ERROR RAISED DURING STEP: Assign taxonomy and QIIME full install test failed
Marcela Villegas
I am running the pick_open_reference_otus.py, and I am having the next issue:
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*** 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}
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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
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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
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Thank you so much for your help!
Barvaz Sini
Marcela Villegas
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