MaayanLab / scAVI

Single-cell RNA-seq data analysis and visualization
http://amp.pharm.mssm.edu/scavi
Apache License 2.0
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Enrichment result too large to be stored for some libraries #31

Open wangz10 opened 6 years ago

wangz10 commented 6 years ago
DocumentTooLarge                          Traceback (most recent call last)
<ipython-input-12-2ab38c04b624> in <module>()
      6                                         er.summarize(db)
      7                                         print 'Finished enrichment analysis on %s for dataset %s' % (gene_set_name, gse_id)
----> 8                                         print er.save(db)
      9                                         er.remove_intermediates(db)

/Users/maayanlab/Documents/Zichen_Projects/scv/enrichment.pyc in save(self, db)
    128                         'top1_terms': self.top1_terms
    129         }
--> 130                 insert_result = db[self.coll].insert_one(doc)
    131                 return insert_result.inserted_id

...

DocumentTooLarge: BSON document too large (196593070 bytes) - the connected server supports BSON document sizes up to 16793598 bytes.
u8sand commented 4 years ago

Perhaps this should be addressed by storing data files in an s3 bucket instead of storing them in mongo.