HITDB classifier

[M_F (Meriem)]

Hello,
I would like to know if there is any update in the newest version of QIIME2 regarding HITDB classifier because when using the following command line
qiime tools import
--type 'FeatureData[Taxonomy]'
--source-format HeaderlessTSVTaxonomyFormat
--input-path HITdb_taxonomy_qiime.txt
--output-path HITdb_taxonomy_qiime.qza

An error message was displayed
No such option: --source-format

Classifer HITdb from Ritari et al. 2015 - suitable for q2

Hi This may be useful to someone. I'm new to qiime but while learning it over the past week I made a q2 usable version of the HITdb classifier from this paper: Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database - PMC "Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database" . It's a gut specific 16S database and here I used their *.fna (fasta) files and the taxonomy text file from the supplement…

Moreover, i will focus on V3-V4 16S rDNA Hypervariables regions, do you know what does 250 in the following command refers to ?
qiime feature-classifier extract-reads
--i-sequences HITdb_sequences.qza
--p-f-primer GTGCCAGCMGCCGCGGTAA
--p-r-primer GGACTACHVGGGTWTCTAAT
--p-trunc-len 250
--o-reads HITdb_sequences_V4.qza

Thanks

.

[colinvwood (Colin Wood)]

Hello @M_F,

Sorry for the long delay, this fell off our radar somehow. I don't have any information about the HITDB classifier. But I can tell you that you probably meant --input-format not --source-format. The --p-trunc-len parameter specifies the length the extracted read should be truncated to. See the command line explanations for more info.