Could you please tell where does the command below lead me? I thought to UNZIP filtered folder?
“~/silva_nr_v132_train_set.fa.gz”,
this part means current working directory. which seems to be C:\Users\salme\Documents/
I didn't know. Yet I placed the files there. Not enough...
dir(path="C:/Users/salme/Documents/UNZIP/filtered")
[1] "rdp_train_set_16.fa.gz" "silva_nr_v128_train_set.fa.gz" "TA-2423-Rhizo2Ser205-1-ENDO_F_filt.fastq.gz"
[4] "TA-2423-Rhizo2Ser205-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser205-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser205-2-ENDO_R_filt.fastq.gz"
[7] "TA-2423-Rhizo2Ser205-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser205-3-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser211-1-ENDO_F_filt.fastq.gz"
[10] "TA-2423-Rhizo2Ser211-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser211-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser211-2-ENDO_R_filt.fastq.gz"
[13] "TA-2423-Rhizo2Ser211-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser211-3-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser229-1-ENDO_F_filt.fastq.gz"
[16] "TA-2423-Rhizo2Ser229-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser229-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser229-2-ENDO_R_filt.fastq.gz"
[19] "TA-2423-Rhizo2Ser229-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser229-3-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser42-1-ENDO_F_filt.fastq.gz"
[22] "TA-2423-Rhizo2Ser42-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser42-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser42-2-ENDO_R_filt.fastq.gz"
[25] "TA-2423-Rhizo2Ser42-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser42-3-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser72-1-ENDO_F_filt.fastq.gz"
[28] "TA-2423-Rhizo2Ser72-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser72-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser72-2-ENDO_R_filt.fastq.gz"
[31] "TA-2423-Rhizo2Ser72-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser72-3-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser97-1-ENDO_F_filt.fastq.gz"
[34] "TA-2423-Rhizo2Ser97-1-ENDO_R_filt.fastq.gz" "TA-2423-Rhizo2Ser97-2-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser97-2-ENDO_R_filt.fastq.gz"
[37] "TA-2423-Rhizo2Ser97-3-ENDO_F_filt.fastq.gz" "TA-2423-Rhizo2Ser97-3-ENDO_R_filt.fastq.gz"
taxa <- assignTaxonomy(seqtab.nochim,
- "~/silva_nr_v132_train_set.fa.gz", multithread=FALSE)
Error: Input/Output
no input files found
dirPath: C:\Users\salme\Documents/silva_nr_v132_train_set.fa.gz
pattern: character(0)
This is a good question! What that means is that you've loaded a package that has a function with the same name as a function in a different package. So in your example, it's telling you that the 'ape' package has a function called 'complement'. The package 'Biostrings' also has a function called 'complement'. Since 'ape' is masking 'Biostrings', if you call 'complement()' in your code, it will automatically use the 'ape' version of 'complement()' instead of the 'Biostrings' version.
You don't really need to do something about right off the bat. That warning is there just to give you a heads up. If you do run into a situation where you need to distinguish between the 'complement()' function in the two different packages, you can be specific by writing 'ape::complement()' or 'Biostrings::complement' to specify.
Q2 Does this mean that using the symbol I can always write just the last part of working directory?
Hi, I started anew: Updated all packages, downloaded last version of DADA2 tutorial (1.16), downloaded last versions of silva files and placed the files into fastq files folder(not into filtered folder as before). Thereafter I applied the commands of the 1.16 tutorial and indeed the assign taxonomy seems to function. Yet it brings to the page below... I don't know what to read out... Eukaryotic sequences? while we studied the 16S sequence of bacteria. Something apparently went wrong in processing the data. Could you please give a hint.
head(track)
input filtered denoisedF denoisedR merged nonchim
TA-2423-Rhizo2Ser205-1-EKTO 88630 85678 72916 81381 18 18
TA-2423-Rhizo2Ser205-2-EKTO 109849 106941 91901 103048 3 3
TA-2423-Rhizo2Ser205-3-EKTO 94610 91885 77732 88214 20 20
TA-2423-Rhizo2Ser211-1-EKTO 81891 79259 62509 74931 28 28
TA-2423-Rhizo2Ser211-2-EKTO 98852 95893 80573 91586 21 21
TA-2423-Rhizo2Ser211-3-EKTO 90015 87377 70476 82730 7 7
taxa <- assignTaxonomy(seqtab.nochim,"~/EKTO/silva_nr_v138_train_set.fa.gz")
taxa <- addSpecies(taxa, "~/EKTO/silva_species_assignment_v138.fa.gz")
taxa.print <- taxa
rownames(taxa.print) <- NULL
head(taxa.print)
Kingdom Phylum Class Order Family Genus Species
[1,] "Eukaryota" NA NA NA NA NA NA
[2,] NA NA NA NA NA NA NA
[3,] "Eukaryota" NA NA NA NA NA NA
[4,] "Eukaryota" NA NA NA NA NA NA
[5,] "Eukaryota" NA NA NA NA NA NA
[6,] "Eukaryota" NA NA NA NA NA NA
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