Logging started at 16:16:18 on 09 Feb 2016
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/macqiime/anaconda/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
assign_taxonomy_reference_seqs_fp	/macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
jobs_to_start	1
denoiser_min_per_core	50
assign_taxonomy_id_to_taxonomy_fp	/macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	60

parameter file values:
beta_diversity:metrics	bray_curtis
alpha_diversity:metrics	observed_otus,chao1
parallel:jobs_to_start	1

Input file md5 sums:
/Users/ciarakeating2/codindex.01.0.01.biom: b03c55151235c24de4e2611394762ce9
/Users/ciarakeating2/mapping_fileCK.txt: b9330b9c0d2f2c31b249770ffd866aec

Executing commands.

# Generate BIOM table summary command 
biom summarize-table -i /Users/ciarakeating2/codindex.01.0.01.biom -o /Users/ciarakeating2/core_diversity01//biom_table_summary.txt 

Stdout:

Stderr:

# Filter low sequence count samples from table (minimum sequence count: 9986) command 
filter_samples_from_otu_table.py -i /Users/ciarakeating2/codindex.01.0.01.biom -o /Users/ciarakeating2/core_diversity01//table_mc9986.biom -n 9986



*** ERROR RAISED DURING STEP: Filter low sequence count samples from table (minimum sequence count: 9986)
Command run was:
 filter_samples_from_otu_table.py -i /Users/ciarakeating2/codindex.01.0.01.biom -o /Users/ciarakeating2/core_diversity01//table_mc9986.biom -n 9986
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/macqiime/anaconda/bin/filter_samples_from_otu_table.py", line 162, in <module>
    main()
  File "/macqiime/anaconda/bin/filter_samples_from_otu_table.py", line 138, in main
    write_biom_table(filtered_otu_table, output_fp)
  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/util.py", line 577, in write_biom_table
    biom_table.to_hdf5(biom_file, generated_by, compress)
  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 3535, in to_hdf5
    self.group_metadata(axis='observation'), 'csr', compression)
  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 3507, in axis_dump
    formatter[category](grp, category, md, compression)
  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 243, in general_formatter
    compression=compression)
  File "/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/group.py", line 99, in create_dataset
    dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
  File "/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 60, in make_new_dset
    raise ValueError("Shape tuple is incompatible with data")
ValueError: Shape tuple is incompatible with data


Logging stopped at 16:17:43 on 09 Feb 2016