sortmerna and sumaclust

[andrefcjp]

Dear Everyone,

I wonder if these softwares sortmerna and sumaclust (green highlighted) are mandatory to be installed to run the QIIME. If yes, why they were not installed when I updated to 1.9.1 version? Please see below the qiime instalation test. In fact I am having some issues when run the core_diversity_analyses.py. Please regard the yellow highlighted. Are they related to these missed softwares?
Can anyone advise me on how to install them? In fact I download some instructions about these softwares (attached files), so I wonder if I need another program to install them or just insert the commands in linux terminal.

Thanks,

Andre

andre2@andrelinux:~/new$ core_diversity_analyses.py -i otusITS/otu_table_mc2_w_tax.biom -o cdoutITS/ -m TsujiITSqiime.txt -e 58698 --nonphylogenetic_diversity
/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2645: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)
/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):
/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):

andre2@andrelinux:~$ print_qiime_config.py -t

System information
==================
         Platform:      linux2
   Python version:      2.7.6 (default, Mar 22 2014, 22:59:56)  [GCC 4.8.2]
Python executable:      /usr/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:        0.17.0
                 pandas version:        0.17.1
             matplotlib version:        1.4.3
            biom-format version:        2.1.5
                   h5py version:        2.2.1 (HDF5 version: 1.8.11)
                   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:        Not installed.
              sumaclust version:        Not installed.
                  swarm version:        Swarm 1.2.19 [Feb 25 2016 17:01:52]
                          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:      /home/andre2/qiime_software/blast-2.2.22-release/data
      pick_otus_reference_seqs_fp:      /usr/local/lib/python2.7/dist-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:      /usr/local/lib/python2.7/dist-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:      /usr/local/lib/python2.7/dist-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:      /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir:      /tmp/
                     slurm_memory:      None
                      slurm_queue:      None
                      blastall_fp:      /home/andre2/qiime_software/blast-2.2.22-release/bin/blastall
                 seconds_to_sleep:      1

QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.163s

OK

[Colin Brislawn]

Hello Andre,

The software packages sortmerna and sumaclust and not part of the default qiime pipeline, so you can run most qiime scripts without having them installed.

Are you planning on using either of these software packages? I can help you install them if you need to.

When you run core_diversity_analyses.py, you receive two warnings. These are warnings (not errors) tell the devs to update our code. You can safely ignore them.

These warnings come from the python packages numpy and matplotlib, which are totally unrelated to sortmerna and sumaclust.

/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py:2645: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)
/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):
/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

Keep in touch,

Colin Brislawn 

[andrefcjp]

Dear Colin,

Thanks for your clarification. Could you please help me to install the sortmerna and sumaclust? You are right, because the warning are not errors thats why I could get the outputs as I planned.
Thanks again

Andre

[Colin Brislawn]

Sure, I can help you install sortmerna and sumaclust if you plan on using them. 

How did you go about installing qiime? If you are using a conda environment, it's pretty easy to install SortMeRNA and sumaclust.

(We can also install them manually, but that's a little harder.)

Colin

[andrefcjp]

Dear Colin,

So could you please guide me on how to install these softwares? sortmerna and sumaclust, I installed the Qiime with Python, and the test results are below. As you can see only the sortmerna and sumaclust are not installed. i really dont know why they did not installed automatically when I downloaded the qiime. In this case I need to do manually.
Thanks in advance

[Colin Brislawn]

OK. Let's start with SortMeRNA

Git clone SortMeRNA from the github repo, here: https://github.com/biocore/sortmerna

Then follow these instruction to compile the program.

https://github.com/biocore/sortmerna#to-compile-on-linux-os 

If you get any errors along the way, let me know and I can help.

Colin

[andrefcjp]

Hi Colin,

I succeeded to install both softwares. thanks for the advising.