assign_tax(analysis_setup,asv_abund_matrix,  retrieve_files=FALSE,  overwrite_existing=FALSE,  db_rps10="oomycetedb.fasta",  db_its="fungidb.fasta",  db_16S="bacteriadb.fasta",  db_other1="otherdb1.fasta",  db_other2="otherdb2.fasta")

# \donttest{# Assign taxonomies to ASVs on by metabarcodeanalysis_setup<-prepare_reads(  data_directory=system.file("extdata", package="demulticoder"),  output_directory=tempdir(),  overwrite_existing=TRUE)#> Existing files found in the output directory. Overwriting existing files.#>Rows:2Columns:25#>──Column specification────────────────────────────────────────────────────────#>Delimiter: ","#>chr  (3): primer_name, forward, reverse#>dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...#>lgl  (4): already_trimmed, count_all_samples, multithread, verbose#>#>ℹ Use `spec()` to retrieve the full column specification for this data.#>ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.#>Rows:2Columns:25#>──Column specification────────────────────────────────────────────────────────#>Delimiter: ","#>chr  (3): primer_name, forward, reverse#>dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...#>lgl  (4): already_trimmed, count_all_samples, multithread, verbose#>#>ℹ Use `spec()` to retrieve the full column specification for this data.#>ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.#>Rows:4Columns:3#>──Column specification────────────────────────────────────────────────────────#>Delimiter: ","#>chr (3): sample_name, primer_name, organism#>#>ℹ Use `spec()` to retrieve the full column specification for this data.#>ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.#> Creating output directory: /tmp/RtmpAtZc28/demulticoder_run/prefiltered_sequencescut_trim(analysis_setup,cutadapt_path="/usr/bin/cutadapt",overwrite_existing=TRUE)#> Running cutadapt 3.5 for its sequence data#> Running cutadapt 3.5 for rps10 sequence datamake_asv_abund_matrix(analysis_setup,overwrite_existing=TRUE)#> 80608 total bases in 307 reads from 2 samples will be used for learning the error rates.#> Error rate plot for the  Forward  read of primer pair  its#>Warning:log-10 transformation introduced infinite values.#> Sample 1 - 163 reads in 84 unique sequences.#> Sample 2 - 144 reads in 96 unique sequences.#> 82114 total bases in 307 reads from 2 samples will be used for learning the error rates.#> Error rate plot for the  Reverse  read of primer pair  its#>Warning:log-10 transformation introduced infinite values.#> Sample 1 - 163 reads in 128 unique sequences.#> Sample 2 - 144 reads in 119 unique sequences.#> 91897 total bases in 327 reads from 2 samples will be used for learning the error rates.#> Error rate plot for the  Forward  read of primer pair  rps10#>Warning:log-10 transformation introduced infinite values.#> Sample 1 - 145 reads in 107 unique sequences.#> Sample 2 - 182 reads in 133 unique sequences.#> 91567 total bases in 327 reads from 2 samples will be used for learning the error rates.#> Error rate plot for the  Reverse  read of primer pair  rps10#>Warning:log-10 transformation introduced infinite values.#> Sample 1 - 145 reads in 114 unique sequences.#> Sample 2 - 182 reads in 170 unique sequences.#> $its#> [1] "/tmp/RtmpAtZc28/demulticoder_run/asvabund_matrixDADA2_its.RData"#>#> $rps10#> [1] "/tmp/RtmpAtZc28/demulticoder_run/asvabund_matrixDADA2_rps10.RData"#>assign_tax(analysis_setup,asv_abund_matrix,retrieve_files=FALSE,overwrite_existing=TRUE)#> Tracking read counts:#>   samplename_barcode input filtered denoisedF denoisedR merged nonchim#> 1             S1_its   299      163       146       141    132     132#> 2             S2_its   235      144       113        99     99      99#> Tracking read counts:#>   samplename_barcode input filtered denoisedF denoisedR merged nonchim#> 1           S1_rps10   196      145       145       145    145     145#> 2           S2_rps10   253      182       181       181    181     181# }