qserenali
commented
5 years ago It works if I run as -j1, but I assume there would be a gain of performance if I run as -j8.
Open qserenali opened 5 years ago
qserenali
commented
5 years ago It works if I run as -j1, but I assume there would be a gain of performance if I run as -j8.
Hi This happened during burden test by gene. I split the jobs by chromosome and use -j8 option (so presumably that is why there are 8 processes). I guess the 8 processes interference with each other and cause the database dock? Does this happen to others when -j8 was listed as an example? or shall I simply remove that option and the run time might be 8x longer? thanks in advance for your advice.
DEBUG: Running query INSERT INTO asso_tmp SELECT DISTINCT variant.variant_id, 0, refGene.refGene.name2 FROM variant, refGene.rng_refGene_hg19_chr_txStart_txEnd, refGene.refGene WHERE (variant.bin = refGene.rng_refGene_hg19_chr_txStart_txEnd.bin AND variant.chr = refGene.__rng_refGene_hg19_chr_txStart_txEnd.chr AND variant.pos >= refGene.rng_refGene_hg19_chr_txStart_txEnd.start AND variant.pos <= refGene.__rng_refGene_hg19_chr_txStart_txEnd.end ) AND (refGene.refGene.rowid = refGene.__rng_refGene_hg19_chr_txStart_txEnd.range_id); 2019-09-17 20:17:39,428: INFO: Grouping variants by 'name2', please be patient ... 2019-09-17 20:17:40,529: INFO: 772 groups are found 2019-09-17 20:17:43,821: DEBUG: Loader 0 is ready 2019-09-17 20:17:46,916: DEBUG: Loader 1 is ready 2019-09-17 20:17:47,145: INFO: Starting 8 processes to load genotypes 2019-09-17 20:17:49,324: DEBUG: Loader 2 is ready 2019-09-17 20:17:51,886: DEBUG: Loader 3 is ready 2019-09-17 20:17:53,383: DEBUG: Loader 4 is ready 2019-09-17 20:17:55,442: DEBUG: Loader 5 is ready 2019-09-17 20:17:58,033: DEBUG: Loader 6 is ready 2019-09-17 20:17:59,907: DEBUG: Loader 7 is ready 2019-09-17 20:19:07,192: ERROR: database is locked