decontam-identify-batches

Technical Support
1

Hi, I am using qiime amplicon 2024.10 installed with conda.

I am having troubles to run quality-control decontam-identify-batches to run decontam by batches.

My command is qiime quality-control decontam-identify-batches --i-table output/asv_seqNcount.qza --m-metadata-file RESDIR/qiime_test.tsv --p-split-column "batch" --p-method "combined" --p-filter-empty-features --o-batch-subset-tables output/decontam/ --o-decontam-scores output/decontam/ --o-score-histograms output/histogram.viz

My metadata file looks like this:
qiime_metadata.tsv (359 Bytes)

My OTU table looks like this:
asv_seqNcount.qza (318.6 KB)

And I am getting this error:

Plugin error from quality-control:

  'batch' is not a column in the metadata. Available columns: 'sample-type'

Debug info has been saved to /tmp/qiime2-q2cli-err-qd86komi.log

The thing is I cannot input which column should the plugin use to identify samples negative controls and neither I have found a standard way to indicate that.

When I input a metadata table that has these two columns, the one indicating which samples are controls and another one indicating how to split the data by batches, I got this error.

Hope you cant help me, thank you very much!

2

PD.: I accidentally pasted an incorrect output.

Here's the one I am getting:

Plugin error from quality-control:

  Column id input error, please select from:
  sample-type, batch

See above for debug info.
4

Hi @jmgs7,
Thanks for providing the data! I just tested and confirmed that I get the same error that you're seeing.

This error message and the documentation for this action could be improved. What seems to be happening is that, since you're providing --p-method combined, the action is expecting you to have provided values for the --p-freq-concentration-column and --p-prev-control-column parameters, though those are not indicated as being required in this case.

@jordenrabasco, could you jump out and help @jmgs7 move forward with this?

@jordenrabasco, it would also be good for us to clarify this error message, and also to indicate in the help text when these parameters are required. Let me know if you need input on how to do that. I created an issue for this here.

6

@gregcaporaso absolutely, no worries! and I totally agree I will take a look at the created issue!

@jmgs7 Thanks for your interest in using decontam-batches! How many samples do you have? From your metadata file it looks like you may need more controls to run the Decontam prevalence method (we recommend at least 3). Do you have dna concentration metadata for your samples?