annotate test-data/summarize_taxa_through_plots/mapping_categories/log_20170501132849.txt @ 0:c11972e98d44 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862

Logging started at 13:28:49 on 01 May 2017
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/Users/bebatut/miniconda3/envs/qiime/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	/Users/bebatut/miniconda3/envs/qiime/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	/Users/bebatut/miniconda3/envs/qiime/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	/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:

Input file md5 sums:
test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
test-data/summarize_taxa_through_plots/Fasting_Map.txt: e16159d7122035797076d66b1a287962

Executing commands.

# Collapse samples in OTU table by categories command 
collapse_samples.py -m test-data/summarize_taxa_through_plots/Fasting_Map.txt -b test-data/summarize_taxa_through_plots/otu_table.biom --output_biom_fp summarize_taxa_through_plots_mapping_categories/Treatment_otu_table.biom --output_mapping_fp summarize_taxa_through_plots_mapping_categories/Treatment_map.txt --collapse_fields 'Treatment' 

Stdout:

Stderr:

# Summarize Taxonomy command 
summarize_taxa.py -i summarize_taxa_through_plots_mapping_categories/Treatment_otu_table.biom -o summarize_taxa_through_plots_mapping_categories 

Stdout:

Stderr:

# Plot Taxonomy Summary command 
plot_taxa_summary.py -i summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.txt -o summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/ 

Stdout:

Stderr:
/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):


Logging stopped at 13:29:07 on 01 May 2017