[Errno 13] and Invalid value... not a QIIME 2 Artifact (.qza) in qiime2-2022.8 in WSL

Technical Support
1

Hello,

I am quite new to qiime, I installed qiime2 2022.8 on the conda environment within the WSL.

I went through the moving pictures tutorial, and everything runs smoothly until the tree generation step.

(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime phylogeny align-to-tree-mafft-fasttree \
>   --i-sequences rep-seqs.qza \
>   --o-alignment aligned-rep-seqs.qza \
>   --o-masked-alignment masked-aligned-rep-seqs.qza \
>   --o-tree unrooted-tree.qza \
>   --o-rooted-tree rooted-tree.qza
Plugin error from phylogeny:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-895f71ul' -> '/tmp/qiime2/cquga/data/c911f1a9-e154-4299-a873-98962b80d832/provenance'

Debug info has been saved to /tmp/qiime2-q2cli-err-rvds8qtr.log

The error:

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: mafft --preservecase --inputorder --thread 1 /tmp/qiime2/cquga/data/608db625-ffbc-465d-ad9a-d6a066f403c0/data/dna-sequences.fasta

inputfile = orig
770 x 120 - 120 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

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done.

Constructing a UPGMA tree (efffree=0) ... 

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done.

Progressive alignment 1/2... 

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Reallocating..done. *alloclen = 1241

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STEP   701 / 769 (thread    0) d h
done.

Making a distance matrix from msa.. 

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done.

Constructing a UPGMA tree (efffree=1) ... 

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done.

Progressive alignment 2/2... 

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Reallocating..done. *alloclen = 1241

STEP   701 / 769 (thread    0) d h
done.

disttbfast (nuc) Version 7.505
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

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: FastTree -quote -nt /tmp/qiime2/cquga/data/0c7194a5-310c-4747-ad43-afad7a1a9a1d/data/aligned-dna-sequences.fasta

FastTree Version 2.1.11 Double precision (No SSE3)
Alignment: /tmp/qiime2/cquga/data/0c7194a5-310c-4747-ad43-afad7a1a9a1d/data/aligned-dna-sequences.fasta
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
      0.10 seconds: Joined    400 of    748
Initial topology in 0.15 seconds
Refining topology: 38 rounds ME-NNIs, 2 rounds ME-SPRs, 19 rounds ML-NNIs
      0.21 seconds: SPR round   1 of   2, 201 of 1500 nodes
      0.31 seconds: SPR round   1 of   2, 901 of 1500 nodes
      0.41 seconds: ME NNI round 14 of 38, 101 of 749 splits, 0 changes
      0.52 seconds: SPR round   2 of   2, 701 of 1500 nodes
      0.63 seconds: SPR round   2 of   2, 1401 of 1500 nodes
Total branch-length 38.282 after 0.67 sec
      0.74 seconds: ML NNI round 1 of 19, 101 of 749 splits, 15 changes (max delta 4.442)
      0.84 seconds: ML NNI round 1 of 19, 501 of 749 splits, 86 changes (max delta 9.712)
ML-NNI round 1: LogLk = -23222.790 NNIs 134 max delta 9.71 Time 0.91
      0.94 seconds: Site likelihoods with rate category 18 of 20
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.994 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
      1.06 seconds: ML NNI round 2 of 19, 501 of 749 splits, 59 changes (max delta 4.035)
ML-NNI round 2: LogLk = -19944.867 NNIs 92 max delta 4.04 Time 1.12
      1.17 seconds: ML NNI round 3 of 19, 301 of 749 splits, 13 changes (max delta 5.208)
ML-NNI round 3: LogLk = -19913.234 NNIs 36 max delta 5.21 Time 1.23
      1.28 seconds: ML NNI round 4 of 19, 301 of 749 splits, 10 changes (max delta 2.133)
ML-NNI round 4: LogLk = -19904.620 NNIs 15 max delta 2.13 Time 1.30
ML-NNI round 5: LogLk = -19903.078 NNIs 7 max delta 0.66 Time 1.34
ML-NNI round 6: LogLk = -19903.055 NNIs 1 max delta 0.00 Time 1.35
Turning off heuristics for final round of ML NNIs (converged)
      1.39 seconds: ML NNI round 7 of 19, 201 of 749 splits, 3 changes (max delta 0.533)
      1.51 seconds: ML NNI round 7 of 19, 601 of 749 splits, 9 changes (max delta 2.161)
ML-NNI round 7: LogLk = -19891.055 NNIs 10 max delta 2.16 Time 1.55 (final)
Optimize all lengths: LogLk = -19889.649 Time 1.60
      1.63 seconds: ML split tests for    100 of    748 internal splits
      1.74 seconds: ML split tests for    400 of    748 internal splits
      1.85 seconds: ML split tests for    700 of    748 internal splits
Total time: 1.87 seconds Unique: 751/770 Bad splits: 0/748
Traceback (most recent call last):
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-409>", line 2, in align_to_tree_mafft_fasttree
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 503, in _callable_executor_
    aliased_result = output._alias(prov)
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 221, in _alias
    alias._archiver = archive.Archiver.from_data(
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 402, in from_data
    Format.write(rec, type, format, data_initializer,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/format/v5.py", line 20, in write
    super().write(archive_record, type, format, data_initializer,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 25, in write
    provenance_capture.finalize(
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 332, in finalize
    raise err
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 325, in finalize
    os.rename(self.path, final_path)
PermissionError: [Errno 13] Permission denied: '/tmp/qiime2-provenance-895f71ul' -> '/tmp/qiime2/cquga/data/c911f1a9-e154-4299-a873-98962b80d832/provenance'

After reading some old topics in the forum, I tried:

  • Running the power-shell as admin -> Did not work

  • Change tmp folder to the current folder -> Worked

(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ mkdir tmp
(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ export TMPDIR=/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial/tmp
(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime phylogeny align-to-tree-mafft-fasttree \
>   --i-sequences rep-seqs.qza \
>   --o-alignment aligned-rep-seqs.qza \
>   --o-masked-alignment masked-aligned-rep-seqs.qza \
>   --o-tree unrooted-tree.qza \
>   --o-rooted-tree rooted-tree.qza
Saved FeatureData[AlignedSequence] to: aligned-rep-seqs.qza
Saved FeatureData[AlignedSequence] to: masked-aligned-rep-seqs.qza
Saved Phylogeny[Unrooted] to: unrooted-tree.qza
Saved Phylogeny[Rooted] to: rooted-tree.qza

However at the next step, I got the error: Invalid value for ... '...' is not a QIIME 2
Artifact (.qza).

(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ 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
Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]

  Applies a collection of diversity metrics (both phylogenetic and non-
  phylogenetic) to a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples over which
                          diversity metrics should be computed.     [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-sampling-depth INTEGER
    Range(1, None)        The total frequency that each sample should be
                          rarefied to prior to computing diversity metrics.
                                                                    [required]
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata to use in the emperor plots.
     will be merged)                                                [required]
  --p-with-replacement / --p-no-with-replacement
                          Rarefy with replacement by sampling from the
                          multinomial distribution instead of rarefying
                          without replacement.                [default: False]
  --p-n-jobs-or-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          [beta/beta-phylogenetic methods only] - The number
                          of concurrent jobs or CPU threads to use in
                          performing this calculation. Individual methods will
                          create jobs/threads as implemented in
                          q2-diversity-lib dependencies. May not exceed the
                          number of available physical cores. If
                          n-jobs-or-threads = 'auto', one thread/job will be
                          created for each identified CPU core on the host.
                                                                  [default: 1]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [required]
  --o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Faith PD values by sample.      [required]
  --o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Observed Features values by sample.
                                                                    [required]
  --o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Shannon diversity values by sample.
                                                                    [required]
  --o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Pielou's evenness values by sample.
                                                                    [required]
  --o-unweighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of unweighted UniFrac distances between
                          pairs of samples.                         [required]
  --o-weighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of weighted UniFrac distances between pairs
                          of samples.                               [required]
  --o-jaccard-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Jaccard distances between pairs of
                          samples.                                  [required]
  --o-bray-curtis-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Bray-Curtis distances between pairs of
                          samples.                                  [required]
  --o-unweighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from unweighted UniFrac
                          distances between samples.                [required]
  --o-weighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from weighted UniFrac
                          distances between samples.                [required]
  --o-jaccard-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Jaccard distances between
                          samples.                                  [required]
  --o-bray-curtis-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Bray-Curtis distances
                          between samples.                          [required]
  --o-unweighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          unweighted UniFrac.                       [required]
  --o-weighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          weighted UniFrac.                         [required]
  --o-jaccard-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Jaccard.                                  [required]
  --o-bray-curtis-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Bray-Curtis.                              [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

                  There were some problems with the command:
 (1/2) Invalid value for '--i-phylogeny': 'rooted-tree.qza' is not a QIIME 2
  Artifact (.qza)
 (2/2) Invalid value for '--i-table': 'table.qza' is not a QIIME 2 Artifact
  (.qza)

The needed files were in the folder and had the .qza extension. I also tried writing the full path to the files and that did not work either.

Extra information: I have run the whole pipeline several times and the [Errno 13] appears at a different step every time. Cleaning the original /tmp folder also worked (sometimes) with

	cd /tmp
	sudo rm -r *

But I thought changing /tmp folder to the working folder would be a better option.

However after solving [Errno 13] the second error appears in the next function.

Anyone knows how to overcome this second error, or a more elegant way of solving the [Errno 13]?
Any help is appreciated :slight_smile:
César.

2 Likes
2

Hello César,

Welcome to the forums! :qiime2:

I'm glad you got the temp folder working for you. Let's investigate the invalid artifacts!

Can you post the two .qza files that are causing this error? We can take a look and see what's wrong with them :mag:

2 Likes
3

Hi Colin,

Thank you for your answer.
Find below the two qza files.

rooted-tree.qza (64.8 KB)

table.qza (52.8 KB)

5

Hello @cquga, sorry about the delay! Assuming you're still having this issue, can you rerun that last core-metrics-phylogenetic command that failed with the not a QIIME 2 Artifact errors with the --verbose flag and post the output from that here? That output should tell us more about what is going on.

1 Like
6

Hi @Oddant1 , thank you for your answer :slight_smile:

Yes, the issue is still there, as I don't know what else to try. If it cannot get it fixed I will try alternatively to install qiime2 in a virtualbox instead of the wsl.

I have just run the code with the verbose flag and somehow now I get the [Errno13] instead of the ...not a QIIME 2 Artifact error. I did not run anything in between the two tries or alter in any way the qza files.

(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ 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 \
> --verbose
/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/sklearn/metrics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard
  warnings.warn(msg, DataConversionWarning)
/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.008860694821538203 and the largest is 3.599672589339156.
  warn(
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/cquga/data/9f2c4362-65d1-4b3a-b54d-c9ef77914259/data/feature-table.biom -t /tmp/qiime2/cquga/data/c9b76c6b-8bd2-49ea-8f80-37e21feed46e/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-gtxh1g1a

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:

ssu -i /tmp/qiime2/cquga/data/9f2c4362-65d1-4b3a-b54d-c9ef77914259/data/feature-table.biom -t /tmp/qiime2/cquga/data/c9b76c6b-8bd2-49ea-8f80-37e21feed46e/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-1q64d30m

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:

ssu -i /tmp/qiime2/cquga/data/9f2c4362-65d1-4b3a-b54d-c9ef77914259/data/feature-table.biom -t /tmp/qiime2/cquga/data/c9b76c6b-8bd2-49ea-8f80-37e21feed46e/data/tree.nwk -m weighted_unnormalized -o /tmp/q2-LSMatFormat-o7vuu_re

/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.009576840846860826 and the largest is 2.382787327600763.
  warn(
/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.019318952670791284 and the largest is 3.182345783846854.
  warn(
Traceback (most recent call last):
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-167>", line 2, in core_metrics_phylogenetic
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 503, in _callable_executor_
    aliased_result = output._alias(prov)
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 221, in _alias
    alias._archiver = archive.Archiver.from_data(
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 402, in from_data
    Format.write(rec, type, format, data_initializer,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/format/v5.py", line 20, in write
    super().write(archive_record, type, format, data_initializer,
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 25, in write
    provenance_capture.finalize(
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 332, in finalize
    raise err
  File "/home/cquga/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 325, in finalize
    os.rename(self.path, final_path)
PermissionError: [Errno 13] Permission denied: '/tmp/qiime2-provenance-2len0z1j' -> '/tmp/qiime2/cquga/data/ba245735-1356-4c08-804e-7469b8a5fc8e/provenance'

Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-2len0z1j' -> '/tmp/qiime2/cquga/data/ba245735-1356-4c08-804e-7469b8a5fc8e/provenance'

See above for debug info.
(qiime2-2022.8) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$

Thank you for your time!
Cesar.

1 Like
7

First of all, I noticed you said you installed 2022.8, you may have better luck with a newer version, we have released 2022.11 and most recently 2023.2. Updating is not guaranteed to fix the issue, but it might. There is a chance this issue is related to a large change we made in 2022.8 and have since polished up in the newer releases, so I recommend upgrading if posssible.

Aside from that, if the permissions issue persists, can you run stat /tmp on WSL and post the output here? It is possible there is something wrong with the permissions on your tmp directory. There might also be permissions issues with the .qzas themselves that caused the second error you saw in a roundabout way. QIIME 2 may have failed to load them as artifacts due to lack of permissions and not understood why it couldn't load them, so the best it could do was "not an artifact"

1 Like
9

Hi @Oddant1 , thank you for your reply.

I updated to Qiime 2023.2 but that did not fix the issue.

Each time the [Errno 13] appears at a different step. This time it appeared when running dada2. Then I run stat /tmp, and I changed the permission from 0777 to 1777. That seemed to solve the issue, at least for this step.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime dada2 denoise-single \
>   --i-demultiplexed-seqs demux.qza \
>   --p-trim-left 0 \
>   --p-trunc-len 120 \
>   --o-representative-sequences rep-seqs-dada2.qza \
>   --o-table table-dada2.qza \
>   --o-denoising-stats stats-dada2.qza
Plugin error from dada2:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-x9p0kcjs' -> '/tmp/qiime2/cquga/processes/299-1679057174.2@cquga/16dec455-c5b1-439c-879d-16744313c0bf.7669074297741152193/16dec455-c5b1-439c-879d-16744313c0bf/provenance'

Debug info has been saved to /tmp/qiime2-q2cli-err-3y3661o1.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp
  File: /tmp
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 3096224745368112  Links: 1
Access: (0777/drwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2023-03-17 13:47:03.198207300 +0100
Modify: 2023-03-17 13:47:03.173959900 +0100
Change: 2023-03-17 13:47:03.173959900 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ sudo chmod 1777 /tmp
[sudo] password for cquga:
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp
  File: /tmp
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 3096224745368112  Links: 1
Access: (1777/drwxrwxrwt)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2023-03-17 13:47:03.198207300 +0100
Modify: 2023-03-17 13:47:03.173959900 +0100
Change: 2023-03-17 13:51:16.242801700 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime dada2 denoise-single \
>   --i-demultiplexed-seqs demux.qza \
>   --p-trim-left 0 \
>   --p-trunc-len 120 \
>   --o-representative-sequences rep-seqs-dada2.qza \
>   --o-table table-dada2.qza \
>   --o-denoising-stats stats-dada2.qza
Saved FeatureTable[Frequency] to: table-dada2.qza
Saved FeatureData[Sequence] to: rep-seqs-dada2.qza
Saved SampleData[DADA2Stats] to: stats-dada2.qza

I continued with the tutorial and [Errno 13] appeared again at the qiime diversity core-metrics-phylogenetic step. I run stat /tmp again and confirmed the permission is still at 1777.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ 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
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-51ltxt_9' -> '/tmp/qiime2/cquga/processes/517-1679057637.86@cquga/3a5f06df-a0cb-4cbb-b2a2-38cd63e5737f.518248944450913471/3a5f06df-a0cb-4cbb-b2a2-38cd63e5737f/provenance'

Debug info has been saved to /tmp/qiime2-q2cli-err-5dj4ma_a.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp
  File: /tmp
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 3096224745368112  Links: 1
Access: (1777/drwxrwxrwt)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2023-03-17 13:54:06.621431900 +0100
Modify: 2023-03-17 13:54:06.536808300 +0100
Change: 2023-03-17 13:54:06.536808300 +0100
 Birth: -

Thank you for your help :slight_smile:
César.

1 Like
10

@cquga That is very interesting. Can you stat /tmp/qiime2/ and /tmp/qiime2/cquga? I'm expecting to see 1777 and 0775 respectively.

Edit: I just noticed something. On your stat /tmp, it says Blocks: 0, can you also run stat /tmp -f in addition to the above commands? This makes me think there is little to no space available to /tmp, but I'm not sure how WSL handles these things.

14

Hi @Oddant1 ,

You were right on the permissions, find also below the stat /tmp -f which I don't know how to interpret it.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp/qiime2/
  File: /tmp/qiime2/
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 25614222880907945  Links: 1
Access: (1777/drwxrwxrwt)  Uid: ( 1000/   cquga)   Gid: ( 1000/   cquga)
Access: 2023-03-17 13:54:06.621431900 +0100
Modify: 2023-03-17 12:38:46.740540700 +0100
Change: 2023-03-17 12:38:46.740540700 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp/qiime2/cquga
  File: /tmp/qiime2/cquga
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 40250921669863351  Links: 1
Access: (0755/drwxr-xr-x)  Uid: ( 1000/   cquga)   Gid: ( 1000/   cquga)
Access: 2023-03-17 13:54:06.652277600 +0100
Modify: 2023-03-17 13:54:06.652277600 +0100
Change: 2023-03-17 13:54:06.652277600 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp -f
  File: "/tmp"
    ID: 100000000 Namelen: 255     Type: wslfs
Block size: 4096       Fundamental block size: 4096
Blocks: Total: 123616255  Free: 62835939   Available: 62835939
Inodes: Total: 999        Free: 1000000```

I changed permissions of /tmp/qiime2/cquga from 0755 to 1777. I run then the tutorial smoothly until the qiime diversity alpha-rarefaction, when again I got [Errno 13]. The above folders where still at 1777, but I saw some subfolders where still at 0755. I run sudo find /tmp -type d -exec chmod 1777 {} \; to set all subfolders to 1777, but that did not solve the issue.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime diversity alpha-rarefaction \
>   --i-table table.qza \
>   --i-phylogeny rooted-tree.qza \
>   --p-max-depth 4000 \
>   --m-metadata-file sample-metadata.tsv \
>   --o-visualization alpha-rarefaction.qzv
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2/cquga/processes/631-1679327016.13@cquga/83d9a973-404f-48e6-9311-85de343b870a.1932667166478762894/83d9a973-404f-48e6-9311-85de343b870a' -> '/tmp/qiime2/cquga/data/83d9a973-404f-48e6-9311-85de343b870a'

Debug info has been saved to /tmp/qiime2-q2cli-err-hxohl_46.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp/qiime2/cquga
  File: /tmp/qiime2/cquga
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 50384020831282374  Links: 1
Access: (1777/drwxrwxrwt)  Uid: ( 1000/   cquga)   Gid: ( 1000/   cquga)
Access: 2023-03-20 16:45:24.383871300 +0100
Modify: 2023-03-20 16:45:24.383871300 +0100
Change: 2023-03-20 16:45:24.383871300 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp/qiime2/cquga/processes
  File: /tmp/qiime2/cquga/processes
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 116530640358346802  Links: 1
Access: (0755/drwxr-xr-x)  Uid: ( 1000/   cquga)   Gid: ( 1000/   cquga)
Access: 2023-03-20 16:45:17.361932400 +0100
Modify: 2023-03-20 16:45:17.361932400 +0100
Change: 2023-03-20 16:45:17.361932400 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ sudo find /tmp -type d -exec chmod 1777 {} \;
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ stat /tmp/qiime2/cquga/processes
  File: /tmp/qiime2/cquga/processes
  Size: 4096            Blocks: 0          IO Block: 4096   directory
Device: 2h/2d   Inode: 116530640358346802  Links: 1
Access: (1777/drwxrwxrwt)  Uid: ( 1000/   cquga)   Gid: ( 1000/   cquga)
Access: 2023-03-20 16:52:22.611301500 +0100
Modify: 2023-03-20 16:45:17.361932400 +0100
Change: 2023-03-20 16:45:17.361932400 +0100
 Birth: -
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime diversity alpha-rarefaction \
>   --i-table table.qza \
>   --i-phylogeny rooted-tree.qza \
>   --p-max-depth 4000 \
>   --m-metadata-file sample-metadata.tsv \
>   --o-visualization alpha-rarefaction.qzv
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-w_5w567f' -> '/tmp/qiime2/cquga/processes/729-1679327578.31@cquga/c0d81e78-dca2-48b7-8a4f-c04a7ca1ed11.4670739441755608869/c0d81e78-dca2-48b7-8a4f-c04a7ca1ed11/provenance'

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

I thought maybe some new subfolders are created each time I run the command, which appear by default with 0755 permission, so cannot be edited afterwards?

Thanks again,
César.

1 Like
17

The Blocks: Available in the output of stats /tmp -f suggests that /tmp has the opportunity to use plenty of disk space if it needs to. I'm wondering if there are some file ownership issues going on here since your inputs are in /mnt/c and you are running this from /mnt/c maybe WSL doesn't understand that you own those files?

Permissions 0755 are read and execute for everyone and read, write, execute only for the file owner. /tmp/qiime2/cquga and everything beneath it should have 0755. We do this as a precaution on multi-user systems, but it may be giving you a headache here since maybe WSL isn't recognizing you as the owner. Maybe try moving your input artifacts out of the Windows part of your hard drive and into a part that belongs to WSL? @colinbrislawn since you use WSL, do you have any input on how to go about doing this/does this seem reasonable to you?

18

I'm not sure if it will fix everything, but I use WSL and it works well for me. I keep all my files in my Linux file system /home/colinbrislawn and not my WIndows one /mnt/c/Users/Colin Brislawn

19

Thank you both :slight_smile:

I tried running the tutorial from my home directory, so /home/cquga but the [Errno 13] keeps appearing.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:~/qiime2-moving-pictures-tutorial$ 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
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-tyk9t3qz' -> '/tmp/qiime2/cquga/processes/572-1679475225.33@cquga/88eefe78-c251-4e79-94c4-9f257cd85e06.361887072292159742/88eefe78-c251-4e79-94c4-9f257cd85e06/provenance'

Debug info has been saved to /tmp/qiime2-q2cli-err-3piqnxjm.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:~/qiime2-moving-pictures-tutorial$ pwd
/home/cquga/qiime2-moving-pictures-tutorial

An IT related person from my institution suggested the problem for me could arise from the very long names qiime tries to give to the subfolders and paths (e.g. '/tmp/qiime2/cquga/processes/572-1679475225.33@cquga/88eefe78-c251-4e79-94c4-9f257cd85e06.361887072292159742/88eefe78-c251-4e79-94c4-9f257cd85e06/provenance'). Somehow the institutional system might see this as a threat and blocks the creation of this long folder names.

I don't know how or whether I could circumvent this though.

Thank you for your help.
César.

1 Like
20

@cquga, we're trying to figure out what's causing this issue right now, but we aren't entirely sure. It's very strange to us that it is breaking on this specific action and it appears to change which file system operation it fails on. Differently configured systems can cause all sorts of different errors for different reasons. Can you give more info on what kind of computer you are running this on? Is it a personal Windows computer you're using to run QIIME 2 through WSL, or is it some sort of institutional cluster?

If it is a computer only you use, can you try explicitly removing /tmp/qiime2 then running your commands? If it is an institutional cluster, can you remove /tmp/qiime2/cquga and try running your commands? Assuming those directories are still around anyway, /tmp is usually cleared when the computer restarts.

21

Hi @Oddant1

My computer is inside my university institutional cluster. I was granted this week local admin rights to see if that solved the problem, and it did not either.

I tried removing /tmp/qiime2/cquga, both before starting the tutorial and after the error appeared, but that did not solve the problem.

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/tmp/qiime2$ ls
cquga
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/tmp/qiime2$ rm -r cquga/
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/tmp/qiime2$ ls
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/tmp/qiime2$
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/tmp/qiime2$ cd /mnt/c/Users/cquga
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga$ mkdir qiime2-moving-pictures-tutorial
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga$ cd qiime2-moving-pictures-tutorial

...

(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime diversity alpha-rarefaction \
>   --i-table table.qza \
>   --i-phylogeny rooted-tree.qza \
>   --p-max-depth 4000 \
>   --m-metadata-file sample-metadata.tsv \
>   --o-visualization alpha-rarefaction.qzv
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2/cquga/processes/757-1679650974.48@cquga/64b0b863-1077-4c8e-aafd-45b4bcbdbb59.2935539040430206534/64b0b863-1077-4c8e-aafd-45b4bcbdbb59' -> '/tmp/qiime2/cquga/data/64b0b863-1077-4c8e-aafd-45b4bcbdbb59'

Debug info has been saved to /tmp/qiime2-q2cli-err-z14i10vd.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ rm -r /tmp/qiime2/cquga
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ ls /tmp/qiime2
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ ls /tmp
hsperfdata_cquga  qiime2  qiime2-q2cli-err-612tbnib.log  qiime2-q2cli-err-z14i10vd.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$ qiime diversity alpha-rarefaction \
>   --i-table table.qza \
>   --i-phylogeny rooted-tree.qza \
>   --p-max-depth 4000 \
>   --m-metadata-file sample-metadata.tsv \
>   --o-visualization alpha-rarefaction.qzv
Plugin error from diversity:

  [Errno 13] Permission denied: '/tmp/qiime2-provenance-oxkgs64c' -> '/tmp/qiime2/cquga/processes/799-1679651113.77@cquga/1be3bfb4-73f6-4e16-9db2-1cb08279538e.3273181839565666210/1be3bfb4-73f6-4e16-9db2-1cb08279538e/provenance'

Debug info has been saved to /tmp/qiime2-q2cli-err-br33xtf0.log
(qiime2-2023.2) cquga@KT-PP-NOTE-0002:/mnt/c/Users/cquga/qiime2-moving-pictures-tutorial$

As another alternative, is it still possible to install qiime2 within VirtualBox? or is that not currently supported? I have seen is not an option anymore in the installation guides, and it gave me an error when I installed in the same way as if it was within the WSL.

22

Hi @cquga,

Yes you can absolutely install QIIME 2 inside a virtualbox image, we just don't distribute those ourselves anymore. You would simply follow the usual instructions inside whatever linux flavor you best prefer.

That said we would definitely like to understand this better, as our goal would be that there's no issues running under WSL.

I wonder what version of WSL is being run, could you run the following in a Windows Powershell session?

wsl --list --verbose

There's technically two versions, and the first one used some Samba magic if I recall, perhaps that's why the filesystem is acting strange for us.

1 Like
24

Hi @ebolyen

Sorry for taking longer to answer. I have been able to fix the problem, now I have run the whole Moving Pictures Tutorial and also my dataset without any error.

This is what I did:

Seeing that this problem was not getting solved I tried installing virtualbox, but every time I run a command I was getting this QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. Illegal instruction (core dumped).

Then I tried installing Docker. It was not working well at the beginning, and searching in forums I followed the recommendation of checking my WSL version, and then seeing it was WSL1 updating to WSL2. Then I could run everything smoothly with no errors.

So, I guess is either the WSL update or Docker.

Thank you very much all of you for your help @colinbrislawn @Oddant1 @ebolyen :slight_smile:

César.

3 Likes
25

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