I have tried and excluded one sample with low number of sequences in the hypothesis that could influence the execution, however I still have problems,
I report hereafter the error I get:
Plugin error from vsearch:
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: vsearch --usearch_global /beegfs/scratch/tmp/tmpegylvue1 --id 0.85 --db /beegfs/scratch/tmp/qiime2-archive-8fawjhsd/2f45e966-178d-4468-901f-5a8de00d8134/data/dna-sequences.fasta --uc /beegfs/scratch/tmp/tmpldr6o3b0 --strand plus --qmask none --notmatched /beegfs/scratch/tmp/tmpilvon15x --threads 1 --minseqlength 1 --fasta_width 0
vsearch v2.7.0_linux_x86_64, 377.4GB RAM, 72 cores
GitHub - torognes/vsearch: Versatile open-source tool for microbiome analysis
Reading file /beegfs/scratch/tmp/qiime2-archive-8fawjhsd/2f45e966-178d-4468-901f-5a8de00d8134/data/dna-sequences.fasta 100%
7276798 nt in 5088 seqs, min 1258, max 2353, avg 1430
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching query sequences: 1148 of 1528 (75.13%)
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: vsearch --sortbysize /beegfs/scratch/tmp/tmpilvon15x --xsize --output /beegfs/scratch/tmp/q2-DNAFASTAFormat-2uf2ow7n --minseqlength 1 --fasta_width 0
vsearch v2.7.0_linux_x86_64, 377.4GB RAM, 72 cores
GitHub - torognes/vsearch: Versatile open-source tool for microbiome analysis
Reading file /beegfs/scratch/tmp/tmpilvon15x 100%
159010 nt in 380 seqs, min 301, max 596, avg 418
Getting sizes 100%
Sorting 100%
Median abundance: 1
Writing output 100%
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: vsearch --cluster_size /beegfs/scratch/tmp/tmpyhsw0iyg --id 0.85 --centroids /beegfs/scratch/tmp/q2-DNAFASTAFormat-b3cbkj4f --uc /beegfs/scratch/tmp/tmp_zq_5m8b --qmask none --xsize --threads 1 --minseqlength 1 --fasta_width 0
vsearch v2.7.0_linux_x86_64, 377.4GB RAM, 72 cores
GitHub - torognes/vsearch: Versatile open-source tool for microbiome analysis
Reading file /beegfs/scratch/tmp/tmpyhsw0iyg 100%
159010 nt in 380 seqs, min 301, max 596, avg 418
Sorting by abundance 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 256 Size min 1, max 9, avg 1.5
Singletons: 190, 50.0% of seqs, 74.2% of clusters
Traceback (most recent call last):
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in cluster_features_open_reference
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 513, in callable_executor
aliased_result = output._alias(prov)
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 199, in _alias
alias._archiver = archive.Archiver.from_data(
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/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/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 18, in write
super().write(archive_record, type, format, data_initializer,
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/core/archive/format/v0.py", line 62, in write
data_initializer(data_dir)
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 194, in clone_original
shutil.copytree(str(self._archiver.data_dir), str(into),
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/shutil.py", line 557, in copytree
return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
File "/home/riba.michela/.conda/envs/Miqiime2-2021.8/lib/python3.8/shutil.py", line 513, in _copytree
raise Error(errors)
shutil.Error: [('/beegfs/scratch/tmp/qiime2-archive-vc4bl7qs/80cfb6ec-e7d0-4ebb-bf94-280d3af5a001/data/feature-table.biom', '/beegfs/scratch/tmp/qiime2-archive-tig60mkf/39192f1d-de4b-47b1-b243-26a62bc0266c/data/feature-table.biom', "[Errno 1] Operation not permitted: '/beegfs/scratch/tmp/qiime2-archive-vc4bl7qs/80cfb6ec-e7d0-4ebb-bf94-280d3af5a001/data/feature-table.biom' -> '/beegfs/scratch/tmp/qiime2-archive-tig60mkf/39192f1d-de4b-47b1-b243-26a62bc0266c/data/feature-table.biom'")]