Install qiime on Windows system for Linux (WSL)

[Pat Schenck]

Hello,

I think this is a new issue. Trying to install qiime on the new-ish (April 2016) WSL interface. Followed the miniconda install procedure then ran test and had two failures. Any ideas?

(qiime1) pitrack01@LAPTOP-4B9AGN4O:/etc/python2.7$ print_qiime_config.py -t

System information

     Platform:      linux2

Python version: 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:42:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Python executable: /home/pitrack01/anaconda3/envs/qiime1/bin/python

QIIME default reference information

For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions

      QIIME library version:        1.9.1
       QIIME script version:        1.9.1

qiime-default-reference version: 0.1.3
NumPy version: 1.10.4
SciPy version: 0.17.1
pandas version: 0.18.1
matplotlib version: 1.4.3
biom-format version: 2.1.5
h5py version: Not installed.
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [Mar 1 2016 23:41:10]
gdata: Installed.

QIIME config values

For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html

                 blastmat_dir:      None
  pick_otus_reference_seqs_fp:      /home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                     sc_queue:      all.q
  topiaryexplorer_project_dir:      None
 pynast_template_alignment_fp:      /home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
              cluster_jobs_fp:      start_parallel_jobs.py

pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp: /home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 1

QIIME base install test results

..F.....F

FAIL: test_cluster_jobs_fp (main.QIIMEDependencyBase)
cluster_jobs_fp is set to a valid path and is executable

Traceback (most recent call last):
File "/home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 224, in test_cluster_jobs_fp
"cluster_jobs_fp set to an invalid file path or is not in $PATH: %s" % fp)
AssertionError: cluster_jobs_fp set to an invalid file path or is not in $PATH: start_parallel_jobs.py

======================================================================
FAIL: test_uclust_supported_version (main.QIIMEDependencyBase)
uclust is in path and version is supported

Traceback (most recent call last):
File "/home/pitrack01/anaconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 336, in test_uclust_supported_version
% ('.'.join(map(str, acceptable_version)), version_string))
AssertionError: Unsupported uclust version. 1.2.22 is required, but running Segmentation fault (core dumped)
.

---

Ran 9 tests in 0.131s

[Antonio González Peña]

The first failure is because QIIME is expecting to have a script to start jobs in a cluster, which I don't think is an issue for your environment. Either way, if you want to configure it suggest checking:

- http://qiime.org/install/qiime_config.html

- http://qiime.org/tutorials/parallel_qiime.html

The latter error is due to having the incorrect version of uclust, perhaps this will give you some solving paths: https://groups.google.com/forum/#!topic/qiime-forum/u6WetsmYi0I

[Michael Baron]

I think I've run into the same issues with uclust. I did a conda install on the Windows 10 Ubuntu bash. First I had issues with libsm6, but that got solved by installing these packages:

sudo apt-get install libsm6 libxrender1 libfontconfig1

System information

==================

         Platform:      linux2

   Python version:      2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15)  [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

Python executable:      /home/Mike/miniconda2/envs/qiime1/bin/python

QIIME default reference information

===================================

For details on what files are used as QIIME's default references, see here:

 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions

===================

          QIIME library version:        1.9.1

           QIIME script version:        1.9.1

qiime-default-reference version:        0.1.3

                  NumPy version:        1.10.4

                  SciPy version:        0.17.1

                 pandas version:        0.18.1

             matplotlib version:        1.4.3

            biom-format version:        2.1.5

                   h5py version:        2.6.0 (HDF5 version: 1.8.16)

                   qcli version:        0.1.1

                   pyqi version:        0.3.2

             scikit-bio version:        0.2.3

                 PyNAST version:        1.2.2

                Emperor version:        0.9.51

                burrito version:        0.9.1

       burrito-fillings version:        0.1.1

              sortmerna version:        sortmerna: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory

              sumaclust version:        Installed, but can't identify version.

                  swarm version:        Swarm 1.2.19 [Mar  5 2016 16:56:02]

                          gdata:        Installed.

QIIME config values

===================

For definitions of these settings and to learn how to configure QIIME, see here:

 http://qiime.org/install/qiime_config.html

 http://qiime.org/tutorials/parallel_qiime.html

                     blastmat_dir:      None

      pick_otus_reference_seqs_fp:      /home/Mike/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                         sc_queue:      all.q

      topiaryexplorer_project_dir:      None

     pynast_template_alignment_fp:      /home/Mike/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

                  cluster_jobs_fp:      start_parallel_jobs.py

pynast_template_alignment_blastdb:      None

assign_taxonomy_reference_seqs_fp:      /home/Mike/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                     torque_queue:      friendlyq

                    jobs_to_start:      1

                       slurm_time:      None

            denoiser_min_per_core:      50

assign_taxonomy_id_to_taxonomy_fp:      /home/Mike/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

                         temp_dir:      /tmp/

                     slurm_memory:      None

                      slurm_queue:      None

                      blastall_fp:      blastall

                 seconds_to_sleep:      1

QIIME base install test results

===============================

........F

======================================================================

FAIL: test_uclust_supported_version (__main__.QIIMEDependencyBase)

uclust is in path and version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/Mike/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 336, in test_uclust_supported_version

    % ('.'.join(map(str, acceptable_version)), version_string))

AssertionError: Unsupported uclust version. 1.2.22 is required, but running Segmentation fault (core dumped)

.

----------------------------------------------------------------------

Ran 9 tests in 0.085s

FAILED (failures=1)

I've already downloaded (http://drive5.com/uclust/downloads1_2_22q.html) and overwritten the uclust in the env's binary files, but to no avail.

Any suggestions?

[Michael Baron]

I can't even seem to execute uclust by itself, that leads straight to a "Segementation faul (core dumped)" error message. Is memory management on the Windows Ubuntu Bash kaputt?

[André Soares]

Same here, core dumped with ./uclustq1.2.22_i86linux64 even after chmod a+x uclustq1.2.22_i86linux64
Any news on this?

[Greg Caporaso]

Hi Andre,

I don't have any experience working on WSL, but it seems like the uclust binary doesn't work in this environment. We don't develop uclust (or have access to it's source code - it's closed source software), so you might need to contact the developer, Robert Edgar about this. His website is drive5.com, and should have contact information on it. 

Sorry to not be able to help more with this - WSL hasn't been a development target for us in QIIME 1. You might try working with QIIME 2 instead (see https://docs.qiime2.org). While we're not explicitly developing QIIME 2 for WSL, we are actively developing the project, unlike QIIME 1 which is now in maintenance mode while we transition to QIIME 2. So, we might be able to help out more with getting QIIME 2 working in this environment. 

Best,

Greg