Hello. I'm running a script on 16S metagenomic data, qiime2-2021.11 on the HPC at my university in a conda environment.
I submitted this qiime script as a job in the HPC.......
conda info --envs
conda activate qiime2-2022.11
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path list.txt --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2
qiime demux summarize --i-data paired-end-demux.qza --o-visualization paired-end-demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-chimera-method pooled --p-trunc-len-f 240 --p-trunc-len-r 222 --p-n-threads 50 --verbose
qiime metadata tabulate --m-input-file denoising-stats.qza --o-visualization denoising-stats.qzv --verbose
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file metadata.tsv
qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv
qiime vsearch cluster-features-de-novo --i-table table.qza --i-sequences rep-seqs.qza --o-clustered-table table-OTU97.qza --o-clustered-sequences rep-seqs-OTU97.qza --p-perc-identity 0.97 --p-threads 50 --verbose
qiime feature-table tabulate-seqs --i-data rep-seqs-OTU97.qza --o-visualization rep-seqs-OTU97.qzv
qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads rep-seqs-OTU97.qza --o-classification taxonomy-silva.qza --verbose --p-n-jobs 50
qiime metadata tabulate --m-input-file taxonomy-silva.qza --o-visualization taxonomy-silva.qzv
qiime taxa barplot --i-table table-OTU97.qza --i-taxonomy taxonomy-silva.qza --m-metadata-file metadata.txt --o-visualization taxa-bar-plots.qzv
qiime phylogeny align-to-tree-mafft-fasttree --i-sequences rep-seqs-OTU97.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
qiime feature-table summarize --i-table table-OTU97.qza --o-visualization table-OTU97.qzv --m-sample-metadata-file metadata.tsv
.....but I keep getting an error code. I tried to run the script line by line on my system with Ubuntu, still conda and the same version, so I can see exactly where the problem starts and I get the paired-end-demux.qza and .qzv files but it starts to go wrong at dada2. I also reduced the number of threads on my system to 7 (same problem still).
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-chimera-method pooled --p-trunc-len-f 240 --p-trunc-len-r 222 --p-n-threads 7 --verbose
Error: I've put the error from just the dada2 step I got on my computer first and a linebreak with fullstops, then the full error report I got for the whole qiime script from my university's HPC.
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: run_dada.R --input_directory /tmp/tmpnu2z9cxh/forward --input_directory_reverse /tmp/tmpnu2z9cxh/reverse --output_path /tmp/tmpnu2z9cxh/output.tsv.biom --output_track /tmp/tmpnu2z9cxh/track.tsv --filtered_directory /tmp/tmpnu2z9cxh/filt_f --filtered_directory_reverse /tmp/tmpnu2z9cxh/filt_r --truncation_length 240 --truncation_length_reverse 222 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method pooled --min_parental_fold 1.0 --allow_one_off False --num_threads 7 --learn_min_reads 1000000
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.9 / RcppParallel: 5.1.6
2) Filtering Error in names(answer) <- names1 :
'names' attribute [81] must be the same length as the vector [36]
4: mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE),
mapply(c, filt, filt.rev, SIMPLIFY = FALSE), MoreArgs = list(truncQ = truncQ,
truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight,
maxLen = maxLen, minLen = minLen, maxN = maxN, minQ = minQ,
maxEE = maxEE, rm.phix = rm.phix, rm.lowcomplex = rm.lowcomplex,
orient.fwd = orient.fwd, matchIDs = matchIDs, id.sep = id.sep,
id.field = id.field, n = n, OMP = OMP, qualityType = qualityType,
compress = compress, verbose = verbose), mc.cores = ncores,
mc.silent = TRUE)
3: filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen,
truncLenR), trimLeft = c(trimLeft, trimLeftR), maxEE = c(maxEE,
maxEER), truncQ = truncQ, rm.phix = TRUE, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(filterAndTrim(unfilts, filts, unfiltsR, filtsR,
truncLen = c(truncLen, truncLenR), trimLeft = c(trimLeft,
trimLeftR), maxEE = c(maxEE, maxEER), truncQ = truncQ,
rm.phix = TRUE, multithread = multithread))
Traceback (most recent call last):
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpnu2z9cxh/forward', '--input_directory_reverse', '/tmp/tmpnu2z9cxh/reverse', '--output_path', '/tmp/tmpnu2z9cxh/output.tsv.biom', '--output_track', '/tmp/tmpnu2z9cxh/track.tsv', '--filtered_directory', '/tmp/tmpnu2z9cxh/filt_f', '--filtered_directory_reverse', '/tmp/tmpnu2z9cxh/filt_r', '--truncation_length', '240', '--truncation_length_reverse', '222', '--trim_left', '0', '--trim_left_reverse', '0', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'pooled', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '7', '--learn_min_reads', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/nengigi/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
...............................................................................................................................
conda environments:
base * /home/crk_w20037292/miniconda3
qiime2-2021.11 /home/crk_w20037292/miniconda3/envs/qiime2-2021.11
qiime2-2022.11 /home/crk_w20037292/miniconda3/envs/qiime2-2022.11
qiime2-2023.2 /home/crk_w20037292/miniconda3/envs/qiime2-2023.2
Imported list.txt as PairedEndFastqManifestPhred33V2 to paired-end-demux.qza
Saved Visualization to: paired-end-demux.qzv
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6
2) Filtering Error in filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen, :
These are the errors (up to 5) encountered in individual cores...
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
failed to write record 17333
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
failed to write record 75223
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
failed to write record 29935
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 249
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
failed to write record 27049
4: stop("These are the errors (up to 5) encountered in individual cores...\n",
rval)
3: filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen,
truncLenR), trimLeft = c(trimLeft, trimLeftR), maxEE = c(maxEE,
maxEER), truncQ = truncQ, rm.phix = TRUE, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(filterAndTrim(unfilts, filts, unfiltsR, filtsR,
truncLen = c(truncLen, truncLenR), trimLeft = c(trimLeft,
trimLeftR), maxEE = c(maxEE, maxEER), truncQ = truncQ,
rm.phix = TRUE, multithread = multithread))
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpkib1gq2y/forward', '--input_directory_reverse', '/tmp/tmpkib1gq2y/reverse', '--output_path', '/tmp/tmpkib1gq2y/output.tsv.biom', '--output_track', '/tmp/tmpkib1gq2y/track.tsv', '--filtered_directory', '/tmp/tmpkib1gq2y/filt_f', '--filtered_directory_reverse', '/tmp/tmpkib1gq2y/filt_r', '--truncation_length', '235', '--truncation_length_reverse', '222', '--trim_left', '0', '--trim_left_reverse', '0', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'pooled', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '120', '--learn_min_reads', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
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: run_dada.R --input_directory /tmp/tmpkib1gq2y/forward --input_directory_reverse /tmp/tmpkib1gq2y/reverse --output_path /tmp/tmpkib1gq2y/output.tsv.biom --output_track /tmp/tmpkib1gq2y/track.tsv --filtered_directory /tmp/tmpkib1gq2y/filt_f --filtered_directory_reverse /tmp/tmpkib1gq2y/filt_r --truncation_length 235 --truncation_length_reverse 222 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method pooled --min_parental_fold 1.0 --allow_one_off False --num_threads 120 --learn_min_reads 1000000
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/util.py", line 288, in load_metadata
metadata = qiime2.Metadata.load(fp)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/metadata/metadata.py", line 396, in load
return MetadataReader(filepath).read(
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/metadata/io.py", line 44, in init
raise MetadataFileError(
qiime2.metadata.io.MetadataFileError: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): denoising-stats.qza
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: Metadata in QIIME 2 — QIIME 2 2023.2.0 documentation
There was an issue with loading the file denoising-stats.qza as metadata:
Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): denoising-stats.qza
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: Metadata in QIIME 2 — QIIME 2 2023.2.0 documentation
See above for debug info.
Usage: qiime feature-table summarize [OPTIONS]
Generate visual and tabular summaries of a feature table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence] The feature table to be summarized. [required]
Parameters:
--m-sample-metadata-file METADATA...
(multiple The sample metadata.
arguments will
be merged) [optional]
Outputs:
--o-visualization VISUALIZATION
[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.
Examples:
### example: feature table summarize
qiime feature-table summarize
--i-table feature-table.qza
--o-visualization table.qzv
There was a problem with the command:
(1/1) Invalid value for '--i-table': table.qza does not exist.
Usage: qiime feature-table tabulate-seqs [OPTIONS]
Generate tabular view of feature identifier to sequence mapping, including
links to BLAST each sequence against the NCBI nt database.
Inputs:
--i-data ARTIFACT FeatureData[Sequence | AlignedSequence]
The feature sequences to be tabulated. [required]
Outputs:
--o-visualization VISUALIZATION
[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.
Examples:
### example: feature table tabulate seqs
qiime feature-table tabulate-seqs
--i-data rep-seqs.qza
--o-visualization rep-seqs.qzv
There was a problem with the command:
(1/1) Invalid value for '--i-data': rep-seqs.qza does not exist.
Usage: qiime vsearch cluster-features-de-novo [OPTIONS]
Given a feature table and the associated feature sequences, cluster the
features based on user-specified percent identity threshold of their
sequences. This is not a general-purpose de novo clustering method, but
rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a single
feature, the frequency of that single feature in a given sample is the sum
of the frequencies of the features that were clustered in that sample.
Feature identifiers and sequences will be inherited from the centroid
feature of each cluster. See the vsearch documentation for details on how
sequence clustering is performed.
Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences corresponding to the features in
table. [required]
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be clustered. [required]
Parameters:
--p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The percent identity at which clustering should be
performed. This parameter maps to vsearch's --id
parameter. [required]
--p-threads INTEGER Range(0, 256, inclusive_end=True)
The number of threads to use for computation.
Passing 0 will launch one thread per CPU core.
[default: 1]
Outputs:
--o-clustered-table ARTIFACT FeatureTable[Frequency]
The table following clustering of features.
[required]
--o-clustered-sequences ARTIFACT FeatureData[Sequence]
Sequences representing clustered features.
[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-table': table.qza does not exist.
(2/2) Invalid value for '--i-sequences': rep-seqs.qza does not exist.
Usage: qiime feature-table tabulate-seqs [OPTIONS]
Generate tabular view of feature identifier to sequence mapping, including
links to BLAST each sequence against the NCBI nt database.
Inputs:
--i-data ARTIFACT FeatureData[Sequence | AlignedSequence]
The feature sequences to be tabulated. [required]
Outputs:
--o-visualization VISUALIZATION
[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.
Examples:
### example: feature table tabulate seqs
qiime feature-table tabulate-seqs
--i-data rep-seqs.qza
--o-visualization rep-seqs.qzv
There was a problem with the command:
(1/1) Invalid value for '--i-data': rep-seqs-OTU97.qza does not exist.
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/zipfile.py", line 1702, in _extract_member
shutil.copyfileobj(source, target)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/shutil.py", line 208, in copyfileobj
fdst_write(buf)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 366, in load
archive.mount(path)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 198, in mount
self.extract(filepath)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 212, in extract
zf.extract(name, path=str(filepath.parent))
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/zipfile.py", line 1630, in extract
return self._extract_member(member, path, pwd)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/zipfile.py", line 1702, in _extract_member
shutil.copyfileobj(source, target)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 79, in load
archiver = archive.Archiver.load(filepath)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 377, in load
cls._destroy_temp_path(archive.uuid)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 300, in _destroy_temp_path
cache.process_pool.remove(str(process_alias))
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/cache.py", line 1541, in remove
with self.cache.lock:
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/core/cache.py", line 290, in enter
self.flufl_lock.lock()
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 328, in lock
self._write()
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 492, in _write
with open(self._claimfile, 'w') as fp:
OSError: [Errno 28] No space left on device: '/tmp/qiime2/crk_w20037292/LOCK|compute004.cm.cluster|25091|1380742089825186126'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/util.py", line 398, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 83, in load
raise ValueError(f'There was not enough space left on '
ValueError: There was not enough space left on '/tmp' to extract the artifact 'silva-138-99-nb-classifier.qza'. (Try setting $TMPDIR to a directory with more space, or increasing the size of '/tmp')
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/click/type.py", line 112, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/util.py", line 352, in _load_input
artifact, error = _load_input_file(fp)
File "/home/crk_w20037292/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/util.py", line 404, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'
There was a problem loading 'silva-138-99-nb-classifier.qza' as an artifact:
It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'
See above for debug info.
slurmstepd: error: *** JOB 1319314 ON compute004 CANCELLED AT 2023-04-04T02:17:13 DUE TO TIME LIMIT ***
