I'm running qiime2 to demultiplex data. I have a forward.fastq.gz file, a reverse.fastq.gz and a barcode.fastq.gz file. So the syntax I used is as below:
After this step I got per sample .fastq files as I expected. However, the size of each fastq file were smaller than the files that have been demultiplexed with qiime1 2 years ago. Below is the file size comparison:
Hi @Leran,
Looks like your original files are fastq files and the new files are compressed fastq files (.gz extension). I believe the reason why the new files are smaller is because the old files were not compressed.
Thanks for your reply @Cherman2! I think you are right and I unzipped the fastq.gz files. The sizes did improved but still not the same with before. I also checked the reads, I took one sample as an example, as shown below:
Old file:
New file:
So the number of reads of the old fastq file is bigger than the number of reads of the new fastq file.
Another thing I have noticed that I'm not sure if it could be related to this. When I ran the "qiime demux emp-paired" step, it takes very long time and then I would received a "broken pipe" notification. When I check the output files, the demux.qza file is there. I'm not sure if this file can be generated even if the process was not fully finished. So I never know if the process has finished or not.
Could the less reads issue be caused by the incompleteness of this step?
