I’m trying to process 16S sequences derived from Tara oceans metagenomic assemblies (miTAGs) with qiime2 in order to best compare them with my own 16S marine amplicon data.
I was able to import the data as a ‘FeatureData[Sequence]’ because I’m dealing with .fna files, not .fastqs.
Now, I’m trying to run dada2 in order to create ASVs, but I’m coming across the problem that dada2 will only run on fastq files.
Is there any way around this, or is it impossible to make ASVs without quality score info? How does qiime2 typically handle metagenome-derived 16S sequences?
I’m running qiime2-2019.4 with conda.
Here is my command:
os.system(‘source activate qiime2-2019.4 && qiime tools import
Here is the error message:
There were some problems with the command:
(1/3) Invalid value for “–i-demultiplexed-seqs”: Expected an artifact of at
least type SampleData[PairedEndSequencesWithQuality]. An artifact of type
FeatureData[Sequence] was provided.
(2/3) Missing option “–p-trunc-len-f”.
(3/3) Missing option “–p-trunc-len-r”.