I put a fastq.gz.temp file into a directory (fastqPath2),

> fastqPath2
[1] "./7051-SLNneg_S3_L001_R1_001.fastq.gz.temp"

and then I try to read in fastq.gz.temp file and get the following error with the script:

> reads2 <- readFastq(fastqPath2)
Error: Input/Output
  file(s):
    ./7051-SLNneg_S3_L001_R1_001.fastq.gz.temp
  message: unexpected empty line ./7051-SLNneg_S3_L001_R1_001.fastq.gz.temp:0

I have gotten separate errors on another occasion when i tried to read, e.g., 0 width fastq record, expected to start with @

I have tried to unzip file to see the structure of the file and nothing happens when I do this (after trying gunzip, zcat, unzip) Also tried 7-zip to unzip which did not work either, said 'cannot archive file'

Maybe my file is not in the ASCII format? Perhaps I need to filter or ignore empty line? I downloaded files directly from Illumina Basespace and did nothing to change their format... Need help! I am a novice at programming so please be gentle :) Thanks!

The extension .temp is often present when a file is only partly downloaded; can you validate that the file is complete? The fact that you can't gunzip it also suggests this.