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Problem in converting the SRA file to fastq file
Error-
fastq-dump --split-3 SRR5873811
sh: 1: fastq-dump: not found
fastq-dump --split-3 SRR5873810
sh: 1: fastq-dump: not found
fastq-dump --split-3 SRR5873809
sh: 1: fastq-dump: not found
fastq-dump --split-3 SRR5873808
sh: 1: fastq-dump: not found

I had install the SRA tool kit using following command-
> tar xzvf sratoolkit.2.9.2-ubuntu64.tar.gz
and
> export PATH=$PATH:/directory/sratoolkit.2.4.1-ubuntu64/bin

Then, i had downloaded the SRA file in R platform using following command line-
> sri<-read.csv("SraRunInfo.csv", stringsAsFactors=FALSE)
> files<-basename(sri$download_path)
> for(i in 1:length(files)) download.file(sri$download_path[i], files[i])

After that i tried to convert the SRA file to fastq file in R platform using following command-
> for(f in files) {
cmd = paste("fastq-dump --split-3", f)
cat(cmd,"\n")#print the current command
system(cmd) # invoke command
}

Awaiting for your kind reply.
Best regard-
Ankur Sahu,
Tezpur University