Mercurial > repos > iuc > qiime_summarize_taxa_through_plots

annotate test-data/summarize_taxa_through_plots/mapping_sort/log_20170501134214.txt @ 7:834ef917138f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 07:54:07 -0500
parents 72b02cea4123
children
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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1 Logging started at 13:42:14 on 01 May 2017
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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2 QIIME version: 1.9.1
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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3
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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4 qiime_config values:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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5 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
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6 sc_queue all.q
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 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
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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8 cluster_jobs_fp start_parallel_jobs.py
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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9 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
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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10 torque_queue friendlyq
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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11 jobs_to_start 1
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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12 denoiser_min_per_core 50
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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13 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
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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14 temp_dir /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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15 blastall_fp blastall
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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16 seconds_to_sleep 1
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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18 parameter file values:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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20 Input file md5 sums:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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21 test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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22 test-data/summarize_taxa_through_plots/Fasting_Map.txt: e16159d7122035797076d66b1a287962
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 Executing commands.
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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26 # Sort OTU Table command
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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27 sort_otu_table.py -i test-data/summarize_taxa_through_plots/otu_table.biom -o summarize_taxa_through_plots_mapping_sort/otu_table_sorted.biom
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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29 Stdout:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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31 Stderr:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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33 # Summarize Taxonomy command
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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34 summarize_taxa.py -i summarize_taxa_through_plots_mapping_sort/otu_table_sorted.biom -o summarize_taxa_through_plots_mapping_sort
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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36 Stdout:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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38 Stderr:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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40 # Plot Taxonomy Summary command
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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41 plot_taxa_summary.py -i summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.txt -o summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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43 Stdout:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45 Stderr:
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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46 /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
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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47 if self._edgecolors == str('face'):
72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72b02cea4123 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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50 Logging stopped at 13:42:34 on 01 May 2017