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:
290394Â : 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:Â Â Â /usr/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
Â
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3Dependency 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):Â Â Â 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:
Â
http://qiime.org/install/qiime_config.htmlÂ
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:Â Â Â None
assign_taxonomy_reference_seqs_fp:Â Â Â /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:Â Â Â /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)