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| author | Frederick Muriuki Muriithi | 2024-04-03 15:31:26 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-04-03 15:31:26 +0300 |
| commit | e3e75ae0e866d3571612b4b769ae5214bf8daf67 (patch) | |
| tree | 84400f0e7fffee52319d804e2fb310e6af211caa /scripts | |
| parent | 60fde66e02dba842b20fa126ff3b2ed9ec2638e6 (diff) | |
| download | gn-uploader-e3e75ae0e866d3571612b4b769ae5214bf8daf67.tar.gz | |
Reduce size of data inserted per query
Reduce the size of data inserted per query since MariDB allows a
packet with a maximum size of 1GB. This should hopefully resolve the
…OperationalError: (2006, 'Server has gone away')
error.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 2 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 709fe0f..d0731a2 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -176,7 +176,7 @@ def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals] cdata = rqtl2.control_data(zfile) genotypes = rqtl2.genotype_data(zfile) while True: - batch = tuple(take(genotypes, 5000)) + batch = tuple(take(genotypes, 1000)) if len(batch) == 0: logger.info("Loading Genotypes complete!") logger.info( diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index 95745d7..b5cab8e 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -111,7 +111,7 @@ def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals] phenorows = 0 datarows = 0 while True: - batch = tuple(take(phenodata, 5000)) + batch = tuple(take(phenodata, 1000)) if len(batch) == 0: logger.info("pheno data loading complete!") logger.info("Inserted a total of %s new ProbeSets and %s " |