assign_taxonomy.py error

james.odon

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Apr 13, 2015, 11:11:31 PM4/13/15

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After putting in a .qiime_config file in my home directory and running assign_taxonomy.py, I am not getting an error (as opposed to it running indefinitely.)

This is the error:

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/assign_taxonomy.py", line 349, in <module>

main()

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/assign_taxonomy.py", line 327, in main

log_path=log_path)

File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/assign_taxonomy.py", line 928, in __call__

dir=get_qiime_temp_dir())

File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/tempfile.py", line 454, in NamedTemporaryFile

(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)

File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/tempfile.py", line 235, in _mkstemp_inner

fd = _os.open(file, flags, 0600)

OSError: [Errno 2] No such file or directory: '/mnt/scratch/someUSER/tmp/UclustConsensusTaxonAssigner_uSNIg1.uc'

-----------

Before it was giving zero errors to print_qiime_config.py -t; now it gives 6 errors.

(BTW, how did this work before when there was apparently no .qiime_config file?

These are the errors outputted by print_qiime_config.py

System information

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

Platform: linux2

Python version: 2.7.3 (default, Dec 19 2013, 03:13:59) [GCC 4.6.3]

Python executable: /home/qiime/qiime_software/python-2.7.3-release/bin/python

Dependency versions

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

PyCogent version: 1.5.3

NumPy version: 1.7.1

matplotlib version: 1.3.1

biom-format version: 1.3.1

qcli version: 0.1.0

QIIME library version: 1.8.0

QIIME script version: 1.8.0

PyNAST version (if installed): 1.2.2

Emperor version: 0.9.3

RDP Classifier version (if installed): rdp_classifier-2.2.jar

Java version (if installed): 1.6.0_34

QIIME config values

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

blastmat_dir: /opt/software/BLAST/2.2.22--GCC-4.4.5/data

sc_queue: all.q

topiaryexplorer_project_dir: None

pynast_template_alignment_fp: None

cluster_jobs_fp: /opt/software/QIIME/1.8.0--GCC-4.4.5/bin/start_parallel_jobs_torque.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: None

torque_queue: main

template_alignment_lanemask_fp: None

jobs_to_start: 100

cloud_environment: False

qiime_scripts_dir: /opt/software/QIIME/1.8.0--GCC-4.4.5/bin

denoiser_min_per_core: 50

working_dir: /mnt/scratch/someUSER

python_exe_fp: python

temp_dir: /mnt/scratch/someUSER/tmp/

blastall_fp: blastall

seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: None

.......F....FF............F...F...F

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

FAIL: test_blastmat_dir (__main__.QIIMEDependencyFull)

blastmat_dir is set to a valid path.

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 136, in test_blastmat_dir

test_qiime_config_variable("blastmat_dir", self.config, self)

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 773, in test_qiime_config_variable

(variable,fp))

AssertionError: blastmat_dir set to an invalid file path: /opt/software/BLAST/2.2.22--GCC-4.4.5/data

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

FAIL: test_cluster_jobs_fp (__main__.QIIMEDependencyFull)

cluster_jobs_fp is set to a valid path and is executable

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 124, 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: /opt/software/QIIME/1.8.0--GCC-4.4.5/bin/start_parallel_jobs_torque.py

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

FAIL: test_denoiser_supported_version (__main__.QIIMEDependencyFull)

denoiser aligner is ready to use

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 579, in test_denoiser_supported_version

"which components of QIIME you plan to use.")

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_qiime_scripts_dir (__main__.QIIMEDependencyFull)

qiime_scripts_dir, if set, is set to a valid path

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 168, in test_qiime_scripts_dir

"qiime_scripts_dir does not exist: %s" % scripts_dir)

AssertionError: qiime_scripts_dir does not exist: /opt/software/QIIME/1.8.0--GCC-4.4.5/bin

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

FAIL: test_temp_dir (__main__.QIIMEDependencyFull)

temp_dir, if set, is set to a valid path

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 182, in test_temp_dir

"temp_dir does not exist: %s" % temp_dir)

AssertionError: temp_dir does not exist: /mnt/scratch/someUSER/tmp/

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

FAIL: test_working_dir (__main__.QIIMEDependencyFull)

working_dir, if set, is set to a valid path

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

Traceback (most recent call last):

File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 196, in test_working_dir

"working dir does not exist: %s" % working_dir)

AssertionError: working dir does not exist: /mnt/scratch/someUSER

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

Ran 35 tests in 2.427s

FAILED (failures=6)

james.odon

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Apr 13, 2015, 11:39:06 PM4/13/15

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This is my qiime_config file, the one that was autogenerated:

# autogenerated by qiime-deploy

cluster_jobs_fp /home/qiime/qiime_software/qiime-1.8.0-release/bin/start_parallel_jobs.py

python_exe_fp /home/qiime/qiime_software/python-2.7.3-release/bin/python

qiime_scripts_dir /home/qiime/qiime_software/qiime-1.8.0-release/bin

blastmat_dir /home/qiime/qiime_software/blast-2.2.22-release/data

blastall_fp /home/qiime/qiime_software/blast-2.2.22-release/bin/blastall

template_alignment_lanemask_fp /home/qiime/qiime_software/lanemask_in_1s_and_0s

pynast_template_alignment_fp /home/qiime/qiime_software/core_set_aligned.fasta.imputed

pynast_template_alignment_blastdb

working_dir /tmp/

jobs_to_start 1

seconds_to_sleep 60

temp_dir /tmp/

cloud_environment False

assign_taxonomy_reference_seqs_fp /home/qiime/qiime_software/gg_otus-13_8-release/rep_set/97_otus.fasta

assign_taxonomy_id_to_taxonomy_fp /home/qiime/qiime_software/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt

John Chase

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Apr 14, 2015, 4:52:08 PM4/14/15

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Hello,

Based on previous threads it sounds like there may be a few different problems that are causing issues with running assign_taxonomy.py. As I understand it the goal here is to have assign_taxonomy.py run using uclust without any errors or with it stalling and not finishing.

My understanding is that you are running assign_taxonomy.py in the QIIME 1.8.0 virtual box, which you had previously attempted to upgrade to 1.9.0. It looks like the 1.8/1.9 partial install may be causing some of the issues you are seeing with assign_taxonomy.py. At this point I recommend installing the QIIME 1.9.0 virtual box fresh and rerunning the analyses there. The QIIME virtual boxes contain a full installation of QIIME (except for usearch due to licensing issues), and they come with the Greengenes database and all other necessary data files in their correct locations. The QIIME config file is also correctly configured so you should not need to make any modifications to it.

Can you try rerunning your assign_taxonomy.py commands on a fresh 1.9.0 virtual box and let me know if you run into any issues?

John

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James O'Donnell

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Apr 14, 2015, 5:32:48 PM4/14/15

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Thanks. I will try to reinstall the virtualbox from scratch and see if assign_taxonomy.py works correctly.

James J. O'Donnell PhD

Postdoctoral Fellow

Boone Lab

Indiana University School of Medicine -- South Bend

John Chase

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Apr 17, 2015, 2:27:27 PM4/17/15

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Hi,

Do you run into this same issue when running the QIIME test data? Or is it only when running your files?

John

James O'Donnell

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Apr 17, 2015, 7:21:18 PM4/17/15

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I haven't run the qiime test data, but that is a good idea. I will try it.

I don't think it is my files, though, since the command works fine on my files when using the desktop (non-virtualbox) version of qiime. For some reason, it's only the virtualbox that doesn't work

-Jim

On Fri, Apr 17, 2015 at 2:27 PM, John Chase <chase...@gmail.com> wrote:

Hi,

Do you run into this same issue when running the QIIME test data? Or is it only when running your files?

John

On Tue, Apr 14, 2015 at 2:32 PM, James O'Donnell <james...@gmail.com> wrote:

Thanks. I will try to reinstall the virtualbox from scratch and see if assign_taxonomy.py works correctly.

James J. O'Donnell PhD

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