Error jaccard_emperor

Technical Support
1

Hello and cordial greetings

I have the version of qiime2 2023.9, installed in conda with windows. I find myself running the motion pictures tutorial, but when performing the alpha and beta diversity analysis under the command for version 2023.9:

qiime diversity core-metrics-phylogenetic
--i-phylogeny phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza
--i-table table.qza
--p-sampling-depth 1103
--m-metadata-file sample-metadata.tsv
--output-dir diversity-core-metrics-phylogenetic

Or the command for version 2024.2:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 1103
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results

I get the following error:

image

Plugin error from diversity:

'jaccard_emperor'

Debug info has been saved to /tmp/qiime2-q2cli-err-qgv5snp0.log

I'm new to the program and I don't understand why this happens. I would be very grateful if someone could help me with a solution for this problem.

2

Hello, cordial greeting

I am doing the ā€œMoving Picturesā€ tutorial version 2023.9, I have qiime2 version 2023.9 installed in conda with Windows. I have a problem when running the command that estimates alpha and beta diversity, which is the following:

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs.qza
--output-dir phylogeny-align-to-tree-mafft-fasttree

and I get this error message:

Plugin error from diversity:
'jaccard_emperor'
Debug info has been saved to /tmp/qiime2-q2cli-err-qgv5snp0.log

It also happens when running version 2024.2 of this tutorial, which is the command:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 1103
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results

I'm new to using qiime2 and I don't understand what's happening. I would be very grateful if someone could help me find a solution.

3

Hello @LisethBolCol,

Welcome to the forums! :qiime2:

Can you post this log file here? This may have more clues!

jaccard_emperor
Jaccard is a beta-diversity distance
emperor is a program for making and viewing PCoA plots

4

How can I view the log file? /tmp/qiime2-q2cli-err-qgv5snp0.log

5

You could use cat to print the full file into your terminal, then copy it into a forum post.

cat /tmp/qiime2-q2cli-err-qgv5snp0.log

Or you could open the folder in Windows then upload the file to the forums:

cd /tmp/       # change directory to the tmp folder
explorer.exe . # use Windows Explorer to open the current folder
6

Hello, I have already managed to view the file.

Traceback (most recent call last):
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 58, in core_metrics_phylogenetic
cr = core_metrics(table=table, sampling_depth=sampling_depth,
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/context.py", line 113, in deferred_action
output = cached_outputs[name]
KeyError: 'jaccard_emperor'

But, now I was running everything again and I got this error using the same command for the diversity metrics, only this time it is with version 2024.2 of qiime. It reported me the error:

Plugin error from diversity:
'bray_curtis_pcoa_results'
Debug info has been saved to /tmp/qiime2-q2cli-err-s7tp4w3w.log

And this is the file:
Traceback (most recent call last):
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 60, in core_metrics_phylogenetic
cr = core_metrics(table=table, sampling_depth=sampling_depth,
File "", line 2, in core_metrics
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 116, in deferred_action
output = cached_outputs[name]
KeyError: 'bray_curtis_pcoa_results'

7

Every time I run the script from the import the error changes, so I'm going to stop running it. In this case the error that was thrown was:

Plugin error from diversity:
'bray_curtis_emperor'
Debug info has been saved to /tmp/qiime2-q2cli-err-6qp7ptxn.log

and the file was:

Traceback (most recent call last):
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 60, in core_metrics_phylogenetic
cr = core_metrics(table=table, sampling_depth=sampling_depth,
File "", line 2, in core_metrics
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 116, in deferred_action
output = cached_outputs[name]
KeyError: 'bray_curtis_emperor'

thank you so much for help me.

8

Thank you for posting all of this! I've confirmed that this specific issue has not been observed before. Thank you for bringing it to our attention.

These two lines appear throughout and point to issues with the Artifact Cache.

I have qiime2 version 2023.9 installed in conda with Windows.

This sounds like WSL, which I also use! Do you know if it's WSL 1 or WSL 2?

Let's see what the Qiime devs recommend.

EDIT: Also, please run qiime info so we can look at the install.

10

Hi

Yes, I have WSL-Ubuntu-22.4. But, I don't know if it is WSL1 or WSL2. and thank you

System versions
Python version: 3.8.15
QIIME 2 release: 2024.2
QIIME 2 version: 2024.2.0
q2cli version: 2024.2.0

Installed plugins
alignment: 2024.2.0
composition: 2024.2.0
cutadapt: 2024.2.0
dada2: 2024.2.0
deblur: 2024.2.0
demux: 2024.2.0
diversity: 2024.2.0
diversity-lib: 2024.2.0
emperor: 2024.2.0
feature-classifier: 2024.2.0
feature-table: 2024.2.2
fragment-insertion: 2024.2.0
longitudinal: 2024.2.0
metadata: 2024.2.0
phylogeny: 2024.2.0
quality-control: 2024.2.0
quality-filter: 2024.2.0
rescript: 2024.2.2
sample-classifier: 2024.2.0
taxa: 2024.2.0
types: 2024.2.0
vsearch: 2024.2.0

Application config directory
/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/var/q2cli

1 Like
11

Hello @LisethBolCol, you can check the version of WSL you are using by running wsl -l -v in either the Windows Terminal or Powershell (NOT in WSL, in the terminal in actual windows).

Inside of the WSL terminal, can you please run the command rm -rf /tmp/qiime2/<your username> then rerun your QIIME commands? Thank you. That ought to resolve this issue although I am unable to replicate it on my end.

2 Likes
14

Hello, thank you very much for helping me

WSL version is 1

After executing the command again according to the instructions given, it gives me the following error:

Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/liseth/data/47cd6ce8-8ea3-46a9-bf9d-e853e21e3cce/data/feature-table.biom', '-t', '/tmp/qiime2/liseth/data/4c5e5202-c60e-4f49-ba3d-a2b84cfb14ba/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-lj_ljn62']' returned non-zero exit status 126.

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

Y el archivo es:

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

faithpd -i /tmp/qiime2/liseth/data/47cd6ce8-8ea3-46a9-bf9d-e853e21e3cce/data/feature-table.biom -t /tmp/qiime2/liseth/data/4c5e5202-c60e-4f49-ba3d-a2b84cfb14ba/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-lj_ljn62

/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/bin/faithpd: line 43: /home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/bin/faithpd_nv_avx2: cannot execute binary file: Exec format error
/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/bin/faithpd: line 43: /home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/bin/faithpd_nv_avx2: Success
Traceback (most recent call last):
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_core_metrics.py", line 65, in core_metrics_phylogenetic
faith_pd_vector, = faith_pd(table=cr.rarefied_table,
File "", line 2, in faith_pd
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "", line 2, in faith_pd
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "", line 2, in faith_pd
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 75, in _validate_tables
return wrapped_function(*args, **kwargs)
File "", line 2, in faith_pd
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 118, in _validate_requested_cpus
return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/alpha.py", line 54, in faith_pd
_omp_cmd_wrapper(threads, cmd)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 134, in _omp_cmd_wrapper
return _run_external_cmd(cmd, verbose=verbose, env=env)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py", line 128, in _run_external_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/liseth/data/47cd6ce8-8ea3-46a9-bf9d-e853e21e3cce/data/feature-table.biom', '-t', '/tmp/qiime2/liseth/data/4c5e5202-c60e-4f49-ba3d-a2b84cfb14ba/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-lj_ljn62']' returned non-zero exit status 126.

15

Hi

Yes, I have WSL-Ubuntu-22.4 WSL1

System versions
Python version: 3.8.15
QIIME 2 release: 2024.2
QIIME 2 version: 2024.2.0
q2cli version: 2024.2.0

Installed plugins
alignment: 2024.2.0
composition: 2024.2.0
cutadapt: 2024.2.0
dada2: 2024.2.0
deblur: 2024.2.0
demux: 2024.2.0
diversity: 2024.2.0
diversity-lib: 2024.2.0
emperor: 2024.2.0
feature-classifier: 2024.2.0
feature-table: 2024.2.2
fragment-insertion: 2024.2.0
longitudinal: 2024.2.0
metadata: 2024.2.0
phylogeny: 2024.2.0
quality-control: 2024.2.0
quality-filter: 2024.2.0
rescript: 2024.2.2
sample-classifier: 2024.2.0
taxa: 2024.2.0
types: 2024.2.0
vsearch: 2024.2.0

Application config directory
/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/var/q2cli
[/quote

16

Hi @LisethBolCol,
Can you confirm that this command successfully deleted that directory? I want to make sure there is nothing cached in your system that could be causing this!

17

Hello

Yes, thank you very much if you eliminated the error

18

@LisethBolCol We have had a lot more success with WSL 2 than WSL 1 if upgrading is a possibility for you.

1 Like
20

How could I install WSL2?

21

These instructions describe how to upgrade from WSL1 to WSL2

22

Thank you very much with the change to WSL2 the problems are no longer being generated

2 Likes