Qiime 2017.6 installs, but doesn't work on Ubuntu 14.04

spikebike · June 28, 2017, 6:40pm

I followed the instructions and am using an ubuntu-14.04 system. I saw no errors during the the conda install, but “qiime --help” doesn’t work.

I was following the instructions at
conda install directions

See below:

$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 14.04.5 LTS
Release:	14.04
Codename:	trusty
$ conda create -n qiime2-2017.6 --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-linux-64.txt
r-cluster-2.0. 100% |################################| Time: 0:00:00  10.39 MB/s
r-ggplot2-2.2. 100% |################################| Time: 0:00:00  19.75 MB/s
r-digest-0.6.1 100% |################################| Time: 0:00:00  17.91 MB/s
r-codetools-0. 100% |################################| Time: 0:00:00  13.32 MB/s
r-colorspace-1 100% |################################| Time: 0:00:00  24.26 MB/s
harfbuzz-0.9.3 100% |################################| Time: 0:00:00  27.00 MB/s
r-tibble-1.2-r 100% |################################| Time: 0:00:00  23.10 MB/s
gstreamer-1.8. 100% |################################| Time: 0:00:00  28.05 MB/s
cairo-1.14.8-0 100% |################################| Time: 0:00:00  22.22 MB/s
r-stringi-1.1. 100% |################################| Time: 0:00:00  27.36 MB/s
r-foreign-0.8_ 100% |################################| Time: 0:00:00  25.11 MB/s
r-3.3.1-r3.3.1 100% |################################| Time: 0:00:00 774.35 kB/s
gst-plugins-ba 100% |################################| Time: 0:00:00  27.73 MB/s
zeromq-4.1.5-0 100% |################################| Time: 0:00:00  28.14 MB/s
vsearch-2.0.3- 100% |################################| Time: 0:00:00 839.60 kB/s
boost-1.61.0-p 100% |################################| Time: 0:00:00  32.45 MB/s
r-scales-0.4.1 100% |################################| Time: 0:00:00  22.24 MB/s
libgcc-5.2.0-0 100% |################################| Time: 0:00:00  32.76 MB/s
glib-2.50.2-1. 100% |################################| Time: 0:00:00  35.28 MB/s
expat-2.1.0-0. 100% |################################| Time: 0:00:00  24.69 MB/s
pango-1.40.3-1 100% |################################| Time: 0:00:00  29.58 MB/s
r-lattice-0.20 100% |################################| Time: 0:00:00  29.76 MB/s
dbus-1.10.10-0 100% |################################| Time: 0:00:00  32.68 MB/s
r-matrix-1.2_7 100% |################################| Time: 0:00:00  33.38 MB/s
libxcb-1.12-1. 100% |################################| Time: 0:00:00  34.02 MB/s
r-lazyeval-0.2 100% |################################| Time: 0:00:00  21.39 MB/s
pixman-0.34.0- 100% |################################| Time: 0:00:00  35.95 MB/s
r-base-3.3.1-6 100% |################################| Time: 0:00:00  38.66 MB/s
libsodium-1.0. 100% |################################| Time: 0:00:00  32.31 MB/s
r-data.table-1 100% |################################| Time: 0:00:00  32.52 MB/s
blast-2.6.0-bo 100% |################################| Time: 0:00:14  18.07 MB/s
bzip2-1.0.6-3. 100% |################################| Time: 0:00:00  14.37 MB/s
qt-5.6.2-4.tar 100% |################################| Time: 0:00:01  38.43 MB/s
r-stringr-1.1. 100% |################################| Time: 0:00:00  18.51 MB/s
r-bh-1.62.0_1- 100% |################################| Time: 0:00:00  40.71 MB/s
r-reshape2-1.4 100% |################################| Time: 0:00:00  30.18 MB/s
libgfortran-3. 100% |################################| Time: 0:00:00  31.58 MB/s
fontconfig-2.1 100% |################################| Time: 0:00:00  40.35 MB/s
r-rcpp-0.12.8- 100% |################################| Time: 0:00:00  41.38 MB/s
r-assertthat-0 100% |################################| Time: 0:00:00  19.71 MB/s
dbus post-link :: /etc/machine-id not found ..
dbus post-link :: .. using /proc/sys/kernel/random/boot_id

But qiime --help doesn’t work

$ source activate qiime2-2017.6
(qiime2-2017.6) user@host:~$ which qiime
/home/user/miniconda2/envs/qiime2-2017.6/bin/qiime
(qiime2-2017.6) user@host:~$ qiime --help
/home/user/miniconda2/envs/qiime2-2017.6/bin/qiime: line 6: syntax error near unexpected token `q2cli.__main__.qiime'
/home/user/miniconda2/envs/qiime2-2017.6/bin/qiime: line 6: `    sys.exit(q2cli.__main__.qiime())'
(qiime2-2017.6) user@host:~$

jairideout · June 28, 2017, 9:36pm

Hi @spikebike! The commands you ran look correct for your system, so I’m not sure immediately what’s going wrong. Let me gather some info:

Are you on a 64-bit or 32-bit operating system?
Did you install Miniconda2 or Miniconda3?
Can you open a new terminal and send the output from these commands? Please don’t activate any QIIME 2 environments in the new terminal.
```
which conda
conda --version
which python
python --version
echo $PATH
echo $PYTHONPATH
```
Activate your QIIME 2 environment and rerun the commands from step 3 above:
```
source activate qiime2-2017.6
# Run commands from step 3 above
```

Thanks!

spikebike · June 28, 2017, 10:31pm

We use miniconda2 heavily, but the system wide minicode + qiime2 created some permission error when it tried to update symbolic links. So we did a install of qiime 2 into the user’s home directory.

1: 64 bit:

user@farm:~$ uname -a
Linux 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
user@farm:~$ file /bin/ls
/bin/ls: ELF 64-bit LSB  executable, x86-64,

2: miniconda2, is 3 better?

3:

user@farm:~$ which conda
/home/dhtaft/miniconda2/bin/conda
user@farm:~$ conda --version
conda 4.3.22
user@farm:~$ which python
/home/user/miniconda2/bin/python
user@farm:~$ python --version
Python 2.7.13 :: Continuum Analytics, Inc.
user@farm:~$ echo $PATH
/home/user/miniconda2/bin:/share/apps/openmpi-2.0.1/gcc-4.8/bin:/share/apps/slurm-16.05.8/bin:/usr/local/bin:/usr/bin:/bin:/opt/puppetlabs/bin

4:

user@farm:~$ source activate qiime2-2017.6
(qiime2-2017.6) user@farm:~$ which conda
/home/user/miniconda2/envs/qiime2-2017.6/bin/conda
(qiime2-2017.6) user@farm:~$ conda --version
conda 4.3.22
(qiime2-2017.6) user@farm:~$ which python
/home/user/miniconda2/envs/qiime2-2017.6/bin/python
(qiime2-2017.6) user@farm:~$ python --version
-su: /home/user/miniconda2/envs/qiime2-2017.6/bin/python: cannot execute binary file: Exec format error
(qiime2-2017.6) user@farm:~$ echo $PATH
/home/user/miniconda2/envs/qiime2-2017.6/bin:/home/user/miniconda2/bin:/share/apps/openmpi-2.0.1/gcc-4.8/bin:/share/apps/slurm-16.05.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/puppetlabs/bin
(qiime2-2017.6) user@farm:~$ echo $PYTHONPATH

(qiime2-2017.6) user@farm:~$

This might be helpful as well:

$ ls -al /home/user/miniconda2/envs/qiime2-2017.6/bin/python
lrwxrwxrwx 1 user user 9 Jun 26 18:14 /home/user/miniconda2/envs/qiime2-2017.6/bin/python -> python3.5
$ ls -al /home/user/miniconda2/envs/qiime2-2017.6/bin/python3.5
-rwxrwxr-x 1 user user  9508 Mar  6 10:17 /home/user/miniconda2/envs/qiime2-2017.6/bin/python3.5
(qiime2-2017.6) user@farm:~$ file /home/user/miniconda2/envs/qiime2-2017.6/bin/python3.5
/home/user/miniconda2/envs/qiime2-2017.6/bin/python3.5: Mach-O 64-bit x86_64 executable

Ah, weird, looks like somehow we ended up with a OSX/Mach python binary.

spikebike · June 28, 2017, 10:50pm

Not sure if it was my error, or an already fixed error elsewhere.

But rm -rf ~/miniconda and starting over fixed it.

Please close this ticket.

thermokarst · June 28, 2017, 11:31pm

@spikebike: it sounds like you might have accidentally used the mac os install file, instead of the linux install file (this has cropped up a few times lately). We have an open issue to revise how those instructions are presented to users. Thanks for the update, and sorry for the troubles!

spikebike · June 29, 2017, 1:42am

Many thanks for the help.

jairideout · July 25, 2017, 10:14pm

QIIME 2 2017.7 is now live and includes the revisions to the install docs @thermokarst mentioned above

system · August 26, 2017, 4:15am

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