Plungin error vsearch

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1

Unable to read from file (/tmp/q2-QIIME1DemuxDirFmt-nv4xlfsv/seqs.fna)
Traceback (most recent call last):
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in dereplicate_sequences
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_vsearch/_cluster_sequences.py", line 37, in dereplicate_sequences
run_command(cmd)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
subprocess.run(cmd, check=True)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['vsearch', '--derep_fulllength', '/tmp/q2-QIIME1DemuxDirFmt-nv4xlfsv/seqs.fna', '--output', '/tmp/q2-DNAFASTAFormat-7hydst2o', '--relabel_sha1', '--relabel_keep', '--uc', '/tmp/tmp7ne4_p81', '--qmask', 'none', '--xsize', '--minseqlength', '1', '--fasta_width', '0']' returned non-zero exit status 1.

2

I have this error when running vsearch

Unable to read from file (/tmp/q2-QIIME1DemuxDirFmt-nv4xlfsv/seqs.fna)
Traceback (most recent call last):
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in dereplicate_sequences
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_vsearch/_cluster_sequences.py", line 37, in dereplicate_sequences
run_command(cmd)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
subprocess.run(cmd, check=True)
File "/home/user/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['vsearch', '--derep_fulllength', '/tmp/q2-QIIME1DemuxDirFmt-nv4xlfsv/seqs.fna', '--output', '/tmp/q2-DNAFASTAFormat-7hydst2o', '--relabel_sha1', '--relabel_keep', '--uc', '/tmp/tmp7ne4_p81', '--qmask', 'none', '--xsize', '--minseqlength', '1', '--fasta_width', '0']' returned non-zero exit status 1.

7

@Nana_Amoako,

Can you post the interface you were using and the command you were trying to run when you got this error?

9

An off-topic reply has been split into a new topic: Trouble with alignment mafft

Please keep replies on-topic in the future.

10

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