marcelm
commented
11 months ago This is not really a question about Cutadapt, but about R. I don’t use R regularly, but you may be able to solve this problem by adding a call to shQuote. So instead of
system2(cutadapt, args = c(R1.flags, "-o", fnFs.cut[i], fnFs.filtN[i]))try running this:
system2(cutadapt, args = shQuote(c(R1.flags, "-o", fnFs.cut[i], fnFs.filtN[i])))
Hi - I am having some trouble with trimming the primers from the sequences (I am using foward reads only for the analysis). A previous similar "issue" I read unfortunately didn't help because I have already accounted for the " and /.
I have quoted and used / in the path name to account for the space between "Processing PC3" which I cannot change. I imagine the space there is the issue - would be grateful for your advice on how to rectify this.
path <- "C:/Users/Processing PC3/Desktop/ITS_FFPE2"
list.files(path)
cutadapt <- "C:/Users/Processing PC3/Downloads/cutadapt.exe" system2(cutadapt, args = "--version")
path.cut <- file.path(path, "cutadapt") if(!dir.exists(path.cut)) dir.create(path.cut) fnFs.cut <- file.path(path.cut, basename(fnFs))
FWD.RC <- dada2:::rc(FWD)
R1.flags <- paste("-g", FWD)
for(i in seq_along(fnFs)) { system2(cutadapt, args = c(R1.flags, "-o", fnFs.cut[i], fnFs.filtN[i])) }
The error message I get is:
This is cutadapt 4.0 with Python 3.9.12 Command line parameters: -g CTTGGTCATTTAGAGGAAGTAA -o C:/Users/Processing PC3/Desktop//ITS_FFPE2/cutadapt/DWE1NegLN_1.fastq.gz C:/Users/Processing PC3/Desktop//ITS_FFPE2/filtN/DWE1NegLN_1.fastq.gz Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation.
cutadapt.exe: error: You provided 3 input file names, but either one or two are expected. The file names were:
Thank you