Specifying directory for emp-paired-end-sequences.qza

Hi everyone - I’m trying to import my sequencing data with the following commands:

cd $WORK/Sequencing

qiime tools import \
–type EMPPairedEndSequences
–input-path 2_fastq \
–output-path emp-paired-end-sequences.qza

The 2_fastq folder contains the sequences and is in the Sequencing folder (my directory).

The problem is that when the emp-paired-end-sequences.qza file is generated it doesn’t go into the 2_fastq folder but in the main directory (Sequencing folder).

Is there a way of specifying the directory so that it goes into the subfolder (2_fastq) instead?


Hi! It’s easy
--output-path 2_fastq/emp-paired-end-sequences.qza

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