amptk database error about amptk

[JonathanVanHamme]

Hi Junli,

It looks like the log file is saying that you have zero errors in the taxonomy information, zero records with no ID, 5208 with length out of range etc. So, I think you are fine on that front.

I had a similar problem with "line 58" (see your error message) as you can read here:

#77

Jon updated the code for AMPtk 1.5.1 to fix a typo in the dereplicate function, so you may need to update your install and run it again. You can read Jon's comment in the link above, this is the command he provided:

python -m pip install --no-deps --force git+https://github.com/nextgenusfs/amptk.git

That worked for me. Good luck!
Jon

[nextgenusfs]

Hi @yuanyuan12543 -- it looks like you've set the minimum read length at 200 bp and then the log file says 5,208 length out of range. So I'm guessing your fragment is shorter than 200 bp? The COI primers typically amplify something around 150 bp if my memory is correct.