ERROR RAISED DURING STEP: Assign taxonomy and QIIME full install test failed

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Marcela Villegas

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Jun 15, 2016, 5:30:47 PM6/15/16
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Hi!

I am running the pick_open_reference_otus.py, and I am having the next issue:

------------------------------------------------------------------------------------------------
*** ERROR RAISED DURING STEP: Assign taxonomy
Command run was:
 assign_taxonomy.py -o OtuPickingV4q30/uclust_assigned_taxonomy -i OtuPickingV4q30/rep_set.fna
Command returned exit status: 2
Stdout:

Stderr
Usage: assign_taxonomy.py [options] {-i/--input_fasta_fp INPUT_FASTA_FP}


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

So I was reading the advices that you gave to some people with the same problem in the past:
1. Check that the Java version is up to 1.6: Checked my Java version is "1.7.0_79"
2. Run the command changing this parameter: assign_taxonomy:rdp_max_memory 2000. I did it but the result is the same one.

3. Run the QIIME full install test: I think somthing there is the problem, but as I am new in this... I honestly don’t know how to fix that. What should I do???

 

The obtained results were:


QIIME full install test results

===============================
.F..........F.F......F.F..F
======================================================================
FAIL: test_INFERNAL_supported_version (__main__.QIIMEDependencyFull)

INFERNAL is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 511, in test_INFERNAL_supported_version

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

AssertionError: Unsupported INFERNAL version. 1.0.2 is required, but running 1.1.1.
======================================================================

FAIL: test_denoiser_supported_version (__main__.QIIMEDependencyFull)

denoiser aligner is ready to use
---------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 569, in test_denoiser_supported_version

    "Denoiser flowgram aligner not found or not "

AssertionError: Denoiser flowgram aligner not found or not executable. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================

FAIL: test_gdata_install (__main__.QIIMEDependencyFull)

gdata is installed
----------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 703, in test_gdata_install

    self.assertTrue(pass_test, "gdata is not installed.")

AssertionError: gdata is not installed.
======================================================================
FAIL: test_raxmlHPC_supported_version (__main__.QIIMEDependencyFull)

raxmlHPC is in path and version is supported
--------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 593, in test_raxmlHPC_supported_version

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

AssertionError: Unsupported raxmlHPC version. (7, 3, 0).(7, 3, 5) is required, but running 8.0.26.
======================================================================
FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull)

sourcetracker is installed
----------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 411, in test_sourcetracker_installed

    ("SOURCETRACKER_PATH is not set. This is "

AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker.
======================================================================
FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)

usearch is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 663, in test_usearch_supported_version

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

AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running

USEARCH is not freely redistributable and is thus not included in the

default QIIME package.  The free VSEARCH will be used in place of USEARCH

where possible, but this does not produce identical results.

You may obtain a personal copy of the 32-bit USEARCH at no charge.

To use this feature, please go to:

    http://www.drive5.com/usearch/download.html

Download USEARCH v5.2.236, then:

    sudo mv usearch* /usr/local/bin/usearch

    sudo chmod a+x /usr/local/bin/usearch

You probably also want to install USEARCH 6.1 as /usr/local/bin/usearch61

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

Thank you so much for your help!

Barvaz Sini

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Jun 16, 2016, 2:24:05 AM6/16/16
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Hi Marcela,
Can you give the exact command you used for the pick_open_reference_otus?
Also, can you attach the print_qiime_config.py -v

Thanks
Amnon

Marcela Villegas

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Jun 16, 2016, 3:06:43 PM6/16/16
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Hi Amnon, When I put he command (print_qiime_config.py -v) , the output was:

System information

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

         Platform: linux2

   Python version: 2.7.6 (default, Jun 22 2015, 17:58:13)  [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+dfsg-1biolinux3

qiime-default-reference version: 0.1.3

                  NumPy version: 1.8.2

                  SciPy version: 0.13.3

                 pandas version: 0.13.1

             matplotlib version: 1.3.1

            biom-format version: 2.1.4

                   h5py version: 2.2.1 (HDF5 version: 1.8.11)

                   qcli version: 0.1.0

                   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 1.0.01

                  swarm version: Swarm 1.2.20 [Feb  1 2015 09:42:15]

                          gdata: Not 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: /usr/share/ncbi/data

                  cluster_jobs_fp: None

      pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                    jobs_to_start: 1

pynast_template_alignment_blastdb: None

                qiime_scripts_dir: /usr/lib/qiime/bin/

                      working_dir: .

     pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed

                    python_exe_fp: python

                         temp_dir: /tmp/

assign_taxonomy_reference_seqs_fp: # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta

                      blastall_fp: blastall

                 seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt


The command to do Otu Picking was:


pick_open_reference_otus.py -i seqs.fna -r ../../../../97_otus.fasta -o OtuPickingV4q20


Thanks for your help!

Marcela




Barvaz Sini

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Jun 17, 2016, 1:37:18 AM6/17/16
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Hi,
It seems the assign taxonomy (final phase of the pick_open_reference_otus.py) fails. 
One option would be to try and remove the relative path from the reference db (in the -r option), so instead of using ../../ try giving the actual absolute path to it.
If the open reference picking was fast, i would recommend just rerunning with the absolute path
otherwise, you can just try to do the assign taxonomy manually, but this could be a bit more complicated.
also, can you find the rep_set_tax_assignments.log rep_set_tax_assignments.txt files and look what they contain?

Amnon

Barvaz Sini

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Jun 17, 2016, 1:37:31 AM6/17/16
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