Error of "Cannot find R. Is it installed? Is it in your path?" when running compare_categories.py
Catie Williams
$ compare_categories.py --method permdisp -m mapping_file.txt -c SeasonCollected -o SeasonAnosimUnweighted -i BetaDiv/unweighted_unifrac_dm.txt
Traceback (most recent call last):
File "/Users/catiewilliams/miniconda3/envs/qiime1/bin/compare_categories.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'compare_categories.py')
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/compare_categories.py", line 189, in <module>
main()
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/compare_categories.py", line 185, in main
categories, opts.num_permutations, out_dir)
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/compare_categories.py", line 145, in compare_categories
rex = RExecutor(TmpDir=get_qiime_temp_dir())
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/burrito-0.9.1-py2.7.egg/burrito/util.py", line 201, in __init__
File "/Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/burrito-0.9.1-py2.7.egg/burrito/util.py", line 468, in _error_on_missing_application
burrito.util.ApplicationNotFoundError: Cannot find R. Is it installed? Is it in your path?
And for print_qiime_config.py -t
System information
==================
Platform: darwin
Python version: 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:43:17) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)]
Python executable: /Users/catiewilliams/miniconda3/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 version 2.0, 29/11/2014
sumaclust version: Not installed.
swarm version: Swarm 1.2.19 [Mar 5 2016 17:12:19]
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: /Users/catiewilliams/miniconda3/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: /Users/catiewilliams/miniconda3/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: /Users/catiewilliams/miniconda3/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: /Users/catiewilliams/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /var/folders/tx/hbfl5qyd4sj9pk5v6nzsrnkw0000gn/T/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 1
QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.161s
OK
Jose
you have probably not installed R after the base install of QIIME. Please see here for details on how to get R installed:
http://qiime.org/install/alternative.html#additional-install-notes-for-some-external-dependencies
Jose
Catie Williams
System information
==================
Platform: darwin
Python version: 2.7.10 |Anaconda 2.2.0 (x86_64)| (default, May 28 2015, 17:04:42) [GCC 4.2.1 (Apple Inc. build 5577)]
Python executable: /macqiime/anaconda/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.2
NumPy version: 1.9.2
SciPy version: 0.15.1
pandas version: 0.16.1
matplotlib version: 1.4.3
biom-format version: 2.1.4
h5py version: 2.4.0 (HDF5 version: 1.8.14)
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 [Jun 2 2015 14:40:16]
gdata: Installed.
RDP Classifier version (if installed): rdp_classifier-2.2.jar
Java version (if installed): 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: None
pick_otus_reference_seqs_fp: /macqiime/anaconda/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: /macqiime/anaconda/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: /macqiime/anaconda/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: /macqiime/anaconda/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: 60
QIIME full install test results
===============================
..FFFE....................F
======================================================================
ERROR: test_blastall_fp (__main__.QIIMEDependencyFull)
blastall_fp is set to a valid path
----------------------------------------------------------------------
Traceback (most recent call last):
File "/macqiime/anaconda/bin/print_qiime_config.py", line 446, in test_blastall_fp
blastall)
ApplicationNotFoundError: blastall_fp set to blastall, but is not in your PATH. Either use an absolute path to or put it in your PATH.
======================================================================
FAIL: test_R_supported_version (__main__.QIIMEDependencyFull)
R is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/macqiime/anaconda/bin/print_qiime_config.py", line 671, in test_R_supported_version
"which components of QIIME you plan to use.")
AssertionError: R not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_ampliconnoise_install (__main__.QIIMEDependencyFull)
AmpliconNoise install looks sane.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/macqiime/anaconda/bin/print_qiime_config.py", line 382, in test_ampliconnoise_install
"$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url)
AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.
======================================================================
FAIL: test_blast_supported_version (__main__.QIIMEDependencyFull)
blast is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/macqiime/anaconda/bin/print_qiime_config.py", line 456, in test_blast_supported_version
"which components of QIIME you plan to use.")
AssertionError: blast not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)
usearch is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/macqiime/anaconda/bin/print_qiime_config.py", line 650, in test_usearch_supported_version
"which components of QIIME you plan to use.")
AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.
----------------------------------------------------------------------
Ran 27 tests in 1.241s
FAILED (failures=4, errors=1)