Issue loading metadata file Qiime2

(Aneth David) #1

Hi,

I am try to get the feature table summary with the following command:

qiime feature-table summarize --i-table table1.qza --o-visualization table1.qzv --m-sample-metadata-file 16s-obj1-metadata.tsv

I keep getting the following error:

**There was an issue with loading the file 16s-obj1-metadata.tsv as metadata:**
**Found unrecognized ID column name '<!DOCTYPE html>' while searching for header. The first column name in the header defines the ID column, and must be one of these values:**
**Case-insensitive: 'feature id', 'feature-id', 'featureid', 'id', 'sample id', 'sample-id', 'sampleid'**
**Case-sensitive: '#OTU ID', '#OTUID', '#Sample ID', '#SampleID', 'sample_name'**
**There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org**
**Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2019.4/tutorials/metadata/**

My metadata file looks like in the attached screenshot. I have successfully validated with Keemei in Safari and then Chrome, changed column names, omitted some columns, nothing works. And I have read and re-read the metadata tutorial. I have run one succesful complete analysis before.

To download the metadata file, I did:

wget -O "16s-obj11-metadata.tsv" "https://docs.google.com/spreadsheets/d/1BOtYXnoCkj3XpnskzcJQyse_8j93Vrtq1ILsJJ0Fkuo/edit#gid=0"

I have read here that other people have experienced a similar problem before but I cant seem to find a solution that works for me.

Please help.

Kind regards,
Aneth.

56

(Matthew Ryan Dillon) #2

Hi @anethdavid!

The problem here is that you aren’t downloading what you think you are downloading. Check this out:

[email protected]:~/Desktop> wget -O "16s-obj11-metadata.tsv" "https://docs.google.com/spreadsheets/d/1BOtYXnoCkj3XpnskzcJQyse_8j93Vrtq1ILsJJ0Fkuo/edit#gid=0"
--2019-05-11 11:00:23--  https://docs.google.com/spreadsheets/d/1BOtYXnoCkj3XpnskzcJQyse_8j93Vrtq1ILsJJ0Fkuo/edit
Resolving docs.google.com (docs.google.com)... 172.217.9.174, 2607:f8b0:4000:814::200e
Connecting to docs.google.com (docs.google.com)|172.217.9.174|:443... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: https://accounts.google.com/ServiceLogin?service=wise&passive=1209600&continue=https://docs.google.com/spreadsheets/d/1BOtYXnoCkj3XpnskzcJQyse_8j93Vrtq1ILsJJ0Fkuo/edit&followup=https://docs.google.com/spreadsheets/d/1BOtYXnoCkj3XpnskzcJQyse_8j93Vrtq1ILsJJ0Fkuo/edit&ltmpl=sheets
Resolving accounts.google.com (accounts.google.com)... 172.217.2.237, 2607:f8b0:4000:811::200d
Connecting to accounts.google.com (accounts.google.com)|172.217.2.237|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: ‘16s-obj11-metadata.tsv’
16s-obj11-metadata.tsv                                                     [ <=>                                                                                                                                                                         ]  55.73K  --.-KB/s    in 0.1s

2019-05-11 11:00:24 (492 KB/s) - ‘16s-obj11-metadata.tsv’ saved [57070]

[email protected]:~/Desktop> head 16s-obj11-metadata.tsv

<!DOCTYPE html>
<html lang="en">
  <head>
  <meta charset="utf-8">
  <meta content="width=300, initial-scale=1" name="viewport">
  <meta name="description" content="Create a new spreadsheet and edit with others at the same time -- from your computer, phone or tablet. Get stuff done with or without an internet connection. Use Sheets to edit Excel files. Free from Google.">
  <meta name="google-site-verification" content="LrdTUW9psUAMbh4Ia074-BPEVmcpBxF6Gwf0MSgQXZs">
  <title>Google Sheets - create and edit spreadsheets online, for free.</title>
  <style>

In case that isn’t clear, you appear to be downloading an HTML document, rather than a TSV.

(Aneth David) #3

Oh, I see now!

But how do I download the google sheet into a recognisable metadata file format?

(Aneth David) #4

I found a solution by downloading it locally, saving as a tab delimited .txt file, then uploading it to the server. It worked.

Thank you very much!