fkingSTDOUT

Run QIIME
###############################################################
check_id_map.py
split_libraries.py
identify_chimeric_seqs.py
pick otus: AbundantOTU+
alnperc changed 0.030000
now read seqfile: ../splits_dir/seqs_gg2013.fna..
totseq 8, max_seqlen 133, min_seqlen 111

now get consensus by consensus alignment

num_seq 8, num_cover_tot 1, highest-one 2 thresh 5
#Consensus 1 len 133, seq-included 2 (tot-assigned 2 25.00% remain 6)
#Consensus 2 len 133, seq-included 1 (tot-assigned 3 37.50% remain 5)
Time used for abundantOTU: 1 sec
pickconsensus: seq 2 10Lf_2, len 133
#greedyrecruit 3 len 133 seq-included 1 (tot-assigned 1 12.50% remain 7)
pickconsensus: seq 6 10Sf_6, len 133
#greedyrecruit 4 len 133 seq-included 2 (tot-assigned 3 37.50% remain 5)
pickconsensus: seq 3 10Sf_3, len 123
#greedyrecruit 5 len 123 seq-included 1 (tot-assigned 4 50.00% remain 4)
pickconsensus: seq 4 10Sf_4, len 119
#greedyrecruit 6 len 119 seq-included 1 (tot-assigned 5 62.50% remain 3)
pickconsensus: seq 7 11L_7, len 115
#greedyrecruit 7 len 115 seq-included 1 (tot-assigned 6 75.00% remain 2)
pickconsensus: seq 1 10Lf_1, len 112
#greedyrecruit 8 len 112 seq-included 1 (tot-assigned 7 87.50% remain 1)
pickconsensus: seq 8 14L_8, len 111
#greedyrecruit 9 len 111 seq-included 1 (tot-assigned 8 100.00% remain 0)
Total clusters: 7
start writing reports
Cluster size saved to file rep_set.clustsize
7 consensus sequences saved to rep_set.cons
Time used: 1 sec
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assign_taxonomy.py
align_seqs.py
filter_alignment.py
make_phylogeny.py
make GG pruned phylogeny
filter_tree.py
make_otu_table.py
filter_otus_from_otu_table
convert_biom.py | biom convert
removeRoot.pl
convert_biom.py | biom convert
Rscript /home/user/sl1p/bin/sl1p_relAbund.R -o otu_table_rdp-training_gg2013_n1_noRoot.txt -m ../map_lucyTest.txt -r otu_table_rdp-training_gg2013_n1_noRoot_relAbund.txt
Loading required package: methods
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2
Converting input file to a table...
Defining OTU table...
Parsing taxonomy table...
Warning message:
In readLines(file) :
  incomplete final line found on 'otu_table_rdp-training_gg2013_n1_noRoot.txt'
summarize_taxa_through_plots.py
Traceback (most recent call last):
  File "/usr/local/bin/summarize_taxa_through_plots.py", line 143, in <module>
    main()
  File "/usr/local/bin/summarize_taxa_through_plots.py", line 140, in main
    status_update_callback=status_update_callback)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 711, in run_summarize_taxa_through_plots
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Plot Taxonomy Summary
Command run was:
 plot_taxa_summary.py -i wf_taxa_summary_rdp-training_gg2013_n1_noRoot/otu_table_rdp-training_gg2013_n1_noRoot_L2.txt,wf_taxa_summary_rdp-training_gg2013_n1_noRoot/otu_table_rdp-training_gg2013_n1_noRoot_L3.txt,wf_taxa_summary_rdp-training_gg2013_n1_noRoot/otu_table_rdp-training_gg2013_n1_noRoot_L4.txt,wf_taxa_summary_rdp-training_gg2013_n1_noRoot/otu_table_rdp-training_gg2013_n1_noRoot_L5.txt,wf_taxa_summary_rdp-training_gg2013_n1_noRoot/otu_table_rdp-training_gg2013_n1_noRoot_L6.txt -o wf_taxa_summary_rdp-training_gg2013_n1_noRoot/taxa_summary_plots/ --chart_type bar
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/plot_taxa_summary.py", line 278, in <module>
    main()
  File "/usr/local/bin/plot_taxa_summary.py", line 274, in main
    resize_nth_label, label_type, include_html_legend)
  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 1138, in make_all_charts
    resize_nth_label, label_type, include_html_legend))
  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 984, in get_counts
    chart_type, False)
  File "/usr/local/lib/python2.7/dist-packages/qiime/plot_taxa_summary.py", line 715, in get_fracs
    frac = float(n) / total
ZeroDivisionError: float division by zero


alpha_rarefaction.py
Traceback (most recent call last):
  File "/usr/local/bin/alpha_rarefaction.py", line 161, in <module>
    main()
  File "/usr/local/bin/alpha_rarefaction.py", line 158, in main
    retain_intermediate_files=retain_intermediate_files)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 342, in run_alpha_rarefaction
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Alpha diversity on rarefied OTU tables
Command run was:
 parallel_alpha_diversity.py -T -i wf_arare_rdp-training_gg2013//rarefaction/ -o wf_arare_rdp-training_gg2013//alpha_div/ --metrics shannon,PD_whole_tree,chao1,observed_species -t rep_phylo_gg2013.tre --jobs_to_start 1
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/parallel_alpha_diversity.py", line 96, in <module>
    main()
  File "/usr/local/bin/parallel_alpha_diversity.py", line 93, in main
    suppress_submit_jobs=opts.suppress_submit_jobs)
  File "/usr/local/lib/python2.7/dist-packages/qiime/parallel/util.py", line 118, in __call__
    input_dir, input_fn = split(input_fp[0])
IndexError: list index out of range


Traceback (most recent call last):
  File "/usr/local/bin/alpha_rarefaction.py", line 161, in <module>
    main()
  File "/usr/local/bin/alpha_rarefaction.py", line 158, in main
    retain_intermediate_files=retain_intermediate_files)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 342, in run_alpha_rarefaction
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Alpha rarefaction
Command run was:
 parallel_multiple_rarefactions.py -T -i otu_table_rdp-training_gg2013_n1_noRoot.biom -m 10 -x 0 -s -1 -o wf_arare_rdp-training_gg2013_n1_noRoot//rarefaction/  --jobs_to_start 1
Command returned exit status: 2
Stdout:

Stderr
Error in parallel_multiple_rarefactions.py: Error: step size must be greater than 0.
If min = max, just leave step size at 1.

If you need help with QIIME, see:
http://help.qiime.org


biom summarize-table
evalue: 1
biom summarize-table
evalue: 0
beta_diversity_through_plots.py
Traceback (most recent call last):
  File "/usr/local/bin/beta_diversity_through_plots.py", line 153, in <module>
    main()
  File "/usr/local/bin/beta_diversity_through_plots.py", line 150, in main
    status_update_callback=status_update_callback)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/downstream.py", line 183, in run_beta_diversity_through_plots
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Make emperor plots, bray_curtis)
Command run was:
 make_emperor.py -i wf_beta_rdp-training_gg2013_e0_n1_noRoot/bray_curtis_pc.txt -o wf_beta_rdp-training_gg2013_e0_n1_noRoot/bray_curtis_emperor_pcoa_plot/ -m ../map_lucyTest.txt
Command returned exit status: 2
Stdout:

Stderr
Error in make_emperor.py: Due to the variation explained, Emperor could not plot at least 3 axes, check the input files to ensure that the percent explained is greater than 0.01 in at least three axes.