AfterQC Cannot Find Output

Question

[alexadeanfitz]

I have run AfterQC using python2.7 on a folder containing fastq files, I get no errors in the terminal window however I cannot locate the generated output folders and it runs too fast for me to think it actually worked, any advice?

Lab-iMac:lab$ cd /Users/Alexa/Alexa/SRP135669/fastq/fastq

Lab-iMac:fastq lab$ python2.7 /Applications/anaconda3/envs/python27/afterqc-0.9.7-2/after.py -f -1 -t -1 -q 20 --input dir /Users/Alexa/Alexa/SRP135669/fastq/fastq

Answer 1

[GenoMax]

Based on the manual the output should be in the same folder where R1 is: Users/Alexa/Alexa/SRP135669/fastq/fastq

In your case something like (don't forget the _ between input and dir, that is missing in your command)

$ python2.7 /Applications/anaconda3/envs/python27/afterqc-0.9.7-2/after.py -f -1 -t -1 -q 20 --input_dir /Users/Alexa/Alexa/SRP135669/fastq/fastq

[alexadeanfitz]

Thank you, the underscore was the issue