probably faulty QIIME installation may be precluding make_otu_table.py
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André Soares
May 13, 2016, 4:14:28 PM5/13/16
to qiime...@googlegroups.com
Hello there,
Trying to run make_otu_table.py from two seemingly 'good' outputs of pick_otus.py (112.6MB) and assign_taxonomy.py (43.1MB), I come across the following error:
Traceback (most recent call last):
File "/usr/local/bin/make_otu_table.py", line 119, in <module>
main()
File "/usr/local/bin/make_otu_table.py", line 115, in main
write_biom_table(biom_otu_table, opts.output_biom_fp)
File "/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 569, in write_biom_table
"Attempting to write an empty BIOM table to disk. "
qiime.util.EmptyBIOMTableError: Attempting to write an empty BIOM table to disk. QIIME doesn't support writing empty BIOM output files.
The .fasta is good, btw:
count_seqs.py output:
290394 : full_fasta_rep_set.fasta (Sequence lengths (mean +/- std): 334.2277 +/- 192.3702)
No problems running any previous commands.
After reinstalling QIIME from scratch, this still happens...
What can I do??
Thanks,
André
Here's my print_qiime_config.py -tf output:
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
qiime-default-reference version: 0.1.3
NumPy version: 1.11.0
SciPy version: 0.17.1
pandas version: 0.18.1
matplotlib version: 1.5.1
biom-format version: 2.1.5
h5py version: 2.5.0 (HDF5 version: 1.8.11)
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 [May 13 2016 21:04:23]
gdata: Installed.
RDP Classifier version (if installed): Not installed.
Java version (if installed): 1.8.0_91
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: /usr/local/lib/python2.7/dist-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/dist-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/dist-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/dist-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.FFE.FFFF.F....FF..FFF..F
======================================================================
ERROR: test_blastall_fp (__main__.QIIMEDependencyFull)
blastall_fp is set to a valid path
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/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_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 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_cdbtools_supported_version (__main__.QIIMEDependencyFull)
cdbtools is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 477, in test_cdbtools_supported_version
"which components of QIIME you plan to use.")
AssertionError: cdbtools not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
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_chimeraSlayer_install (__main__.QIIMEDependencyFull)
no obvious problems with ChimeraSlayer install
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 429, in test_chimeraSlayer_install
self.assertTrue(chim_slay, "ChimeraSlayer was not found in your $PATH")
AssertionError: ChimeraSlayer was not found in your $PATH
======================================================================
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_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 558, in test_mothur_supported_version
% ('.'.join(map(str, acceptable_version)), version_string))
AssertionError: Unsupported mothur version. 1.25.0 is required, but running 1.36.1.
======================================================================
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 0.096s
FAILED (failures=14, errors=1)
Trying to run make_otu_table.py from two seemingly 'good' outputs of pick_otus.py (112.6MB) and assign_taxonomy.py (43.1MB), I come across the following error:
Traceback (most recent call last):
File "/usr/local/bin/make_otu_table.py", line 119, in <module>
main()
File "/usr/local/bin/make_otu_table.py", line 115, in main
write_biom_table(biom_otu_table, opts.output_biom_fp)
File "/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 569, in write_biom_table
"Attempting to write an empty BIOM table to disk. "
qiime.util.EmptyBIOMTableError: Attempting to write an empty BIOM table to disk. QIIME doesn't support writing empty BIOM output files.
The .fasta is good, btw:
count_seqs.py output:
290394 : full_fasta_rep_set.fasta (Sequence lengths (mean +/- std): 334.2277 +/- 192.3702)
No problems running any previous commands.
After reinstalling QIIME from scratch, this still happens...
What can I do??
Thanks,
André
Here's my print_qiime_config.py -tf output:
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
qiime-default-reference version: 0.1.3
NumPy version: 1.11.0
SciPy version: 0.17.1
pandas version: 0.18.1
matplotlib version: 1.5.1
biom-format version: 2.1.5
h5py version: 2.5.0 (HDF5 version: 1.8.11)
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 [May 13 2016 21:04:23]
gdata: Installed.
RDP Classifier version (if installed): Not installed.
Java version (if installed): 1.8.0_91
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: /usr/local/lib/python2.7/dist-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/dist-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/dist-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/dist-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.FFE.FFFF.F....FF..FFF..F
======================================================================
ERROR: test_blastall_fp (__main__.QIIMEDependencyFull)
blastall_fp is set to a valid path
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/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_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 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_cdbtools_supported_version (__main__.QIIMEDependencyFull)
cdbtools is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 477, in test_cdbtools_supported_version
"which components of QIIME you plan to use.")
AssertionError: cdbtools not found. This may or may not be a problem depending on which components of QIIME you plan to use.
======================================================================
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_chimeraSlayer_install (__main__.QIIMEDependencyFull)
no obvious problems with ChimeraSlayer install
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 429, in test_chimeraSlayer_install
self.assertTrue(chim_slay, "ChimeraSlayer was not found in your $PATH")
AssertionError: ChimeraSlayer was not found in your $PATH
======================================================================
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_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 558, in test_mothur_supported_version
% ('.'.join(map(str, acceptable_version)), version_string))
AssertionError: Unsupported mothur version. 1.25.0 is required, but running 1.36.1.
======================================================================
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 0.096s
FAILED (failures=14, errors=1)
Kyle Bittinger
May 14, 2016, 2:10:35 PM5/14/16
to Qiime 1 Forum
Andre, this is most likely a problem with your input files. Can you send me the exact command you used as well as the first few lines of each input file?
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