issues with paired end import QIIME 2023.9: incorrect demultiplexed sequence counts summary


I am have trouble importing my paired end data into QIIME2 using 2023.9. I am not receiving any error messages but my demultiplexed sequence counts summary visualization is not correct. I am receiving multiple sequence summaries instead of a single mean/median/max/min (see image below).

I am importing paired end reads for each sample (for example, P001_S1_L001_R1_001.fastq.gz and P001_S1_L001_R2_001.fastq.gz) using:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path {metadata_p}/sample_manifest_2023.txt \ --output-path {step_1_p}/1a_paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

followed by:

qiime demux summarize --i-data {step_1_p}/1a_paired-end-demux.qza --o-visualization {step_1_p}/1a_raw_data_quality.qzv

It appears that my paired end reads might not be lining up for each sample. I have checked my sample manifest and paths and sample ID are correct. But the output visualization is as follows.

Please let me know if you have any suggestions!

Hi @cannec,

This is a bug that has been fixed internally as of today. Just your luck!
To fix it on your end you just need to update your qiime2 environment (you can do this by creating a new environment ), after that it re run your commands, the results should be in correct alignment.
Let me know if that is not the case or if you have any other questions.


1 Like

Great! It worked, thank you!!