plotQualityProfile

General
1

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Does Quality Profile function in DADA2
Error in plotQualityProfile(fnFs[1:2]) : could not find function "plotQualityProfile" > plotQualityProfile(fnFs[1:2]) Error in plotQualityProfile(fnFs[1:2]) : could not find function "plotQualityProfile"

2

Have you loaded the library that defines plotQualityProfile?

If you would like a better answer, please tell us more than just the error message.

3

Hi, I am running into a problem when trying to visualize the quality profile of the forward and reverse reads. I followed all the instructions in the DADA2 tutorial, but I have not be able to fix this problem. I have loaded ggplot2.

4

I have Rstudio 3.6.2 and library ggplot2. I wonder if the combination defines plot Quality Profile

5

do you have library(DADA2) in your code ?

6

I attempted library "ggplot2" and warning message came that the package was built under R 363. I have R 362. Do i need to download the 363 version?

7

Are you saying this because your original issue has been solved ?
I thought you were struggling to find the function plotQualityProfile, I assumed this was because you omitted library("DADA2")

please clarify

8

My original issue was solved after I downloaded 363 version.
I now got smoothly through the DADA2 tutorial until the species assignment. I downloaded the silva_nr_v132_train_set.fa and placed it to the directory, into the folder with my fastq sequences.
Yet below the error message. What could be wrong?
taxa <- assignTaxonomy(seqtab.nochim,

  • "C: /Users/salme/Desktop/SYNCdata/NGS2019/2423 endo/UNZIP/silva_nr_v132_train_set.fa",
  • multithread=TRUE)
    Error: Input/Output
    no input files found
    dirPath: C: /Users/salme/Desktop/SYNCdata/NGS2019/2423 endo/UNZIP/silva_nr_v132_train_set.fa
    pattern: character(0)
9

The error is saying it can't find your files at the given path.

Maybe take a look, you can use dir() to see what files are in some path.

dir(path="C:/Users/salme/Desktop/SYNCdata/NGS2019/2423 endo/UNZIP")

an invalid path will give you character(0) result

maybe its a typo but looks like you had an odd gap between C: and /Users

10

Yes, I did. Please find below. Still smth wrong....what possibly?

dir(path = "C:/Users/salme/Desktop/SYNCdata/NGS 2019/2423 endo/UNZIP"
+ )
 [1] "~$st tutorial.docx"                                "~WRL1522.tmp"                                      "24 jul"                                           
 [4] "2423UNZIP"                                         "30 juuli"                                          "30 juuli history"                                 
 [7] "filtered"                                          "last tutorial.docx"                                "SILVA_LICENSE"                                    
[10] "silva_nr_v128_train_set.fa.gz"                     "silva_species_assignment_v128.fa.gz"               "TA-2423-Rhizo2Ser205-1-ENDO_S58_L001_R1_001.fastq"
[13] "TA-2423-Rhizo2Ser205-1-ENDO_S58_L001_R2_001.fastq" "TA-2423-Rhizo2Ser205-2-ENDO_S59_L001_R1_001.fastq" "TA-2423-Rhizo2Ser205-2-ENDO_S59_L001_R2_001.fastq"
[16] "TA-2423-Rhizo2Ser205-3-ENDO_S60_L001_R1_001.fastq" "TA-2423-Rhizo2Ser205-3-ENDO_S60_L001_R2_001.fastq" "TA-2423-Rhizo2Ser211-1-ENDO_S64_L001_R1_001.fastq"
[19] "TA-2423-Rhizo2Ser211-1-ENDO_S64_L001_R2_001.fastq" "TA-2423-Rhizo2Ser211-2-ENDO_S65_L001_R1_001.fastq" "TA-2423-Rhizo2Ser211-2-ENDO_S65_L001_R2_001.fastq"
[22] "TA-2423-Rhizo2Ser211-3-ENDO_S66_L001_R1_001.fastq" "TA-2423-Rhizo2Ser211-3-ENDO_S66_L001_R2_001.fastq" "TA-2423-Rhizo2Ser229-1-ENDO_S70_L001_R1_001.fastq"
[25] "TA-2423-Rhizo2Ser229-1-ENDO_S70_L001_R2_001.fastq" "TA-2423-Rhizo2Ser229-2-ENDO_S71_L001_R1_001.fastq" "TA-2423-Rhizo2Ser229-2-ENDO_S71_L001_R2_001.fastq"
[28] "TA-2423-Rhizo2Ser229-3-ENDO_R_filt.fastq.gz"       "TA-2423-Rhizo2Ser229-3-ENDO_S72_L001_R1_001.fastq" "TA-2423-Rhizo2Ser229-3-ENDO_S72_L001_R2_001.fastq"
[31] "TA-2423-Rhizo2Ser42-1-ENDO_S55_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser42-1-ENDO_S55_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser42-2-ENDO_S56_L001_R1_001.fastq" 
[34] "TA-2423-Rhizo2Ser42-2-ENDO_S56_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser42-3-ENDO_S57_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser42-3-ENDO_S57_L001_R2_001.fastq" 
[37] "TA-2423-Rhizo2Ser72-1-ENDO_S61_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser72-1-ENDO_S61_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser72-2-ENDO_S62_L001_R1_001.fastq" 
[40] "TA-2423-Rhizo2Ser72-2-ENDO_S62_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser72-3-ENDO_S63_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser72-3-ENDO_S63_L001_R2_001.fastq" 
[43] "TA-2423-Rhizo2Ser97-1-ENDO_S67_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser97-1-ENDO_S67_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser97-2-ENDO_S68_L001_R1_001.fastq" 
[46] "TA-2423-Rhizo2Ser97-2-ENDO_S68_L001_R2_001.fastq"  "TA-2423-Rhizo2Ser97-3-ENDO_S69_L001_R1_001.fastq"  "TA-2423-Rhizo2Ser97-3-ENDO_S69_L001_R2_001.fastq" 
[49] "tax"                                              
> taxa <- assignTaxonomy(seqtab.nochim,
+ "C:/Users/salme/Desktop/SYNCdata/NGS 2019/2423 endo/UNZIP", multithread=TRUE)
Error in .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec,  : 
  reading FASTA file C:/Users/salme/Desktop/SYNCdata/NGS 2019/2423 endo/UNZIP/~$st tutorial.docx: ">" expected at beginning of line 1
>
11

if you are taking all files, and not just those with fastq in the suffix , then you will try and fail to treat a ~$st tutorial.docx as though it were a fastq.

12

Than you but i dont get it. Should i take all files....

13 
(files_to_do <- dir(path = "C:/Users/salme/Desktop/SYNCdata/NGS 2019/2423 endo/UNZIP/*.fastq"))
 taxa <- assignTaxonomy(seqtab.nochim, files_to_do, multithread=TRUE)
14

Thank you! I got the message below. How to proceed?

files_to_do <- dir(path = "C:/Users/salme/Desktop/SYNCdata/NGS 2019/2423 endo/UNZIP/*.fastq")

taxa <- assignTaxonomy(seqtab.nochim, files_to_do, multithread=TRUE)
Error in tax[[1]] : subscript out of bounds

15

I've never used this function. Is it in principle able to process multiple files or not?
If not you would iterate using purrr map functions

16

I am afraid I don't understand. what does it mean tax[[1]] : subscript out of bounds?

17

Here is an explanation.
Run it and think about what it shows

var <- c("a","b")

var[[1]]
var[[2]]
var[[3]]
18

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I started anew and seems multithreading not possible....what does it mean?
frrom the console :
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(200,200), + maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE, + compress=TRUE, multithread=TRUE) # On Windows set multithread=FALSE Multithreading has been DISABLED, as forking is not supported on .Platform$OS.type 'windows' > head(out) reads.in reads.out TA-2423-Rhizo2Ser205-1-ENDO_S58_L001_R1_001.fastq 80846 79511 TA-2423-Rhizo2Ser205-2-ENDO_S59_L001_R1_001.fastq 88318 86841 TA-2423-Rhizo2Ser205-3-ENDO_S60_L001_R1_001.fastq 74490 72962 TA-2423-Rhizo2Ser211-1-ENDO_S64_L001_R1_001.fastq 89280 87813 TA-2423-Rhizo2Ser211-2-ENDO_S65_L001_R1_001.fastq 74096 72708 TA-2423-Rhizo2Ser211-3-ENDO_S66_L001_R1_001.fastq 84392 82972 >

19

so set multithread to false, its not supported in windows. you are limited to one cpu core

20

seems still problem...

out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(200,200),
+                      maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
+ compress=TRUE, multithread=FALSE)
Error: UserArgumentMismatch
  file 'C:\Users\salme\Desktop\SYNCdata\NGS 2019\2423 endo\UNZIP\filtered\TA-2423-Rhizo2Ser205-1-ENDO_F_filt.fastq.gz' exists, but mode is not 'a'
> head(out)