test_result.log

1..33
ok 1 Variable set: version
ok 2 silva_db database file
ok 3 silva_udb database file
ok 4 typestrains_udb database file
ok 5 Variable set: denovo_prefix
ok 6 Variable set: maxthreads
ok 7 usearch in $PATH
ok 8 sina in $PATH
ok 9 R in $PATH
ok 10 Rscript in $PATH
ok 11 Check installed R packages
ok 12 Echo with timestamp
ok 13 Shell is BASH
ok 14 Error if temp/ folder exists
ok 15 Error if output/ folder exists
ok 16 Check input data
ok 17 Step: Orient
ok 18 Step: Dereplication
ok 19 Step: Denoise
ok 20 Step: Find longest and rename
ok 21 Step (optional): Add additional FLASVs to DB
ok 22 Step: Global alignment against SILVA
ok 23 Step: Trim and strip alignment
ok 24 Step: Sort FLASVs by ID (i.e. highest coverage)
ok 25 Step: Obtaining the taxonomy of the best hit in the SILVA database
ok 26 Step: Obtaining the taxonomy of species (>98.7% id) in the SILVA typestrains database
ok 27 Step: Cluster at species level
ok 28 Step: Cluster at genus level
ok 29 Step: Cluster at family level
ok 30 Step: Cluster at order level
ok 31 Step: Cluster at class level
ok 32 Step: Cluster at phylum level
ok 33 Step: Merge and output taxonomy