jvfe / kraken2_latch Goto Github PK
View Code? Open in Web Editor NEWA LatchBio workflow for running Kraken2
Home Page: https://console.latch.bio/explore/82006/info
License: MIT License
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microview fails
hello mr jvfe, thanks for your work
this workflow fails at the microview step for the attached tsv, providing the traceback below:
Running MicroView 👓 v0.9.4
Found 1 reports...
/opt/conda/lib/python3.9/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide
proportion_explained = eigvals / sum_eigenvalues
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /opt/conda/lib/python3.9/site-packages/microview/cli.py:75 in main │
│ │
│ 72 │ │ │ if parsed_result is not None: │
│ 73 │ │ │ │ tax_plots = generate_taxo_plots(tax_results, parsed_res │
│ 74 │ │ │ else: │
│ ❱ 75 │ │ │ │ tax_plots = generate_taxo_plots(tax_results) │
│ 76 │ │ │ render_base(tax_plots=tax_plots, dir_path=data_source, outp │
│ 77 │ │ console.print(f"\n Done!\n", style="bold green") │
│ 78 │ except Exception: │
│ │
│ ╭───────────────────────────────── locals ─────────────────────────────────╮ │
│ │ console = <console width=80 None> │ │
│ │ csv_file = None │ │
│ │ data_source = PosixPath('/root/tsv_only') │ │
│ │ output = PosixPath('/root/microview_report.html') │ │
│ │ parsed_result = None │ │
│ │ reports = [ │ │
│ │ │ Sample( │ │
│ │ │ │ report=PosixPath('/root/tsv_only/L01.tsv'), │ │
│ │ │ │ report_type='kraken' │ │
│ │ │ ) │ │
│ │ ] │ │
│ │ tax_results = { │ │
│ │ │ 'sample n reads': index variable value │ │
│ │ 0 L01.tsv assigned 94.554794 │ │
│ │ 1 L01.tsv unassigned 5.445206, │ │
│ │ │ 'common taxas': index │ │
│ │ variable value │ │
│ │ 1 L01.tsv unclassified 5.450000 │ │
│ │ 5 L01.tsv other 3.528075 │ │
│ │ 3 L01.tsv cellular organisms 0.550000 │ │
│ │ 2 L01.tsv Saccharomycetaceae 0.840000 │ │
│ │ 0 L01.tsv Saccharomyces cerevisiae S288C 89.180000 │ │
│ │ 4 L01.tsv Saccharomyces 0.450000, │ │
│ │ │ 'abund and div': index Shannon Diversity N │ │
│ │ Taxas Pielou Evenness │ │
│ │ 0 L01.tsv 0.896088 3013 0.111862, │ │
│ │ │ 'beta div': │ │
│ │ <skbio.stats.ordination._ordination_results.OrdinationR… │ │
│ │ object at 0x7f4fb1ed6a30> │ │
│ │ } │ │
│ │ taxonomy = PosixPath('/root/tsv_only') │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │
│ │
│ /opt/conda/lib/python3.9/site-packages/microview/plotting.py:134 in │
│ generate_taxo_plots │
│ │
│ 131 │ # Beta diversity plots │
│ 132 │ │
│ 133 │ pcoa_embed = ( │
│ ❱ 134 │ │ tax_data["beta div"].samples[["PC1", "PC2"]].rename_axis("samp │
│ 135 │ ) │
│ 136 │ var_explained = ( │
│ 137 │ │ tax_data["beta div"] │
│ │
│ ╭───────────────────────────────── locals ─────────────────────────────────╮ │
│ │ assigned = Figure({ │ │
│ │ │ 'data': [{'alignmentgroup': 'True', │ │
│ │ │ │ │ 'hovertemplate': │ │
│ │ 'Category=assigned<br>Sample name=%{x}<br>% of │ │
│ │ reads=%{y}<extra></extra>', │ │
│ │ │ │ │ 'legendgroup': 'assigned', │ │
│ │ │ │ │ 'marker': {'color': '#636efa', 'pattern': │ │
│ │ {'shape': ''}}, │ │
│ │ │ │ │ 'name': 'assigned', │ │
│ │ │ │ │ 'offsetgroup': 'assigned', │ │
│ │ │ │ │ 'orientation': 'v', │ │
│ │ │ │ │ 'showlegend': True, │ │
│ │ │ │ │ 'textposition': 'auto', │ │
│ │ │ │ │ 'type': 'bar', │ │
│ │ │ │ │ 'x': array(['L01.tsv'], dtype=object), │ │
│ │ │ │ │ 'xaxis': 'x', │ │
│ │ │ │ │ 'y': array([94.55479444]), │ │
│ │ │ │ │ 'yaxis': 'y'}, │ │
│ │ │ │ │ {'alignmentgroup': 'True', │ │
│ │ │ │ │ 'hovertemplate': │ │
│ │ 'Category=unassigned<br>Sample name=%{x}<br>% of │ │
│ │ reads=%{y}<extra></extra>', │ │
│ │ │ │ │ 'legendgroup': 'unassigned', │ │
│ │ │ │ │ 'marker': {'color': '#EF553B', 'pattern': │ │
│ │ {'shape': ''}}, │ │
│ │ │ │ │ 'name': 'unassigned', │ │
│ │ │ │ │ 'offsetgroup': 'unassigned', │ │
│ │ │ │ │ 'orientation': 'v', │ │
│ │ │ │ │ 'showlegend': True, │ │
│ │ │ │ │ 'textposition': 'auto', │ │
│ │ │ │ │ 'type': 'bar', │ │
│ │ │ │ │ 'x': array(['L01.tsv'], dtype=object), │ │
│ │ │ │ │ 'xaxis': 'x', │ │
│ │ │ │ │ 'y': array([5.44520556]), │ │
│ │ │ │ │ 'yaxis': 'y'}], │ │
│ │ │ 'layout': {'barmode': 'relative', │ │
│ │ │ │ │ 'legend': {'title': {'text': 'Category'}, │ │
│ │ 'tracegroupgap': 0}, │ │
│ │ │ │ │ 'margin': {'t': 60}, │ │
│ │ │ │ │ 'template': '...', │ │
│ │ │ │ │ 'xaxis': {'anchor': 'y', │ │
│ │ │ │ │ │ │ │ 'categoryorder': 'category │ │
│ │ ascending', │ │
│ │ │ │ │ │ │ │ 'domain': [0.0, 1.0], │ │
│ │ │ │ │ │ │ │ 'title': {'text': 'Sample │ │
│ │ name'}}, │ │
│ │ │ │ │ 'yaxis': {'anchor': 'x', 'domain': [0.0, │ │
│ │ 1.0], 'title': {'text': '% of reads'}}} │ │
│ │ }) │ │
│ │ assigned_html = '<div> <div │ │
│ │ id="assigned-plot" class="plotly-graph-div'+8550 │ │
│ │ contrast_df = None │ │
│ │ tax_data = { │ │
│ │ │ 'sample n reads': index variable value │ │
│ │ 0 L01.tsv assigned 94.554794 │ │
│ │ 1 L01.tsv unassigned 5.445206, │ │
│ │ │ 'common taxas': index │ │
│ │ variable value │ │
│ │ 1 L01.tsv unclassified 5.450000 │ │
│ │ 5 L01.tsv other 3.528075 │ │
│ │ 3 L01.tsv cellular organisms 0.550000 │ │
│ │ 2 L01.tsv Saccharomycetaceae 0.840000 │ │
│ │ 0 L01.tsv Saccharomyces cerevisiae S288C 89.180000 │ │
│ │ 4 L01.tsv Saccharomyces 0.450000, │ │
│ │ │ 'abund and div': index Shannon Diversity N │ │
│ │ Taxas Pielou Evenness │ │
│ │ 0 L01.tsv 0.896088 3013 0.111862, │ │
│ │ │ 'beta div': │ │
│ │ <skbio.stats.ordination._ordination_results.OrdinationR… │ │
│ │ object at 0x7f4fb1ed6a30> │ │
│ │ } │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │
│ │
│ /opt/conda/lib/python3.9/site-packages/pandas/core/frame.py:3811 in │
│ __getitem__ │
│ │
│ 3808 │ │ else: │
│ 3809 │ │ │ if is_iterator(key): │
│ 3810 │ │ │ │ key = list(key) │
│ ❱ 3811 │ │ │ indexer = self.columns._get_indexer_strict(key, "columns │
│ 3812 │ │ │
│ 3813 │ │ # take() does not accept boolean indexers │
│ 3814 │ │ if getattr(indexer, "dtype", None) == bool: │
│ │
│ ╭──────────── locals ────────────╮ │
│ │ indexer = None │ │
│ │ is_single_key = False │ │
│ │ key = ['PC1', 'PC2'] │ │
│ │ self = │ │ PC1 │ │
│ │ L01.tsv 0.0 │ │
│ ╰────────────────────────────────╯ │
│ │
│ /opt/conda/lib/python3.9/site-packages/pandas/core/indexes/base.py:6113 in │
│ _get_indexer_strict │
│ │
│ 6110 │ │ else: │
│ 6111 │ │ │ keyarr, indexer, new_indexer = self._reindex_non_unique(k │
│ 6112 │ │ │
│ ❱ 6113 │ │ self._raise_if_missing(keyarr, indexer, axis_name) │
│ 6114 │ │ │
│ 6115 │ │ keyarr = self.take(indexer) │
│ 6116 │ │ if isinstance(key, Index): │
│ │
│ ╭───────────────────── locals ──────────────────────╮ │
│ │ axis_name = 'columns' │ │
│ │ indexer = array([ 0, -1]) │ │
│ │ key = ['PC1', 'PC2'] │ │
│ │ keyarr = Index(['PC1', 'PC2'], dtype='object') │ │
│ │ self = Index(['PC1'], dtype='object') │ │
│ ╰───────────────────────────────────────────────────╯ │
│ │
│ /opt/conda/lib/python3.9/site-packages/pandas/core/indexes/base.py:6176 in │
│ _raise_if_missing │
│ │
│ 6173 │ │ │ │ raise KeyError(f"None of [{key}] are in the [{axis_na │
│ 6174 │ │ │ │
│ 6175 │ │ │ not_found = list(ensure_index(key)[missing_mask.nonzero() │
│ ❱ 6176 │ │ │ raise KeyError(f"{not_found} not in index") │
│ 6177 │ │
│ 6178 │ @overload │
│ 6179 │ def _get_indexer_non_comparable( │
│ │
│ ╭───────────────────────── locals ─────────────────────────╮ │
│ │ axis_name = 'columns' │ │
│ │ indexer = array([ 0, -1]) │ │
│ │ key = Index(['PC1', 'PC2'], dtype='object') │ │
│ │ missing_mask = array([False, True]) │ │
│ │ nmissing = 1 │ │
│ │ not_found = ['PC2'] │ │
│ │ self = Index(['PC1'], dtype='object') │ │
│ │ use_interval_msg = False │ │
│ ╰──────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────╯
KeyError: "['PC2'] not in index"
====================
2022-12-05 15:09:13,269 flytekit ERROR Failed to convert return value for var o0 with error <class 'flytekit.exceptions.user.FlyteAssertion'>: Failed to put data from /root/microview_report.html to latch:///kraken2/microview_report.html (recursive=False).
Original exception: [Errno 2] No such file or directory: '/root/microview_report.html'
====================
====================
2022-12-05 15:09:13,270 flytekit.entrypoint ERROR !! Begin System Error Captured by Flyte !!
====================
====================
2022-12-05 15:09:13,270 flytekit.entrypoint ERROR Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/flytekit/exceptions/scopes.py", line 166, in system_entry_point
return wrapped(*args, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/flytekit/core/base_task.py", line 525, in dispatch_execute
raise TypeError(
Message:
Failed to convert return value for var o0 for function wf.__init__.run_microview with error <class 'flytekit.exceptions.user.FlyteAssertion'>: Failed to put data from /root/microview_report.html to latch:///kraken2/microview_report.html (recursive=False).
Original exception: [Errno 2] No such file or directory: '/root/microview_report.html'
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