clawback error message

Community Plugin Support
1

Hello everyone, I’ve used qiime2 version qiime2-2019.7 and q2-clawback for assign taxonomy to 16S sequences but I found the error message in assemble-weights-from-Qiita step

error message

    Plugin error from clawback:

      EVALSHA : b''

    Debug info has been saved to /tmp/qiime2-q2cli-err-iaduchl2.log

qiime2-q2cli-err-iaduchl2.log file

    Traceback (most recent call last):
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
    results = action(**arguments)
      File "</home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-488>", line 2, in assemble_weights_from_Qiita
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 477, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_clawback/_clawback.py", line 101, in assemble_weights_from_Qiita
    metadata_key=metadata_key)
      File "</home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-495>", line 2, in fetch_Qiita_samples
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_clawback/_clawback.py", line 60, in fetch_Qiita_samples
    samples, ambig = redbiom.fetch.data_from_samples(context, sample_ids)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/redbiom/fetch.py", line 263, in data_from_samples
    return _biom_from_samples(context, samples)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/redbiom/fetch.py", line 320, in _biom_from_samples
    data = se(fetch_sample, 0, context, id_)
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/redbiom/_requests.py", line 105, in f
    return json.loads(_parse_validate_request(s.get(url), 'EVALSHA'))
      File "/home_bif/61110700601/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/redbiom/_requests.py", line 5, in _parse_validate_request
    raise requests.HTTPError("%s : %s" % (command, req.content))
    requests.exceptions.HTTPError: EVALSHA : b''

what should I do next? Many thanks.

2

Welcome to the forum @MMaetha!

It looks like either you are making an invalid request or redbiom (a dependency of clawback) is acting up. Could you please post the command that you used?

3

Hi @MMaetha,

I had that error message, too, yesterday. It has gone away now. I speculate that it was due to some transient issue on the server side for redbiom.

There is another issue now, however. q2-clawback is broken with qiime2-2019.7. We will rush a fix, but in the mean time please use qiime2-2019.4 if you wish to use clawback.

Thanks,
Ben

4

I run these commands and got the error alert

qiime clawback summarize-Qiita-metadata-category-and-contexts \
  --p-category empo_3 \
  --o-visualization vs12.available_empo3.qzv
qiime clawback assemble-weights-from-Qiita \
  --i-classifier 00.classifier_v3-4.qza \
  --i-reference-taxonomy 00.ref-taxonomy.qza \
  --i-reference-sequences 00.silva_132_97_v3-4.qza \
  --p-metadata-key empo_3 \
  --p-metadata-value "Animal distal gut" \
  --p-context Pick_closed-reference_OTUs-Greengenes-Illumina-16S-V4-5c6506 \
  --o-class-weight 13.assemble-weights.qza
5

Thank you @MMaetha. As @BenKaehler mentioned above, this appears to have been a transient issue that fixed itself (my guess is QIITA may have been down, possibly for maintenance?)

So is this working for you now with QIIME 2 version 2019.4?

6

For anyone who is tracking this issue, we have released a new version of q2-clawback on conda.

Anyone using QIIME 2 version 2019.7 should use q2-clawback version 2019.7.0 from conda.

Anyone using QIIME 2 version 2019.4 must use q2-clawback version 0.0.6 from conda.

@MMaetha, I am now seeing no trace of the EVALSH error (after significant testing). Please let us know if you are still experiencing that problem.

2 Likes
7

after I updated q2-clawback in conda. It works. But I have new error alert

%E0%B8%A0%E0%B8%B2%E0%B8%9E
%E0%B8%A0%E0%B8%B2%E0%B8%9E837×442 34.8 KB

Command

time qiime clawback assemble-weights-from-Qiita \
>   --i-classifier 00.classifier_v3-4.qza \
>   --i-reference-taxonomy 00.ref-taxonomy.qza \
>   --i-reference-sequences 00.silva_132_97_v3-4.qza \
>   --p-metadata-key empo_3 \
>   --p-metadata-value "Animal distal gut" \
>   --p-context Pick_closed-reference_OTUs-Greengenes-Illumina-16S-V4-5c6506 \
>   --o-class-weight 14.assemble-weights.qza
9

Hi @MMaetha,
This new error does not appear to be related to clawback, rather there appears to be something wrong with your sequence files.

Can you run qiime tools validate on your reference sequences artifact? That may provide some more information — otherwise you should check out the fasta file that you imported, there may be spaces in that file.