Mercurial > repos > iuc > qiime_split_libraries
diff 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
author | iuc |
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date | Thu, 18 May 2017 09:38:55 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize_taxa_through_plots/mapping_categories/log_20170501132849.txt Thu May 18 09:38:55 2017 -0400 @@ -0,0 +1,50 @@ +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