pathway_pipeline.py - KeyError: 'Sample-Name'

[Afrina Ad]

Hi all,

I am trying to run the code below to get the output as shown in the tutorial but I keep getting key error with the sample name eventhough my file has the same format/column as in the tutorial.

pathway_pipeline.py -i EC_metagenome_out/pred_metagenome_contrib.tsv.gz --no_regroup -o pathways_out -p 1

This is the error that I got:

Traceback (most recent call last):
  File "/home/customercare/miniconda3/envs/picrust2/bin/pathway_pipeline.py", line 272, in <module>
    main()
  File "/home/customercare/miniconda3/envs/picrust2/bin/pathway_pipeline.py", line 210, in main
    verbose=args.verbose)
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/pathway_pipeline.py", line 398, in pathway_pipeline
    for sample_id in samples)
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/site-packages/joblib/parallel.py", line 1017, in __call__
    self.retrieve()
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/site-packages/joblib/parallel.py", line 909, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 562, in wrap_future_result
    return future.result(timeout=timeout)
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "/home/customercare/miniconda3/envs/picrust2/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
KeyError: 'G25Wk16'

Can anyone point out which part should I edit? Or is it because my pred_metagenome_contrib.tsv.gz is too big (9 Gb)?

[Gavin Douglas]

Hey there,

How many samples do you have and would you mind sharing the head of the input file?

Thanks,

Gavin

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[Afrina Ad]

I have about 300+ samples which then produced about 100+ m rows in my pred_metagenome_contrib.tsv.gz.

Here is the head of the input file:

sample    function    taxon      taxon_abun   taxon_rel_abun      genome_function_count  taxon_function_abun  taxon_rel_function_abun
G25Wk16   EC:1.1.1.1  OTU_1      830.0        3.931059633701022      2                   1660.0               7.862119267402044
G25Wk16   EC:1.1.1.1  OTU_10     359.0        1.7003016969863456     2                   718.0                3.400603393972691
G25Wk16   EC:1.1.1.1  OTU_1002   3.0          0.01420864927843743    2                   6.0                  0.02841729855687486

Gavin

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[Gavin Douglas]

Hey again,

I think the issue is that when you’re using the —no_regroup option that the tool is unable to identify any pathways as present and is returning an empty object. I’ll be sure to make the tool throw a warning and end gracefully in these cases for a future release.

In the meantime, you actually need to use the “—no_regroup” option if you’re using the default pathway inference pipeline - this option prevents the EC numbers from being regrouped to MetaCyc reactions, which is necessary for inferring the MetaCyc pathways. 

Best,

Gavin

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