I’m using qiime version 2018.11.0 on an Oracle VM Virtual box
I sequenced 89 samples using the EMP protocol on Miseq. I performed the extra steps required to convert the output to fastq as described here
This resulted in 3 files, read 1, read 2 and index files. The read 1 and read 2 files are about 1.2GB big, and the index file is 188MB big. I did the following on qiime 2
qiime tools import
This generated the folder emp-paired-end-sequences.qza
qiime demux emp-paired
This generated the folder demux.qza
After this, I did
qiime tools export --input-path demux.qza --output-path demux.fastq
But this generated a demux.fastq folder with only 8 samples instead of 89! And most these 8 files are only 360 bytes big. I don’t know if I’m doing anything wrong here. I called Illumina, but they weren’t able to help.
I would really appreciate any help!