Plugin error - feature-table

User Support
1

Hello, Kindly help me with the below given error:

Plugin error from feature-table:

Linkage must be computed on at least two observations.

Debug info has been saved to /tmp/qiime2-q2cli-err-o96vsxid.log
Usage: qiime tools export [OPTIONS] PATH

Error: Invalid value for “path”: Path “feature_heatmap/L1/heatmap.qzv” does not exist.
html: No such file or directory
mv: cannot stat ‘OTU/feature-barplots.qzv’: No such file or directory
Usage: qiime taxa collapse [OPTIONS]

Error: Invalid value for “–i-table”: Path “feature-table.qza” does not exist.
Usage: qiime feature-table heatmap [OPTIONS]

Error: Invalid value for “–i-table”: Path “feature_heatmap/L1/collapsed_table.qza” does not exist.
Usage: qiime tools export [OPTIONS] PATH

Error: Invalid value for “path”: Path “feature_heatmap/L1/heatmap.qzv” does not exist.
Usage: qiime taxa collapse [OPTIONS]

Error: Invalid value for “–i-table”: Path “feature-table.qza” does not exist.
Usage: qiime feature-table heatmap [OPTIONS]

2

Hi, please, attach screenshots of the terminal with command and with opened working directory

3

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5

Hi @anu - your script is generating a bunch of noise, since it looks like it doesn’t terminate on the first non-zero exit code (I usually join my commands with && in bash to make that work). Anyway, I suspect the issue is with your feature table - can you run feature-table summarize on the table you are generating the heatmap for and return the results here?

6

Thank you for the response.
I am running the feature table in a .sh script. As I am new to this, I am not sure about running the script/command separately. Can you please explain it elaborately so that I can understand it in a better way.

7

Let's circle back on this later, for now:

9

hello
I ran the feature table summarize and came across below given error.

Warning message:
package ‘ggplot2’ was built under R version 3.4.3
Warning message:
package ‘gdtools’ was built under R version 3.4.3
Plugin error from feature-table:

Linkage must be computed on at least two observations.

Debug info has been saved to /tmp/qiime2-q2cli-err-5m1ckt8e.log
Usage: qiime tools export [OPTIONS] PATH

Error: Invalid value for “path”: Path “feature_heatmap/L1/heatmap.qzv” does not exist.

10

Please run the command directly, rather than putting the command in your broken script file, the script is getting in the way:

qiime feature-table summarize \
   --i-table MY_FEATURE_TABLE.QZA \
   --o-visualization table_summary.qzv

Please copy-and-paste this command into your terminal (after activating QIIME 2), replace MY_FEATURE_TABLE.QZA with the feature table filename, then press the enter/return key. Once it is done, please share the table_summary.qzv file here.

11

Hi @thermokarst

Thanks for your help. I ran the commands and it was successful. The .qzv file was generated and unzipped using

unzip table_summary.qzv

Which file should i share?

12

Hey @anu,

I think @thermokarst was interested in the qzv file itself, as it contains provenance and other important details.

1 Like
13

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