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I have checked many times that fastqc is installed in bin folder and 

library("fastqcr")

is also not giving any error still I am getting error of sh: 1: fastqc: not found for the following command

fastqc(fq.dir = "~/WES_Pipeline/Data",   # FASTQ files directory       
       qc.dir = "~/WES_Pipeline/FASTQC", # Results direcory
       threads = 4                       # Number of threads
      )

I am not able to figure out what is the possible reason for this error.

I am currently using R-version 3.4.3, Bioconductor 3.6 in ubuntu 14.04.

zx8754
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    Does this also return an error: `system("fastqc --version")`? – pogibas Jan 07 '18 at 11:09
  • @PoGibas: It is also giving the same error. I have started working on bioinformatics few days before. I have developed a pipeline and want to test it. So I have downloaded the data and testing my codes on Linux pc. – Lot_to_learn Jan 07 '18 at 11:27
  • Try with specified path: `system("/PATH1/PATH2/bin/fastqc --version")` – pogibas Jan 07 '18 at 11:30
  • now it says `sh: 1: ~/bin/FastQC: Permission denied` even I always start rstudio from the terminal with the command `sudo rstudio` . – Lot_to_learn Jan 07 '18 at 15:40
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    Well, it's R and external program permission problem. You should google or look for similar problems on SO. – pogibas Jan 07 '18 at 15:43

0 Answers0