Diagnostic.py or Mask-alignment.py filtered my important sequences

I started using nextstrain only two days ago) My question is about filtering. I take 2 samples from example folder and 5 my samples (with bad quality). I see that there is problem with my seqs - they were filtered on the step python3 scripts/diagnostic.py, as I could understand from log-file. In results/aligned.fasta there are all 5 samples, but in aligned-filtered.fasta only 2 good samples from examples.
It is not a problem about wrong dates or locations, etc, because when changed only sequences in my samples it worked well. Also I add samples to “include-file” and it did not help
Could you help me, please: how could I change a filter to have my bad samples in results?