I am totally new in Qiime and Qiime2. I am running the clustering step as below:
Import reference sequence
qiime tools import _
_ --input-path silva.nr_v132.align _
_ --output-path reference-seqs.qza _
_ --type 'FeatureData[Sequence]'
Closed-reference clustering
qiime vsearch cluster-features-closed-reference _
_ --i-table feature-frequency-filtered-table.qza _
_ --i-sequences rep-seqs-filtered.qza _
_ --i-reference-sequences reference-seqs.qza_
_ --p-perc-identity 0.97 _
_ --o-clustered-table table-cr-97.qza _
_ --o-clustered-sequences rep-seqs-cr-97.qza _
_ --o-unmatched-sequences unmatched-cr-97.qza
But there was always error info as:
Plugin Error from vsearch: Command '['vsearch', '--usearch_global',....returned non-zero exit status 1.
Here is the log info:
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 /tmp/tmpbr_9gead --id 0.97 --db /tmp/qiime2-archive-xodkr3r6/fadebd06-b0b6-43e6-a3a7-2f731302270d/data/dna-sequences.fasta --uc /tmp/tmpcyed42k0 --strand plus --qmask none --notmatched /tmp/tmpl64pqv9h --threads 1
vsearch v2.7.0_linux_x86_64, 31.4GB RAM, 8 cores
Reading file /tmp/qiime2-archive-xodkr3r6/fadebd06-b0b6-43e6-a3a7-2f731302270d/data/dna-sequences.fasta
Fatal error: illegal character '.' on line 2 in FASTA file
Traceback (most recent call last):
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in cluster_features_closed_reference
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
output_types, provenance)
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 367, in callable_executor
output_views = self._callable(**view_args)
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 256, in cluster_features_closed_reference
run_command(cmd)
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
subprocess.run(cmd, check=True)
File "/home/xyz/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['vsearch', '--usearch_global', '/tmp/tmpbr_9gead', '--id', '0.97', '--db', '/tmp/qiime2-archive-xodkr3r6/fadebd06-b0b6-43e6-a3a7-2f731302270d/data/dna-sequences.fasta', '--uc', '/tmp/tmpcyed42k0', '--strand', 'plus', '--qmask', 'none', '--notmatched', '/tmp/tmpl64pqv9h', '--threads', '1']' returned non-zero exit status 1
What can I do to debug?
Thank you very much.
Chloe