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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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User request for sumstats harmonisation #1300

Closed ljwh2 closed 3 months ago

ljwh2 commented 5 months ago

Please prioritise the sumstats associated with this publication for harmonisation https://www.ebi.ac.uk/gwas/publications/36474045

karatugo commented 5 months ago

Job <97669165> is submitted to default queue .

Update. Failed.

karatugo commented 5 months ago

As the prev LSF job submission failed, I submit again. 

Job <98014643> is submitted to default queue <standard>.
karatugo commented 5 months ago

LSF job failed again. Submitted in SLURM. 

Submitted batch job 4623821
karatugo commented 5 months ago

SLURM job failed too according to the logs. Asked for @jiyue1214 help.

karatugo commented 4 months ago

Need to restart again as Yue updated the code.

karatugo commented 4 months ago

Restarted /hps/software/users/parkinso/spot/gwas/prod/scripts/cron/start_harmonisation_pre_standard_slurm_goci1300.sh

         JOBID PARTITION NAME                                                    USER     ST TIME       NODES  NODELIST
       8384004 standard  pre_gwas_ssf_harmo                                      gwas_lsf R  0:23       1      hl-codon-05-01
karatugo commented 4 months ago

Failed again, need help from @jiyue1214

jiyue1214 commented 4 months ago

The harmonised result is available on the FTP right now and could @karatugo double-check if the data is correct?

karatugo commented 4 months ago

Looks good to me, thanks @jiyue1214

karatugo commented 4 months ago

http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90132001-GCST90133000/GCST90132314/harmonised/

http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90132001-GCST90133000/GCST90132315/harmonised/

ljwh2 commented 4 months ago

@ljwh2 to confirm

ljwh2 commented 3 months ago

confirmed