[1] "Usage: my_program.R [options]\n--help           show this screen\n--binDIR PATH    hard path to bin dir [default: 'getwd()/TEDreadsTAX/bin']\n--sccList NAME   hard path and name of file listing successful sample names [default: 'SccList.txt']\n--outdir NAME    path to & name of output directory to create [default: 'getwd()/TEDreadsTAX/merged_tables']\n--genesDIR PATH  hard path to bin dir for KO/EC genes [None for TAX mode, but flag is needed]"
List of 10
 $ --help    : logi FALSE
 $ --binDIR  : chr "/outputs/TAXprofiles/readsTAX_plusPFV/bin/"
 $ --sccList : chr "/outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt"
 $ --outdir  : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ --genesDIR: chr "NA"
 $ help      : logi FALSE
 $ binDIR    : chr "/outputs/TAXprofiles/readsTAX_plusPFV/bin/"
 $ sccList   : chr "/outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt"
 $ outdir    : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ genesDIR  : chr "NA"
NULL
[1] "------> detecting input files:"
[1] "/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904817_wTAXid_4krona.txt"
[2] "/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904818_wTAXid_4krona.txt"
[3] "/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904821_wTAXid_4krona.txt"
[1] "------> naming input files:"
                                                               SRR12904817 
"/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904817_wTAXid_4krona.txt" 
                                                               SRR12904818 
"/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904818_wTAXid_4krona.txt" 
                                                               SRR12904821 
"/outputs/TAXprofiles/readsTAX_plusPFV/bin//SRR12904821_wTAXid_4krona.txt" 
[1] "------> load data from files"
[1] "------> checking data loading objects:"
# A tibble: 6 × 10
# Groups:   Kingdom, Phylum, Class, Order, Family, Genus, Species [6]
  Counts Kingdom  Phylum         Class Order Family Genus Species  TAXid Lineage
   <int> <chr>    <chr>          <chr> <chr> <chr>  <chr> <chr>    <int> <chr>  
1     12 Bacteria Actinomycetota Acti… Acti… Actin… Acti… Actino… 1.65e3 Bacter…
2     14 Bacteria Actinomycetota Acti… Acti… Actin… Acti… Actino… 1.66e3 Bacter…
3      2 Bacteria Actinomycetota Acti… Acti… Actin… Acti… Actino… 5.45e5 Bacter…
4      3 Bacteria Actinomycetota Acti… Acti… Actin… Acti… Actino… 1.85e6 Bacter…
5      0 Bacteria Actinomycetota Acti… Acti… Actin… Paul… Paulje… 2.74e6 Bacter…
6     15 Bacteria Actinomycetota Acti… Acti… Actin… Paul… Paulje… 1.78e5 Bacter…
# A tibble: 6 × 10
# Groups:   Kingdom, Phylum, Class, Order, Family, Genus, Species [6]
  Counts Kingdom Phylum       Class    Order Family Genus Species  TAXid Lineage
   <int> <chr>   <chr>        <chr>    <chr> <chr>  <chr> <chr>    <int> <chr>  
1      2 Viruses Pisuviricota Pisoniv… Pico… Picor… Ente… Entero… 1.21e4 Viruse…
2      0 Viruses Pisuviricota Pisoniv… Pico… Picor… <NA>  Picorn… 1.21e4 Viruse…
3      0 Viruses Pisuviricota Pisoniv… Pico… <NA>   <NA>  Picorn… 4.64e5 Viruse…
4      0 Viruses Pisuviricota Pisoniv… <NA>  <NA>   <NA>  Pisoni… 2.73e6 Viruse…
5      0 Viruses Pisuviricota <NA>     <NA>  <NA>   <NA>  Pisuvi… 2.73e6 Viruse…
6      0 Viruses <NA>         <NA>     <NA>  <NA>   <NA>  Viruse… 1.02e4 Viruse…
[1] "SRR12904817" "SRR12904818" "SRR12904821"
[1] "------> merging data"
[1] "------> checking merged object:"
           Kingdom          Phylum         Class           Order
id204434  Bacteria Acidobacteriota   Terriglobia   Terriglobales
id2789425 Bacteria  Actinomycetota Actinomycetes Actinomycetales
id1659    Bacteria  Actinomycetota Actinomycetes Actinomycetales
id461393  Bacteria  Actinomycetota Actinomycetes Actinomycetales
id1655    Bacteria  Actinomycetota Actinomycetes Actinomycetales
id706438  Bacteria  Actinomycetota Actinomycetes Actinomycetales
                     Family       Genus                    Species SRR12904817
id204434  Acidobacteriaceae        <NA>       Acidobacteriaceae_sp           0
id2789425  Actinomycetaceae Actinomyces        Actinomyces_HMT_175           0
id1659     Actinomycetaceae Actinomyces       Actinomyces_israelii           0
id461393   Actinomycetaceae Actinomyces   Actinomyces_massiliensis           0
id1655     Actinomycetaceae Actinomyces     Actinomyces_naeslundii          14
id706438   Actinomycetaceae Actinomyces Actinomyces_oral_taxon_171           0
          SRR12904818 SRR12904821
id204434            0           1
id2789425           0           1
id1659              0           1
id461393            0           1
id1655              0           1
id706438            2           0
[1] 580  11
[1] "------> exporting data at: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
