Recently I (finally) got around to finishing up analysis of some old(er) 16S data, where I discovered an error in my bash script that ignored one sample during a .fasta file exporting process post cleanup/chimera filtering process in QIIME2.
So I decide to re-run the .fasta export steps using the QIIME2 version 2019.1, which I was using before and also for cleaning up the raw sequences leading up to that point. This is where I got an error saying
filter-seqs that says
Plugin error from feature-table: All features were filtered out of the data.
I looked through few posts on the same error (this, and this, and also this), but they don't seem to quite help with whatever it is that I'm missing or doing wrong. The main thing I saw that got suggested were the input file formats, which I checked for
filter-seqs and they were both
FeatureData[Sequence] so I know it's not the file formatting there.
To get .fasta files from a filtered rep-seqs.qza (post-chimera filtering) per sample, I had some little scripts I used before (last in 2019) that does the following:
my_path/ is whatever relevant path for each file &
sampleID# is the individual sample ID for each sample)
- Imports all the individual names of the sequence samples
qiime feature-table filter-samplesto get filtered-table.qza per sample:
feature-table filter-samples\ --i-table my_path/table-nonchimeric-wo-borderline.qza\ --m-metadata-file names.tsv (has individual sample names)\ --p-where "SampleID='sampleID#'"\ --o-filtered-table sampleID#.qza
qiime feature-table filter-seqson the tables from step 2:
qiime feature-table filter-seqs\ --i-data my_path/rep-seqs-nonchimeric-wo-borderline.qza\ --i-table my_path/sampleID#.qza\ --o-filtered-data my_path/seq-sampleID#.qza
qiime tools exporton outputs from step 3 and get .fasta:
qiime tools export --input-path my_path/seq-sampleID#.qza\ --output-path my_pathq/sampleID#.biom
and the attached(?)
dna-sequences.fastafiles are renamed and moved into a final directory
Looking back the scripts are not the prettiest, but they did at some point, actually gave me the outputs I needed.
At this point, I feel like I am either making the silliest mistake somewhere, or the version I'm using no longer works due to time/newer updates. If it is the latter, how okay is it to use a newer version for the export steps? I know versions can make enough difference in data and I really don't want to introduce any inconsistencies and inaccuracies.
Sorry for such a long post! & Thank you in advance!