[1] "------> start of PWY Diversity Plots <------"
[1] "------> docopt settings ------"
[1] "Usage: DiversityPlots_v3.R [options]\n  --help            show this screen.\n  --wdir PATH       give path to working dir /project main dir  [default: pwd ].\n  --indir PATH      give path to input files directory [default: profiles/merged_tables ].\n  --mfile NAME      give name of mapping file [default: mapping.txt ].\n  --outdir NAME     give path & name of output directory to create [default: pwd/profiles/DiversityPlots]."
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 $ --help  : logi FALSE
 $ --wdir  : chr "/outputs/tmp"
 $ --indir : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ --mfile : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt"
 $ --outdir: chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/"
 $ help    : logi FALSE
 $ wdir    : chr "/outputs/tmp"
 $ indir   : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ mfile   : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt"
 $ outdir  : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/"
NULL
[1] "-----------> docopt settings------^^^^"
[1] "-----------> reading in mapping file:"
               SampleID Description TreatmentGroup
SRR12904817 SRR12904817 SRR12904817       12 month
SRR12904818 SRR12904818 SRR12904818       12 month
SRR12904821 SRR12904821 SRR12904821        1 month
                                ForwardFastqFile
SRR12904817 /inputs/SRR12904817_1_2Msub.fastq.gz
SRR12904818 /inputs/SRR12904818_1_2Msub.fastq.gz
SRR12904821 /inputs/SRR12904821_1_2Msub.fastq.gz
                                ReverseFastqFile
SRR12904817 /inputs/SRR12904817_2_2Msub.fastq.gz
SRR12904818 /inputs/SRR12904818_2_2Msub.fastq.gz
SRR12904821 /inputs/SRR12904821_2_2Msub.fastq.gz
[1] "-----------> done importing mapping file^^^"
[1] "-----------> prepping AMPVIS2 object"
                     Phylum                 Order                      Species
map04214 Cellular Processes Cell growth and death              Apoptosis - fly
map04112 Cellular Processes Cell growth and death     Cell cycle - Caulobacter
map04111 Cellular Processes Cell growth and death           Cell cycle - yeast
map04110 Cellular Processes Cell growth and death                   Cell cycle
map04113 Cellular Processes Cell growth and death              Meiosis - yeast
map04820 Cellular Processes         Cell motility Cytoskeleton in muscle cells
              OTU SRR12904817 SRR12904818 SRR12904821
map04214 map04214       44.75        10.0       16.50
map04112 map04112       22.31        28.9       28.05
map04111 map04111        0.00         0.0       16.73
map04110 map04110        0.00         0.0       22.07
map04113 map04113        0.00         0.0       15.58
map04820 map04820        0.00         0.0       29.67
[1] "-----------> making PCOA plot"
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[1] "-----------> making nMDS plot"
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[1] "-----------> making heatmap profile graph"
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