Silve132_STDOUT

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_silva132_n1_noRoot.txt -m ../map_lucyTest.txt -r otu_table_rdp-training_silva132_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...
There were 50 or more warnings (use warnings() to see the first 50)
summarize_taxa_through_plots.py
alpha_rarefaction.py
biom summarize-table
evalue: 10899
biom summarize-table
evalue: 10773
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, weighted_unifrac)
Command run was:
 make_emperor.py -i wf_beta_rdp-training_silva132_e10899/weighted_unifrac_pc.txt -o wf_beta_rdp-training_silva132_e10899/weighted_unifrac_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.


sh: 1: tree: not found
###############################################################
R Analysis
###############################################################

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> params= list( otutable='otu_table_rdp-training_silva132_n1_noRoot.txt', mapfile='../map_lucyTest.txt',trefile='silva132_97_pruned.tre',pwd='/home/user/sl1p/picked_otus_abundantotu_silva132', L6file='wf_taxa_summary_rdp-training_silva132_n1_noRoot/otu_table_rdp-training_silva132_n1_noRoot_L6.txt', L2file='wf_taxa_summary_rdp-training_silva132/otu_table_rdp-training_silva132_L2.txt', libstats='library_stats_rdp-training_silva132.txt'); rmarkdown::render('sl1p_analysis.Rmd')


processing file: sl1p_analysis.Rmd
  |..                                                               |   4%
  ordinary text without R code

  |.....                                                            |   7%
label: unnamed-chunk-1 (with options)
List of 1
 $ include: logi FALSE

  |.......                                                          |  11%
  ordinary text without R code

  |..........                                                       |  15%
label: unnamed-chunk-2 (with options)
List of 1
 $ include: logi FALSE

  |............                                                     |  19%
  ordinary text without R code

  |..............                                                   |  22%
label: unnamed-chunk-3 (with options)
List of 1
 $ include: logi FALSE

Quitting from lines 33-37 (sl1p_analysis.Rmd)
Error in file(file, "r") : cannot open the connection
Calls: <Anonymous> ... withVisible -> eval -> eval -> read.newick -> scan -> file

Execution halted
###############################################################
#Cleaning up
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align_silva132/