qiime-deploy environment variable mis-match

[avoorhis]

Hi QIIME People,

I'm having trouble installing QIIME version 1.7 correctly from the qiime-deploy.py script. Once it finishes and

I run print_qiime_config.py -t I see different paths for the environment variables than what is in the qiime_config file.

The paths in the qiime_config file are correct so I'm not sure where the print_qiime_config.py script is getting

its values.

[bpcweb7.bpcservers.private]-avoorhis /xraid2-2/vampsweb/vampsdev> which print_qiime_config.py

/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py

[bpcweb7.bpcservers.private]-avoorhis /xraid2-2/vampsweb/vampsdev> cat qiime_software/qiime_config 

# autogenerated by qiime-deploy

cluster_jobs_fp /xraid2-2/vampsweb/vamps/qiime_software/qiime-1.7.0-release/bin/start_parallel_jobs.py

python_exe_fp /xraid2-2/vampsweb/vamps/qiime_software/python-2.7.3-release/bin/python

qiime_scripts_dir /xraid2-2/vampsweb/vamps/qiime_software/qiime-1.7.0-release/bin

blastmat_dir /xraid2-2/vampsweb/vamps/qiime_software/blast-2.2.22-release/data

blastall_fp /xraid2-2/vampsweb/vamps/qiime_software/blast-2.2.22-release/bin/blastall

template_alignment_lanemask_fp /xraid2-2/vampsweb/vamps/qiime_software/lanemask_in_1s_and_0s

pynast_template_alignment_fp /xraid2-2/vampsweb/vamps/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 /xraid2-2/vampsweb/vamps/qiime_software/gg_otus-12_10-release/rep_set/97_otus.fasta

assign_taxonomy_id_to_taxonomy_fp /xraid2-2/vampsweb/vamps/qiime_software/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt

Output from print_qiime_config.py -t

(the path, /bioware/qiime_software/, exists so no path errors are found)

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

[bpcweb7.bpcservers.private]-avoorhis /xraid2-2/vampsweb/vampsdev> print_qiime_config.py -t

System information

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

         Platform: linux2

   Python version: 2.7.3 (default, Jun 19 2013, 13:38:33)  [GCC 4.6.2 20111027 (Red Hat 4.6.2-1)]

Python executable: /xraid2-2/vampsweb/vampsdev/qiime_software/python-2.7.3-release/bin/python

Dependency versions

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

                     PyCogent version: 1.5.3

                        NumPy version: 1.5.1

                   matplotlib version: 1.1.0

                  biom-format version: 1.1.2

                QIIME library version: 1.7.0

                 QIIME script version: 1.7.0

        PyNAST version (if installed): 1.2

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

          Java version (if installed): 1.7.0_04

QIIME config values

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

                     blastmat_dir: /bioware/qiime_software/blast-2.2.22-release/data

                         sc_queue: all.q

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /bioware/qiime_software/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /bioware/qiime_software/qiime-1.5.0-release/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /bioware/qiime_software/gg_otus-4feb2011-release/rep_set/gg_97_otus_4feb2011.fasta

                     torque_queue: friendlyq

   template_alignment_lanemask_fp: /bioware/qiime_software/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /bioware/qiime_software/qiime-1.5.0-release/bin

            denoiser_min_per_core: 50

                      working_dir: /tmp/

                    python_exe_fp: /bioware/qiime_software/python-2.7.1-release/bin/python

                         temp_dir: /tmp/

                      blastall_fp: /bioware/qiime_software/blast-2.2.22-release/bin/blastall

                 seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: /bioware/qiime_software/gg_otus-4feb2011-release/taxonomies/greengenes_tax_rdp_train.txt

running checks:

test_FastTree_supported_version (__main__.Qiime_config)

FastTree is in path and version is supported ... ok

test_INFERNAL_supported_version (__main__.Qiime_config)

INFERNAL is in path and version is supported ... ok

test_ParsInsert_supported_version (__main__.Qiime_config)

ParsInsert is in path and version is supported ... ok

test_R_supported_version (__main__.Qiime_config)

R is in path and version is supported ... ok

test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane. ... FAIL

test_blast_supported_version (__main__.Qiime_config)

blast is in path and version is supported ... ok

test_blastall_fp (__main__.Qiime_config)

blastall_fp is set to a valid path ... ok

test_blastmat_dir (__main__.Qiime_config)

blastmat_dir is set to a valid path. ... ok

test_cdbtools_supported_version (__main__.Qiime_config)

cdbtools is in path and version is supported ... ok

test_cdhit_supported_version (__main__.Qiime_config)

cd-hit is in path and version is supported ... ok

test_chimeraSlayer_install (__main__.Qiime_config)

no obvious problems with ChimeraSlayer install ... ok

test_clearcut_supported_version (__main__.Qiime_config)

clearcut is in path and version is supported ... ok

test_cluster_jobs_fp (__main__.Qiime_config)

cluster_jobs_fp is set to a valid path and is executable ... ok

test_denoiser_supported_version (__main__.Qiime_config)

denoiser aligner is ready to use ... FAIL

test_for_obsolete_values (__main__.Qiime_config)

local qiime_config has no extra params ... ok

test_gdata_install (__main__.Qiime_config)

gdata is installed ... ok

test_matplotlib_suported_version (__main__.Qiime_config)

maptplotlib version is supported ... ok

test_mothur_supported_version (__main__.Qiime_config)

mothur is in path and version is supported ... ok

test_muscle_supported_version (__main__.Qiime_config)

muscle is in path and version is supported ... ok

test_numpy_suported_version (__main__.Qiime_config)

numpy version is supported ... ok

test_pplacer_supported_version (__main__.Qiime_config)

pplacer is in path and version is supported ... FAIL

test_pynast_suported_version (__main__.Qiime_config)

pynast version is supported ... ok

test_pynast_template_alignment_blastdb_fp (__main__.Qiime_config)

pynast_template_alignment_blastdb, if set, is set to a valid path ... ok

test_pynast_template_alignment_fp (__main__.Qiime_config)

pynast_template_alignment, if set, is set to a valid path ... ok

test_python_exe_fp (__main__.Qiime_config)

python_exe_fp is set to a working python env ... FAIL

test_python_supported_version (__main__.Qiime_config)

python is in path and version is supported ... ok

test_qiime_scripts_dir (__main__.Qiime_config)

qiime_scripts_dir, if set, is set to a valid path ... ok

test_raxmlHPC_supported_version (__main__.Qiime_config)

raxmlHPC is in path and version is supported ... ok

test_rtax_supported_version (__main__.Qiime_config)

rtax is in path and version is supported ... ok

test_sourcetracker_installed (__main__.Qiime_config)

sourcetracker is installed ... ok

test_temp_dir (__main__.Qiime_config)

temp_dir, if set, is set to a valid path ... ok

test_template_alignment_lanemask_fp (__main__.Qiime_config)

template_alignment_lanemask, if set, is set to a valid path ... ok

test_uclust_supported_version (__main__.Qiime_config)

uclust is in path and version is supported ... ok

test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported ... FAIL

test_working_dir (__main__.Qiime_config)

working_dir, if set, is set to a valid path ... ok

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

FAIL: test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane.

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

Traceback (most recent call last):

  File "/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 144, 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_denoiser_supported_version (__main__.Qiime_config)

denoiser aligner is ready to use

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

Traceback (most recent call last):

  File "/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 542, 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_pplacer_supported_version (__main__.Qiime_config)

pplacer is in path and version is supported

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

Traceback (most recent call last):

  File "/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 633, in test_pplacer_supported_version

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

AssertionError: pplacer not found. This may or may not be a problem depending on which components of QIIME you plan to use.

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

FAIL: test_python_exe_fp (__main__.Qiime_config)

python_exe_fp is set to a working python env

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

Traceback (most recent call last):

  File "/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 89, in test_python_exe_fp

    self.fail("Calling python failed. Check you python_exe_fp:%s" %python)

AssertionError: Calling python failed. Check you python_exe_fp:/bioware/qiime_software/python-2.7.1-release/bin/python

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

FAIL: test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported

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

Traceback (most recent call last):

  File "/xraid2-2/vampsweb/vampsdev/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 692, 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 5.2.32

.

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

Ran 35 tests in 1.792s

FAILED (failures=5)

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

So how do I get print_qiime_config.py  to show the correct environment variable paths?

Andy Voorhis

VAMPS

[Yoshiki Vázquez Baeza]

Hello Andy,

Can you check if you have an additional .qiime_config that you are using maybe in the home directory? I think the configuration files are getting messed up.

Also, can you send us the output of env?

Thanks!

Yoshiki.

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[avoorhis]

THANK YOU Yoshiki!  The .qiime_config was hanging out in my home directory causing trouble.

[Yoshiki Vázquez Baeza]

Good to hear that Andy!

Thanks!

Yoshiki.