Cluster-features-closed-reference file not qza file

User Support
1

Hello, Im studying microbial community in the Korea. I was doing this tutorial(https://github.com/shu251/V4_tagsequencing_18Sdiversity_qiime2), but suddenly many error message appear. Please see below.

(qiime2-2018.6) LabOfMarineProtistanEcophysioloygy:test lompe$ qiime vsearch cluster-features-closed-reference \
 --i-table derep_table.qza \
 --i-sequences derep_seqs.qza \
 --i-reference-sequences /Users/lompe/test/pr2.qza \
 --o-clustered-table closedref/table_closed_97.qza \
 --o-unmatched-sequences closedref/unmatched_seqs.qza \
 --o-clustered-sequences closedref/rep-seqs_closed_97.qza \
 --p-perc-identity 0.97 \
 --p-threads 8
Traceback (most recent call last):
  File "/miniconda2/envs/qiime2-2018.6/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 244, in __call__
    arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 326, in handle_in_params
    kwargs, fallback=cmd_fallback)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/handlers.py", line 375, in get_value
    artifact = qiime2.sdk.Result.load(path)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 65, in load
    archiver = archive.Archiver.load(filepath)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 293, in load
    archive = cls.get_archive(filepath)
  File "/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 258, in get_archive
    raise ValueError("%s is not a QIIME archive." % filepath)
ValueError: /Users/lompe/murder/pr2.qza is not a QIIME archive.

When I first doing that pipe line. There is no error message like that. Why suddenly appear? Please help me

3

Hi @Don,
Thank you for sharing the full error message.

It looks like your reference database was not imported correctly. Did you use the import command listed in that tutorial?

So you successfully ran this command previously? If that is the case, my guess is that you accidentally overwrote this file at some point. You should try re-importing following the instructions in the tutorial you are following and try again.

I hope that helps!

1 Like
5

I solve it. Thank you very much

6

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