bio-0.5.1-np113py35_0/lib/python3.5/site-packages/skbio/diversity/beta/tests/data/qiime-191-tt
/opt/apps/Miniconda3/envs/qiime2-2017.10

Does anyone have any clues?

3

@hotblast, sorry to hear things aren't going so well!

I just performed a fresh install of Miniconda2 last week and installed QIIME 2 2017.11 in it, everything looked good from this end. The big red flag here for me is the installation hanging while downloading pygments.

Everything you are describing in this post is making me lean towards blaming the network connection while you were doing these tests. This doesn't necessarily mean your network connection - we have seen weird network hiccups from anaconda.org plenty of times in the past. :ghost: :imp:

Is it possible for you to try this all over again? If it still doesn't work, are you able to attempt on a different computer/location/etc? What happens then?

Please keep us posted! :t_rex:

5

I just followed the suggestion to try the Miniconda3 & QIIME 2 2017.11 on another host.

Since we have two clusters on different networks, I have now unsuccessfully tried installing into a shared directory from both cluster master nodes. And the result is always the same.

The last file (zlib-1.2.8-3) completes download (entire liine of #) but never gives back the shell prompt.

7

Hello Folks,

This line caught my eye:

This makes me think you have two versions of conda; 1) a module installed by admins on the supercomputer, 2) the version you just downloaded and installed to your user account.

When I have used conda on supercomputers before, I was careful to NOT use the module load ... version, and only use my local copy. This has worked well for me and avoided strange interactions with system software.

Let me know if this is relevant to your setup,
Colin

1 Like
8

Hi @halesch! I’ve seen conda take awhile to install and link packages after the package download step completes. This is limited by hard disk speed, and I’ve seen it happen on laptops, as well as a couple of institutional clusters.

Can you try reinstalling qiime2, and wait for the process to finish? It can take some time to complete, and you won’t necessarily see any output during this stage of the install process.

1 Like
10

Colin,

Actually I installed both Miniconda2 and Miniconda3 as modules to be available to the LANL Biology Division.

There is no locally installed version.

Chuck

1 Like
11

jairideout,

I have gone back to the starting point and reinstalled Minicond3. And this time I just waited (~20 minutes) for the Qiime2 installation to finish. And when I just looked back at that session I now see the shell prompt.

The “source activate qiime2-2017.10” seems to work since the test command, “qiime --help” returns appropriate help information.

I appreciate your help and will try to be more patient in the future.

Chuck

1 Like
12

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