outOfMemory error when running on PharmGKB genes.tsv - Githubissues

MaastrichtU-IDS / AutoR2RML

http://d2s.semanticscience.org/

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outOfMemory error when running on PharmGKB genes.tsv #20

Open vemonet opened 5 years ago

vemonet commented 5 years ago

genes.tsv from https://www.pharmgkb.org/downloads raise a stackOverflow outOfMemory error issue when running r2rml after AutoR2RML. Even if the genes.tsv files is only a couple Mo

What have been tried by Ammar:

Loading the TSV file in LibreOffice, saving it and processing it
- Solves the issue. LibreOffice might do some preprocessing solving our error. But they also modify the content of some files
Removing some columns from the mapping.trig

Note: could be related to COHD issue (outOfMemory error on 1G SQL table)

vemonet commented 4 years ago

Still same issue with the new Apache Drill configuration for COHD 27G dataset

R2RML aborting generation of triples after getting error:

2020-03-25 11:15:03 ERROR TriplesMap:293 - R2RMLException.
r2rml.engine.R2RMLException: RESOURCE ERROR: 
   External Sort encountered an error while spilling to disk