taxa collapse - Requested level of 6 is larger than the maximum level available in taxonomy data

Greetings!

While i am entering my command like this for ANCOM analysis

qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table gut-table-l6.qza

I am getting the error message
Plugin error from taxa:

Requested level of 6 is larger than the maximum level available in taxonomy data (1).

Debug info has been saved to /tmp/qiime2-q2cli-err-csfj54uo.log

Error message
Traceback (most recent call last):
File “/apps/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</apps/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-136>”, line 2, in collapse
File “/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/apps/qiime2-2019.1/lib/python3.6/site-packages/q2_taxa/_method.py”, line 27, in collapse
(level, max_observed_level))
ValueError: Requested level of 6 is larger than the maximum level available in taxonomy data (1).

Please help me to sort this issue

Hi! Can you please attach your taxonomy file?

Hi
My taxonomy taxonomy.qza (39.2 KB)

This file i downloaded and converted from
gg-13-8-99-515-806-nb-classifier

I attempted with level 1 also. If doing that the error message is

Traceback (most recent call last):
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</apps/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-136>", line 2, in collapse
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 393, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view
result = transformation(view)
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py", line 220, in wrapped
file_view = transformer(view)
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/q2_types/feature_table/_transformer.py", line 152, in _10
return _table_to_v210(_dataframe_to_table(df))
File "/apps/qiime2-2019.1/lib/python3.6/site-packages/q2_types/feature_table/_transformer.py", line 85, in _dataframe_to_table
raise TypeError("Please provide a DataFrame with a string-based Index")
TypeError: Please provide a DataFrame with a string-based Index

Plugin error from taxa:

Please provide a DataFrame with a string-based Index

See above for debug info.

Thank you

In your taxonomy.qza all features assigned only to the bacteria level or unassigned at all.
You should check your taxonomy classification step with a classifier

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Following up on this, could you describe which database you used, where/what you are sampling, and your primer pair? That will help us understand if there was a mismatch.

Thank you Evan

The sequences are from local 16s rRNA analysis service provider. They provided one forward and one reverse sequence per sample - FASTQ format -totally 34 samples. and no other files like manifest/ mapping file.

The database you are mentioning is taxonomy /
gg-13-8-99-515-806-nb-classifier

There is no primer pair details given with the data. JK-1_S13_L001_R1_001_tr.fastq (5.3 MB) JK-1_S13_L001_R2_001_tr.fastq (5.3 MB) JK-2_S13_L001_R1_001_tr.fastq (3.2 MB) JK-2_S13_L001_R2_001_tr.fastq (3.2 MB) JK-3_S13_L001_R1_001_tr.fastq (7.3 MB) JK-3_S13_L001_R2_001_tr.fastq (7.3 MB) JK-4_S13_L001_R1_001_tr.fastq (3.2 MB) JK-4_S13_L001_R2_001_tr.fastq (3.2 MB) JK-5_S13_L001_R1_001_tr.fastq (4.3 MB) JK-5_S13_L001_R2_001_tr.fastq (4.3 MB) JK-6_S13_L001_R1_001_tr.fastq (1.7 MB) JK-6_S13_L001_R2_001_tr.fastq (1.7 MB) JK-7_S13_L001_R1_001_tr.fastq (5.8 MB) JK-7_S13_L001_R2_001_tr.fastq (5.8 MB) JK-8_S13_L001_R1_001_tr.fastq (5.8 MB) JK-8_S13_L001_R2_001_tr.fastq (5.8 MB) JK-9_S13_L001_R1_001_tr.fastq (2.5 MB) JK-9_S13_L001_R2_001_tr.fastq (2.5 MB) JK-10_S13_L001_R1_001_tr.fastq (3.1 MB) JK-10_S13_L001_R2_001_tr.fastq (3.1 MB)

I attempted to import through paired end multiplexed sequence and done with some error message.

HI @srini,

Sorry for the delay on my part. What region of 16S? I suspect you are not sequencing the V4 region, which is why the trimmed classifier for the V4 region is only able to get an assignment of bacteria.

Hi Evan

Thank you for your reply. Initially, I raised the question about “Requested level of 6 is larger than the maximum level available in taxonomy data”
But later i raised an entirely different topic importing the data. In this data importing, I found the file names should be in a format ends with R1_001.fastq which is wrong in my filename. After deleting the _tr from the file name, the importing problem is over.

Regarding the “Requested level of 6 is larger than the maximum level available in taxonomy data” , the data is originally from V4 region only according to our request and the supplier information. I felt the problem is with the quality of the base pairs and most of the sequence (around 50%) are less than 20 quality score. I suspect this might be the problem I lose the taxonomical classification and hence fail to continue further analysis.

Thank you for the replies. It helped me a lot to understand my data quality and analysis tactics.

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