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Wendy Demos
Mar 30, 2016, 4:58:19 PM3/30/16
to Qiime 1 Forum
Greetings.
My sys admin has assured me the update and dependencies have been installed correctly, however, I am running into an error with ChimeraSlayer. Any suggestions for the fix? Thank you in advance
Here is the call and error:
identify_chimeric_seqs.py -m ChimeraSlayer -i Pick_open_ref_out/pynast_aligned_seqs/rep_set_aligned.fasta -a /usr/local/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta -o Pick_open_ref_out/chimeric_seq.txt
Traceback (most recent call last):
File "/usr/local/bin/identify_chimeric_seqs.py", line 354, in <module>
main()
File "/usr/local/bin/identify_chimeric_seqs.py", line 328, in main
keep_intermediates=keep_intermediates)
File "/usr/local/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 159, in chimeraSlayer_identify_chimeras
keep_intermediates=keep_intermediates):
File "/usr/local/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 143, in __call__
keep_intermediates=keep_intermediates)
File "/usr/local/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 637, in get_chimeras_from_Nast_aligned
app_results = app()
File "/usr/local/lib/python2.7/site-packages/burrito/util.py", line 295, in __call__
result_paths = self._get_result_paths(data)
File "/usr/local/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 419, in _get_result_paths
raise ApplicationError("Calling ChimeraSlayer failed.")
burrito.util.ApplicationError: Calling ChimeraSlayer failed.
Qiime config output:
System information
==================
Platform: linux2
Python version: 2.7.9 (default, Apr 21 2015, 14:09:41) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
Python executable: /usr/local/bin/python2.7
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: 0.1.3
NumPy version: 1.10.4
SciPy version: 0.17.0
pandas version: 0.18.0
matplotlib version: 1.5.1
biom-format version: 2.1.5
h5py version: Not installed.
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 [Mar 18 2016 16:56:18]
gdata: Installed.
RDP Classifier version (if installed): Not installed.
Java version (if installed): 1.7.0_21
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
blastmat_dir: None
pick_otus_reference_seqs_fp: /usr/local/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: /usr/local/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: /usr/local/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: /usr/local/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: 1
QIIME full install test results
===============================
.F.FF...F.F.F...FFF..FFF..F
======================================================================
FAIL: test_INFERNAL_supported_version (__main__.QIIMEDependencyFull)
INFERNAL is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 498, in test_INFERNAL_supported_version
"which components of QIIME you plan to use.")
AssertionError: Infernal 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 "/usr/local/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 "/usr/local/bin/print_qiime_config.py", line 470, in test_blast_supported_version
% ('.'.join(map(str, acceptable_version)), version_string))
AssertionError: Unsupported blast version. 2.2.22 is required, but running 2.2.26.
======================================================================
FAIL: test_cdhit_supported_version (__main__.QIIMEDependencyFull)
cd-hit is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 621, in test_cdhit_supported_version
"which components of QIIME you plan to use.")
AssertionError: cd-hit not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_clearcut_supported_version (__main__.QIIMEDependencyFull)
clearcut is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 601, in test_clearcut_supported_version
"which components of QIIME you plan to use.")
AssertionError: clearcut not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_denoiser_supported_version (__main__.QIIMEDependencyFull)
denoiser aligner is ready to use
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 570, 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_h5py (__main__.QIIMEDependencyFull)
h5py is installed
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 709, in test_h5py
"h5py is not installed. You should install this for "
AssertionError: h5py is not installed. You should install this for improved performance with large BIOM files or if working with BIOM format version 2.x files. For more information, see http://qiime.org/documentation/file_formats.html#biom-file-format-versions
======================================================================
FAIL: test_mothur_supported_version (__main__.QIIMEDependencyFull)
mothur is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 540, in test_mothur_supported_version
"which components of QIIME you plan to use.")
AssertionError: mothur not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_muscle_supported_version (__main__.QIIMEDependencyFull)
muscle is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 519, in test_muscle_supported_version
"which components of QIIME you plan to use.")
AssertionError: muscle not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_raxmlHPC_supported_version (__main__.QIIMEDependencyFull)
raxmlHPC is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 580, in test_raxmlHPC_supported_version
"which components of QIIME you plan to use.")
AssertionError: raxmlHPC not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull)
rtax is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 629, in test_rtax_supported_version
"which components of QIIME you plan to use.")
AssertionError: rtax not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull)
sourcetracker is installed
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 412, 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/local/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 0.043s
FAILED (failures=13)
Jenya Kopylov
Mar 30, 2016, 10:30:53 PM3/30/16
to Qiime 1 Forum
Hi Wendy,
Something that pops up immediately is the error "AssertionError: Unsupported blast version. 2.2.22 is required, but running 2.2.26.". ChimeraSlayer uses blast (see more here) and the blast version supported by QIIME 1.9.1 is 2.2.22 (see here for installation). It's possible the command given by ChimeraSlayer is not supported by blast 2.2.26 and thus the call error.
Alternatively, you can also try UCHIME (via usearch or vsearch) which can be faster (see this thread) and does not require blast.
Hope this helps,
Jenya
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