Set up environment¶

In [1]:
import scanpy as sc
In [2]:
output_folder = './'

Load data¶

In [3]:
adata = sc.read(output_folder + "1_All_Annotated_Triku.h5ad")
adata
Out[3]:
AnnData object with n_obs × n_vars = 27925 × 14582
    obs: 'sample_id', 'run_id', 'probe_barcode_ids', 'subject', 'line', 'specimen', 'stage', 'condition', 'notes', 'seqRun', 'original_name', 'project', 'who', 'SC_derivation', 'micoplasma', 'mosaic', 'genSite', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mito', 'log1p_total_counts_mito', 'pct_counts_mito', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'gene_UMI_ratio', 'log1p_gene_UMI_ratio', 'scDblFinder_score', 'scDblFinder_class', 'n_counts', 'n_genes', 'leiden', 'score_pluripotency', 'score_mesoderm', 'score_PS', 'score_EM', 'score_AM', 'score_Endo', 'score_Epi', 'score_HEP', 'score_NM', 'score_ExM', 'score_Ery', 'score_EAE', 'score_Amnion_LC', 'score_AxM', 'score_Amnion', 'score_NNE', 'score_PGC', 'score_hPGCLCs', 'score_DE1', 'score_DE2', 'score_Hypoblast', 'score_YS', 'score_EMPs', 'score_Endothelium', 'score_Myeloid_Progenitors', 'score_Megakaryocyte_Erythroid_progenitors', 'CellTypes'
    var: 'n_cells', 'mito', 'ribo', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection', 'triku_distance', 'triku_distance_uncorrected', 'triku_highly_variable'
    uns: 'CellTypes_colors', 'dendrogram_CellTypes', 'dendrogram_leiden', 'dendrogram_specimen', 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'rank_genes_groups', 'run_id_colors', 'sample_id_colors', 'specimen_colors', 'stage_colors', 'triku_params', 'umap'
    obsm: 'X_pca', 'X_pca_harmony', 'X_umap'
    varm: 'PCs'
    layers: 'raw'
    obsp: 'connectivities', 'distances'
In [4]:
sc.pl.umap(adata, color = 'leiden', legend_loc = 'on data')

Run enrichement¶

In [5]:
from subprocess import run

# run(["cd ./pattern_1_2_3_1/"], shell = True)

for i in adata.obs.leiden.unique():
    print('Executing GO for cluster ', i)
    run(["./../../../../quarto_folder/quarto render GenericGO.ipynb --to html -P N:" + str(i) + " -o GO_cluster_" + str(i) + ".html"], shell=True)

Executing GO for cluster  2

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pandoc -o GO_cluster_2.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_2.html


Executing GO for cluster  6

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pandoc -o GO_cluster_6.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_6.html


Executing GO for cluster  10

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pandoc -o GO_cluster_10.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_10.html


Executing GO for cluster  5

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pandoc -o GO_cluster_5.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_5.html


Executing GO for cluster  8

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
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  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_8.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_8.html


Executing GO for cluster  12

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
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  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_12.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_12.html


Executing GO for cluster  11

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
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  Cell 163/174...Done
  Cell 164/174...Done
  Cell 165/174...Done
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  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_11.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_11.html


Executing GO for cluster  4

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
  Cell 7/174...Done
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  Cell 31/174...Done
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  Cell 50/174...Done
  Cell 51/174...Done
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  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_4.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_4.html


Executing GO for cluster  9

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
  Cell 7/174...Done
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  Cell 10/174...Done
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  Cell 12/174...Done
  Cell 13/174...Done
  Cell 14/174...Done
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  Cell 19/174...Done
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  Cell 22/174...Done
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  Cell 24/174...Done
  Cell 25/174...Done
  Cell 26/174...Done
  Cell 27/174...Done
  Cell 28/174...Done
  Cell 29/174...Done
  Cell 30/174...Done
  Cell 31/174...Done
  Cell 32/174...Done
  Cell 33/174...Done
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  Cell 39/174...Done
  Cell 40/174...Done
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  Cell 45/174...Done
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  Cell 47/174...Done
  Cell 48/174...Done
  Cell 49/174...Done
  Cell 50/174...Done
  Cell 51/174...Done
  Cell 52/174...Done
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  Cell 54/174...Done
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  Cell 59/174...Done
  Cell 60/174...Done
  Cell 61/174...Done
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  Cell 63/174...Done
  Cell 64/174...Done
  Cell 65/174...Done
  Cell 66/174...Done
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  Cell 68/174...Done
  Cell 69/174...Done
  Cell 70/174...Done
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  Cell 72/174...Done
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  Cell 74/174...Done
  Cell 75/174...Done
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  Cell 85/174...Done
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  Cell 87/174...Done
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  Cell 89/174...Done
  Cell 90/174...Done
  Cell 91/174...Done
  Cell 92/174...Done
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  Cell 95/174...Done
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  Cell 98/174...Done
  Cell 99/174...Done
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  Cell 105/174...Done
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  Cell 107/174...Done
  Cell 108/174...Done
  Cell 109/174...Done
  Cell 110/174...Done
  Cell 111/174...Done
  Cell 112/174...Done
  Cell 113/174...Done
  Cell 114/174...Done
  Cell 115/174...Done
  Cell 116/174...Done
  Cell 117/174...Done
  Cell 118/174...Done
  Cell 119/174...Done
  Cell 120/174...Done
  Cell 121/174...Done
  Cell 122/174...Done
  Cell 123/174...Done
  Cell 124/174...Done
  Cell 125/174...Done
  Cell 126/174...Done
  Cell 127/174...Done
  Cell 128/174...Done
  Cell 129/174...Done
  Cell 130/174...Done
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  Cell 132/174...Done
  Cell 133/174...Done
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  Cell 151/174...Done
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  Cell 153/174...Done
  Cell 154/174...Done
  Cell 155/174...Done
  Cell 156/174...Done
  Cell 157/174...Done
  Cell 158/174...Done
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  Cell 160/174...Done
  Cell 161/174...Done
  Cell 162/174...Done
  Cell 163/174...Done
  Cell 164/174...Done
  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_9.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_9.html


Executing GO for cluster  1

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
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  Cell 23/174...Done
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  Cell 26/174...Done
  Cell 27/174...Done
  Cell 28/174...Done
  Cell 29/174...Done
  Cell 30/174...Done
  Cell 31/174...Done
  Cell 32/174...Done
  Cell 33/174...Done
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  Cell 36/174...Done
  Cell 37/174...Done
  Cell 38/174...Done
  Cell 39/174...Done
  Cell 40/174...Done
  Cell 41/174...Done
  Cell 42/174...Done
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  Cell 44/174...Done
  Cell 45/174...Done
  Cell 46/174...Done
  Cell 47/174...Done
  Cell 48/174...Done
  Cell 49/174...Done
  Cell 50/174...Done
  Cell 51/174...Done
  Cell 52/174...Done
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  Cell 54/174...Done
  Cell 55/174...Done
  Cell 56/174...Done
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  Cell 59/174...Done
  Cell 60/174...Done
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  Cell 64/174...Done
  Cell 65/174...Done
  Cell 66/174...Done
  Cell 67/174...Done
  Cell 68/174...Done
  Cell 69/174...Done
  Cell 70/174...Done
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  Cell 109/174...Done
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  Cell 134/174...Done
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  Cell 136/174...Done
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  Cell 145/174...Done
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  Cell 147/174...Done
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  Cell 149/174...Done
  Cell 150/174...Done
  Cell 151/174...Done
  Cell 152/174...Done
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  Cell 154/174...Done
  Cell 155/174...Done
  Cell 156/174...Done
  Cell 157/174...Done
  Cell 158/174...Done
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  Cell 160/174...Done
  Cell 161/174...Done
  Cell 162/174...Done
  Cell 163/174...Done
  Cell 164/174...Done
  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_1.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_1.html


Executing GO for cluster  7

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
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  Cell 50/174...Done
  Cell 51/174...Done
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  Cell 70/174...Done
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  Cell 80/174...Done
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  Cell 109/174...Done
  Cell 110/174...Done
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  Cell 115/174...Done
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  Cell 142/174...Done
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  Cell 154/174...Done
  Cell 155/174...Done
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  Cell 161/174...Done
  Cell 162/174...Done
  Cell 163/174...Done
  Cell 164/174...Done
  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_7.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_7.html


Executing GO for cluster  0

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
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  Cell 31/174...Done
  Cell 32/174...Done
  Cell 33/174...Done
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  Cell 35/174...Done
  Cell 36/174...Done
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  Cell 38/174...Done
  Cell 39/174...Done
  Cell 40/174...Done
  Cell 41/174...Done
  Cell 42/174...Done
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  Cell 44/174...Done
  Cell 45/174...Done
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  Cell 47/174...Done
  Cell 48/174...Done
  Cell 49/174...Done
  Cell 50/174...Done
  Cell 51/174...Done
  Cell 52/174...Done
  Cell 53/174...Done
  Cell 54/174...Done
  Cell 55/174...Done
  Cell 56/174...Done
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  Cell 59/174...Done
  Cell 60/174...Done
  Cell 61/174...Done
  Cell 62/174...Done
  Cell 63/174...Done
  Cell 64/174...Done
  Cell 65/174...Done
  Cell 66/174...Done
  Cell 67/174...Done
  Cell 68/174...Done
  Cell 69/174...Done
  Cell 70/174...Done
  Cell 71/174...Done
  Cell 72/174...Done
  Cell 73/174...Done
  Cell 74/174...Done
  Cell 75/174...Done
  Cell 76/174...Done
  Cell 77/174...Done
  Cell 78/174...Done
  Cell 79/174...Done
  Cell 80/174...Done
  Cell 81/174...Done
  Cell 82/174...Done
  Cell 83/174...Done
  Cell 84/174...Done
  Cell 85/174...Done
  Cell 86/174...Done
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  Cell 91/174...Done
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  Cell 99/174...Done
  Cell 100/174...Done
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  Cell 105/174...Done
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  Cell 109/174...Done
  Cell 110/174...Done
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  Cell 112/174...Done
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  Cell 114/174...Done
  Cell 115/174...Done
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  Cell 117/174...Done
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  Cell 121/174...Done
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  Cell 125/174...Done
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  Cell 128/174...Done
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  Cell 131/174...Done
  Cell 132/174...Done
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  Cell 134/174...Done
  Cell 135/174...Done
  Cell 136/174...Done
  Cell 137/174...Done
  Cell 138/174...Done
  Cell 139/174...Done
  Cell 140/174...Done
  Cell 141/174...Done
  Cell 142/174...Done
  Cell 143/174...Done
  Cell 144/174...Done
  Cell 145/174...Done
  Cell 146/174...Done
  Cell 147/174...Done
  Cell 148/174...Done
  Cell 149/174...Done
  Cell 150/174...Done
  Cell 151/174...Done
  Cell 152/174...Done
  Cell 153/174...Done
  Cell 154/174...Done
  Cell 155/174...Done
  Cell 156/174...Done
  Cell 157/174...Done
  Cell 158/174...Done
  Cell 159/174...Done
  Cell 160/174...Done
  Cell 161/174...Done
  Cell 162/174...Done
  Cell 163/174...Done
  Cell 164/174...Done
  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_0.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_0.html


Executing GO for cluster  3

Starting python3 kernel...Done

Executing 'GenericGO.ipynb'
  Cell 1/174...Done
  Cell 2/174...Done
  Cell 3/174...Done
  Cell 4/174...Done
  Cell 5/174...Done
  Cell 6/174...Done
  Cell 7/174...Done
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  Cell 19/174...Done
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  Cell 21/174...Done
  Cell 22/174...Done
  Cell 23/174...Done
  Cell 24/174...Done
  Cell 25/174...Done
  Cell 26/174...Done
  Cell 27/174...Done
  Cell 28/174...Done
  Cell 29/174...Done
  Cell 30/174...Done
  Cell 31/174...Done
  Cell 32/174...Done
  Cell 33/174...Done
  Cell 34/174...Done
  Cell 35/174...Done
  Cell 36/174...Done
  Cell 37/174...Done
  Cell 38/174...Done
  Cell 39/174...Done
  Cell 40/174...Done
  Cell 41/174...Done
  Cell 42/174...Done
  Cell 43/174...Done
  Cell 44/174...Done
  Cell 45/174...Done
  Cell 46/174...Done
  Cell 47/174...Done
  Cell 48/174...Done
  Cell 49/174...Done
  Cell 50/174...Done
  Cell 51/174...Done
  Cell 52/174...Done
  Cell 53/174...Done
  Cell 54/174...Done
  Cell 55/174...Done
  Cell 56/174...Done
  Cell 57/174...Done
  Cell 58/174...Done
  Cell 59/174...Done
  Cell 60/174...Done
  Cell 61/174...Done
  Cell 62/174...Done
  Cell 63/174...Done
  Cell 64/174...Done
  Cell 65/174...Done
  Cell 66/174...Done
  Cell 67/174...Done
  Cell 68/174...Done
  Cell 69/174...Done
  Cell 70/174...Done
  Cell 71/174...Done
  Cell 72/174...Done
  Cell 73/174...Done
  Cell 74/174...Done
  Cell 75/174...Done
  Cell 76/174...Done
  Cell 77/174...Done
  Cell 78/174...Done
  Cell 79/174...Done
  Cell 80/174...Done
  Cell 81/174...Done
  Cell 82/174...Done
  Cell 83/174...Done
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  Cell 85/174...Done
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  Cell 91/174...Done
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  Cell 99/174...Done
  Cell 100/174...Done
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  Cell 110/174...Done
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  Cell 133/174...Done
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  Cell 139/174...Done
  Cell 140/174...Done
  Cell 141/174...Done
  Cell 142/174...Done
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  Cell 164/174...Done
  Cell 165/174...Done
  Cell 166/174...Done
  Cell 167/174...Done
  Cell 168/174...Done
  Cell 169/174...Done
  Cell 170/174...Done
  Cell 171/174...Done
  Cell 172/174...Done
  Cell 173/174...Done
  Cell 174/174...Done

pandoc -o GO_cluster_3.html
  to: html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  number-sections: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  theme: minty
  highlight: pygments
  toc-location: left
  fontsize: 20px
  page-layout: full
  width: 2000
  grid:
    sidebar-width: 0px
    body-width: 2000px
    margin-width: 0px
    gutter-width: 1.5rem
  
Output created: GO_cluster_3.html