Qiime2 installed, but command not found when I run command

Hi all,

I installed qiime2 on Mac, activated and checked the installation with qiime--help, everything is fine. however, when I running command, such as_ _ join_paired_ends.py -i $PWD/R1Index.fastq, -r $PWD/R1Index.fastq, -o $PWD/Barcode.fastq

it showed:
-bash: join_paired_ends.py: command not found

Could you please let me know what’s run? Thanks a lot!

Hi @savan - join_paired_ends.py is not a QIIME 2 command, which is why this is failing for you. Please take a look at docs.qiime2.org to get started with QIIME 2. Thanks!

Hi Matthew, I did follow it. For example, when I follow the 454 Overview Tutoria, 454 Overview Tutoria,
turns out: -bash: validate_mapping_file.py: command not found.

I think you might be confusing QIIME 1 and QIIME 2. Please follow the link I provided above for information on QIIME 2.

An off-topic reply has been split into a new topic: How to import demultiplexed paired-end reads?

Please keep replies on-topic in the future.

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