Thank you, the underscore was the issue
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AfterQC Cannot Find Output
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
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GenoMax
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1 answer
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
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