Fastqc - fastq file not found

Question

[leonmcswain]

I am attempting to run fastqc on a single read fastq file. I used sra toolkit to convert sra file to a fastq file. I checked that the file was not paired in and then converted to fastq so I know its correctly formatted (I think). I then closed out the terminal and set the PATH to my FastQC file to run commands but when try to run QC on my file it tells me that "Skipping 'fastq/SRR9019705_1.fastq' which didn't exist, or couldn't be read". I though this was initially because I processed the file as paired end when it was single but after converting for single I am still getting this error. The PATH was set to FastQC location while the directory was set to the fastq file location. I have very minimal experience with terminal.

leonfoymcswain@Leons-MBP ~ % export PATH=$PATH:/Users/leonfoymcswain/Desktop/Bio_Packages/FastQC
leonfoymcswain@Leons-MBP ~ % cd /Users/leonfoymcswain/Desktop/NCBI_Datasets/Ovchinnikov_2020/SRR9019705/fastq       
leonfoymcswain@Leons-MBP fastq % fastqc -t 8 fastq/SRR9019705_1.fastq fastq/SRR9019705_1.fastq
Skipping 'fastq/SRR9019705_1.fastq' which didn't exist, or couldn't be read
Skipping 'fastq/SRR9019705_1.fastq' which didn't exist, or couldn't be read

[leonmcswain]

Thank you! I realized the file name was also typed incorrectly -_-

[ATpoint]

If the answer solve the issue please accept it (the green checkmark below the bookmark sign of the answer).

Answer 1

[Mensur Dlakic]

It seems that you are already in a directory that contains the file. This command:

fastqc -t 8 fastq/SRR9019705_1.fastq

tells the program to look for file SRR9019705_1.fastq which is in fastq subdirectory relative to your present position. Since you already appear to be inside fastq, your command probably should be:

fastqc -t 8 SRR9019705_1.fastq

In the future, you can always type the full path to your file, which includes all the directories leading to it plus the file name:

fastqc -t 8  /Users/leonfoymcswain/Desktop/NCBI_Datasets/Ovchinnikov_2020/SRR9019705/fastq/SRR9019705_1.fastq

That command will work regardless of where you are in the directory hierarchy.