Complete QIIME beginner here. I have been using Mothur and now want to use MacQIIME for my core diversity etc analysis. However, I am encountering error messages and the only output I get is the log file, rarefied number biom and biom table summary. I've the log below and have attached the mapping file (it appears that the other files are too large to attach). I'd appreciate any help or advice you could give. I've been researching myself to figure it out but I've been unsuccessful! I'm wondering is it maybe to do with my negative control being in the sample which would be one sample on its own different to all the others?
The command I ran was: (9986 being my lowest sample count/selected non phylogenetic diversity as I had issues making the tree [I had the same tree issue in Mothur as my distance file was 249gb])
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