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mcurto / SSR-GBS-pipeline

Pipeline to analyse SSR-GBS data (microsatellite loci sequenced with Illumina) based on amplicon length and sequence identity.
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errors in CountLengths.bash script? #1

Open Robvh-git opened 4 years ago

Robvh-git commented 4 years ago

Hello,

I'm experimenting with your SSR-GBS pipeline with your SRA data from Tibihika et al. 2019 regarding the East African Nile Tilapia. I'm trying to run CountLengths.bash on the output of script 1 using following code: bash CountLengths.bash /home/my-workstation/Documents/script1_output /home/my-workstation/Documents/output but I receive following error: ls: cannot access '/home/my-workstation/Documents/output/SeparatOut': No such file or directory.

Upon inspecting the script I see that it appears that the input/output directory variables are mixed up in the script. e.g. for filename in $(ls $Outputdir/SeparatOut); do. So it looks in the Output directory instead of the input directory.

Even when changing it to Input it does not work and I receive the same error. What exactly is this /SeparatOut? I have also deleted this from the script but it still doesn't work.

Could you please advice me on how to fix the issue?

mcurto commented 4 years ago

Hi, thanks for your interest in the pipeline and for pointing out the issue. You are correct there was a mistake on the input and output directory variables. This code was part of a larger script and since I use SeparatOut as a standard directory I didn't noticed the mistake when I tested it. I changed the script and now it should work. Please, let me know of further questions or issues. Best regards, Manuel

Robvh-git commented 4 years ago

Hi Manuel,

thank you for your quick reply. Indeed, the script does work now.

Thank you very much!

Kind regards, Robbert