# login with bioinfo
cd /ceph_disk3/lx/ws/user_dir_for_bioinfo/qiime_train_classifier
conda activate qiime2-2020.2

导入数据

qiime tools import \
  --type 'FeatureData[Sequence]' \
  --input-path bacteria_unaligned_08_14_2020.fasta \
  --output-path bacteria_unaligned_08_14_2020.qza

qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-format HeaderlessTSVTaxonomyFormat \
  --input-path taxonomy.txt \
  --output-path ref-taxonomy.qza

抽取序列

qiime feature-classifier extract-reads \
  --i-sequences bacteria_unaligned_08_14_2020.qza \
  --p-f-primer GTGCCAGCMGCCGCGGTAA \
  --p-r-primer GGACTACHVGGGTWTCTAAT \
  --p-trunc-len 120 \
  --p-min-length 100 \
  --p-max-length 400 \
  --o-reads xxxx.qza
  

构建分类器

qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads bacteria_unaligned_08_14_2020.qza \
--i-reference-taxonomy ref-taxonomy.qza \
--o-classifier rdp_bacteria_unaligned_classifier_08_14_2020.qza