quality-control decontam-identify

Technical Support
1

I am performing **
M2.txt (24.0 KB)
** and I am getting in Metadata file, I have attached metadata file here.

2

Hi @Vilaspatel,
Thank you for linking your metadata. Can you give me more details about the issue you are having?
--Hannah

3

I have to remove contaminated ASVs/OTUs from sample based control ASVs. I am doing 16S analysis in QIIME, I have run dada2 denoise-paired and have pet-table.qza, rep-sees-dada2.qza and denoising stats.qza in my directory. and then I am running following command
"qiime quality-control decontam-identify --i-table pet-table.qza --m-metadata-file M6.txt --p-method 'combined' --p-freq-concentration-column DNA-Conc --p-prev-control-column Sample-Type --p-prev-control-indicator "Control" --o-decontam-scores decontam-scores-comb-method.qza --verbose"

I am getting error in metadata which I tried to solve but still I am getting error in metadata
Traceback (most recent call last):
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in _execute_action
results = action(**arguments)
File "", line 2, in decontam_identify
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/q2_quality_control/decontam.py", line 132, in decontam_identify
_check_column_inputs(table, metadata, method, freq_concentration_column,
File "/apps/eb/QIIME2/2023.7/lib/python3.8/site-packages/q2_quality_control/decontam.py", line 101, in _check_column_inputs
raise ValueError('Column id input error, please '
ValueError: Column id input error, please select from:
Aphid

Plugin error from quality-control:

Column id input error, please select from:
Aphid

I am attaching here my modified metadata
M6.txt (7.1 KB)

Control and Blank labels are my negative control.
Thank You
Vilas

4

Hi @Vilaspatel,
Looking at your metadata file, it only has "aphid" as a column but you pass in "DNA-Conc" as a column in your command.

I would suggesting using a different metadata that has the information that decontam is requesting.

Hope this helps!

1 Like
5

I could run qiime quality-control decontam-identify, and got output "decontam-scores-comb-method.qza", Now I want to remove contaminants reads from experimental samples and run this following command
"qiime feature-table filter-features --i-table table3.qza --m-metadata-file decontam-scores-comb-method.qza --o-filtered-table table3-filtered.qza"
and from this command size of table3-filtered.qza bigger than table3.qza, Am I running correct command for filtering out reads?

6

Hi @Vilaspatel,
That is really weird.
Would you mind sending me your feature tables.qzv(before and after filtering) so I can take a look?

Also would you send your decontam-scores-comb-method.qza so I can take a look at that too!

7

Hi @Vilaspatel there is actually a dedicated function within quality-control to remove contaminants from your feature tables (called decontam-remove), however you will need to supply a threshold value as a contaminant cutoff. I would suggest following the tutorial which can be found here. Let me know if you have any other questions or concerns!

2 Likes
8

Thanks Jorden for the insight!

1 Like