Importing and Demultiplex process for 4 Fastq Files: R1, R2, Index1 and Index2

[Sara_Jeanne08 (Sara D.)]

Hi Nicolas,

I was able to complete denovo and reference based chimera checking and now moving on to OTU picking with VSearch. I am having a hard time importing my Silva taxonomy following the format below:

@Nicholas_Bokulich

qiime tools import
--type 'FeatureData[Taxonomy]'
--source-format HeaderlessTSVTaxonomyFormat
--input-path 99_otu_taxonomy.txt
--output-path ref-taxonomy.qza

This the command I passed:

(qiime2-2017.12) bash-3.2$ qiime tools import --type FeatureData[Taxonomy] --source-format HeaderLessTSVTaxonomyFormat --input-path ./consensus_taxonomy_7_levels.txt --output-path ref-taxonomy.qza
Traceback (most recent call last):
  File "/Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/util.py", line 91, in parse_format
    format_record = pm.formats[format_str]
KeyError: 'HeaderLessTSVTaxonomyFormat'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/tools.py", line 116, in import_data
    view_type=source_format)
  File "/Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/result.py", line 180, in import_data
    view_type = qiime2.sdk.parse_format(view_type)
  File "/Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/util.py", line 93, in parse_format
    raise TypeError("No format: %s" % format_str)
TypeError: No format: HeaderLessTSVTaxonomyFormat

An unexpected error has occurred:

  No format: HeaderLessTSVTaxonomyFormat

See above for debug info.

Thank you very much for your time and help with this,

Sara

[Nicholas_Bokulich]

@Sara_Jeanne08

HeaderLessTSVTaxonomyFormat

Try HeaderlessTSVTaxonomyFormat instead — sorry, I had copied/pasted the above command from elsewhere and obviously propagated a typo. You can see the correct command in this tutorial, and I have corrected this typo above.

I hope that helps!

EDIT: the original command I wrote (copied/pasted) above is correct, but for some reason the forum is automatically capitalizing the "less" in "Headerless". Make sure that the "less" is lowercase. HeaderlessTSVTaxonomyFormat. Thanks!