Cornbob plugin-qiime2 2021.4 version

Hello everyone!

I have qiime2 2021.4 version. I want to use q2-corncob for my analysis. I saw the release was for qiime2-2018.8. It is compatible with more recent qiime2 versions?

Thanks!

Hello,

I was able to install corncob using my qiime2 version. But I am getting this error:
Plugin error from corncob:

Command '['differentialtest.R', '/tmp/tmp3fovlbdn/table.tsv', '/tmp/tmp3fovlbdn/metadata.tsv', '/tmp/qiime2-archive-nmml2htc/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv', 'Diet', '/tmp/tmp3fovlbdn/data.tsv']' returned non-zero exit status 1.

Any idea of what this means will be appreciated.

Thanks!

Hi @idapantoja,
I'm not familiar with corncob errors themselves, but this part of the error

reminds me of times I've seen something similar in R when one of its causes was when an input ends up being empty for some reason during a step.

I'm tagging one of the q2-corncob developers to see if they have any ideas. @Pauline_Trinh.

In the meantime could you provide some more details such as the exact commands you are running, add the --verbose tag in your command in case that gives a bit more detailed error message, and the QIIME 2 version you are using.

Hello @Mehrbod_Estaki !
Thanks so much for your response!

I ran the command again adding --verbose and this is what get:

qiime corncob differentialtest
--i-table ASV-table-dada2_ResistantStarch_Only65_Orderedbytimepoints.qza
--m-metadata-file mapping_file_RS_corncob_feb3_2022.txt
--p-variable Time_Point
--i-taxonomy taxonomy_ResistantStarch_Only65_orderedbytimepoints.qza
--verbose
--o-output corncobresults

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: differentialtest.R /tmp/tmp0c999aao/table.tsv /tmp/tmp0c999aao/metadata.tsv /tmp/qiime2-archive-hzu_922i/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv Time_Point /tmp/tmp0c999aao/data.tsv

R version 4.0.3 (2020-10-10)
Great! phyloseq is already available

Thank goodness! devtools is already available

You have magrittr installed!

Error: tidyr needs to be installed!

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘cli’ 2.4.0 is being loaded, but >= 3.0.0 is required
Calls: :: ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
Traceback (most recent call last):
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in differentialtest
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_corncob/_differentialtest.py", line 56, in differentialtest
run_commands([cmd])
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_corncob/_differentialtest.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/var/opt/miniconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['differentialtest.R', '/tmp/tmp0c999aao/table.tsv', '/tmp/tmp0c999aao/metadata.tsv', '/tmp/qiime2-archive-hzu_922i/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv', 'Time_Point', '/tmp/tmp0c999aao/data.tsv']' returned non-zero exit status 1.

Plugin error from corncob:

Command '['differentialtest.R', '/tmp/tmp0c999aao/table.tsv', '/tmp/tmp0c999aao/metadata.tsv', '/tmp/qiime2-archive-hzu_922i/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv', 'Time_Point', '/tmp/tmp0c999aao/data.tsv']' returned non-zero exit status 1.

See above for debug info.

I am using qiime2-2021.4

Hope you can help me figure out what's the error. Let me know if you need additional information.

Thanks again!

1 Like

Hi @idapantoja,
Thanks for the additional info.
From a first glance, it looks to me that there is some missing packages in the R environment:

and also

You can try downloading the newest QIIME 2 version to see if that resolves the issue, but I'm not sure if the newest version comes with any of these.
Other options is to manually install the newest version of those 2 packages in your QIIME 2's R environment. There's no guarantee that this is the sole problem and that would resolve it, but might be a start.
Another option is also to simply use the stand-alone R version of corncob which should hopefully not have these compatibility issues.

Sorry I couldn't give you more of a straight forward solution.

Hi @Mehrbod_Estaki !

Thanks so much for the response and suggestions. Very helpful.
I will probably go with the stand-alone R version.

Best regards,
@idapantoja

1 Like

Hi @Mehrbod_Estaki ,

Hope you are well.

I updated qiime2 to the 2021.11 version but still getting:

qiime corncob differentialtest --i-table ASV-table-dada2_ResistantStarch_Only65_Orderedbytimepoints.qza --m-metadata-file mapping_file_RS_corncob_feb3_2022.txt --p-variable Diet --i-taxonomy taxonomy_ResistantStarch_Only65_orderedbytimepoints.qza --o-output corncobresults --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: differentialtest.R /tmp/tmp24kbe9y3/table.tsv /tmp/tmp24kbe9y3/metadata.tsv /tmp/qiime2-archive-7pe5kguq/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv Diet /tmp/tmp24kbe9y3/data.tsv

R version 4.0.5 (2021-03-31)
Great! phyloseq is already available

Thank goodness! devtools is already available

You have magrittr installed!

You have tidyr installed!

Downloading GitHub repo hadley/[email protected]
Error: Failed to install 'tidyr' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.
Execution halted
Traceback (most recent call last):
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in differentialtest
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_corncob/_differentialtest.py", line 56, in differentialtest
run_commands([cmd])
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_corncob/_differentialtest.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/var/opt/miniconda3/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['differentialtest.R', '/tmp/tmp24kbe9y3/table.tsv', '/tmp/tmp24kbe9y3/metadata.tsv', '/tmp/qiime2-archive-7pe5kguq/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv', 'Diet', '/tmp/tmp24kbe9y3/data.tsv']' returned non-zero exit status 1.

Plugin error from corncob:

Command '['differentialtest.R', '/tmp/tmp24kbe9y3/table.tsv', '/tmp/tmp24kbe9y3/metadata.tsv', '/tmp/qiime2-archive-7pe5kguq/bb9d7034-6704-44b2-bc8f-ee1e14db2c85/data/taxonomy.tsv', 'Diet', '/tmp/tmp24kbe9y3/data.tsv']' returned non-zero exit status 1.

See above for debug info.

It says that
You have tidyr installed!

But then:
Downloading GitHub repo hadley/[email protected]
Error: Failed to install 'tidyr' from GitHub:
Could not find tools necessary to compile a package

I am using a Linux Server. How will be the command to try to fix this?

I would appreciate our help again!

Thanks!
Ida

1 Like

Hi @idapantoja,

That is odd indeed, though this is now a different error than the original. Did you run into any issues when you tried to install q2-corncob within the new conda environment?, or see any warning messages? It's odd to me that corncob is trying to install tidyr again when its already there.
Unfortunately, beyond this I'm not sure I can be of help troubleshooting this as it seems very specific to corncob and that help would have to come from its developer.

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