Hi, I'm trying to extract reference reads from a qiime2 compatible PhytoRef database. [ Oceanic_database/PhytoRef at master · ndu-bioinfo/Oceanic_database · GitHub ]. I have worked with this database before (trained the classifier with the provided files : Phyto_16S_plastid_qiime2.qza and Phyto_16S_…

Hi @uth , Can you tell us what QIIME 2 version you are running and the OS, as well as copy & paste the exact commands you ran, as well as the full error message you get. Adding the --verbose flag would be very useful as well. In future posts, these would be a great a minimum info starting point. T…

Hi, Thanks a lot for the response. I apologise for the late reply!!! Below is the command I used qiime feature-classifier extract-reads --i-sequences qiime2-compatible-phytoref-files/Phyto_16S_plastid_qiime2.qza --p-f-primer GTGCCAGCMGCCGCGGTAA --p-r-primer GGACTACHVGGGTWTCTAAT --o-reads referenc…

Hi @uth , Thanks for the update. [image] Mehrbod_Estaki: Can you tell us what QIIME 2 version you are running The error is telling you that it can't find the qiime2-compatible-phytoref-files/Phyto_16S_plastid_qiime2.qza file in the directory you are telling it to. Can you double-check to mak…

Hi @Mehrbod_Estaki , Thanks a lot for the response. The qiime2 version I'm running is 2019.10. "And is this command exactly as you typed it into terminal?"...I usually type the command and tab complete it. I also copy pasted the command you have posted but the error is the same. "Check with ls q…

Hi @uth , I don't think you typed ls qiime2-compatible-phytoref-files/ as I mentioned but rather you typed ll -h while you were in the qiime2-compatible-phytoref-files directory itself. Anyways, I believe the issue is as before, you are just not providing the right path to the file. If you are run…

Hi @Mehrbod_Estaki , I'm extremely sorry for the late reply. I couldn't get anything to work so I went ahead with a classifier I trained with the same files a long time ago without extracting reads. I have copy pasted the error again. I ran the codes with and without specifying paths (by changing t…

Hi @uth , This is a bit odd because I'm able to run this command with no problems using the latest Q2-2020.8 version when I download that file from the github page. You are using a rather old version of Qiime2 (qiime2-2019.10 if I'm not mistaken) and it's possible that just updating to the newest v…

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Error feature classifier:extract reference reads

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