Failed to open error: RNAseq Analysis

Question

[Chelsea]

I am getting an error message saying that the files failed to open but it is only the second read for each file not the first read. They are in the same directory as the first read so I am not sure why this is occuring. The code does not look different between the first and second input besides indicating read one and read two

[Ram]

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Answer 1

[GenoMax]

Issue probably is in this part

{}_R2_002.fastq.gz

that should be

{}_R2_001.fastq.gz

Both R1/R2 read files should have 001 in name. That is a left over from ancient times when that number used to be incremented for file pieces (a fixed number of reads used to be put in each file like ~2 M).