Karatuğ Ozan Bircan

Submitted a SLURM job for copying Quant files to the private ftp for test submission in sandbox. 23899637 datamover cp-ukbb-quant-private-ftp spotbot R 2:57:34 1 codon-dm-04

Submission template is now ready. Lizzy updated it and fixed the errors.

Possible errors found during the merge of Binary studies: ``` gzip: /hps/nobackup/parkinso/spot/gwas/scratch/goci-1267/aws/gwas_summary_stats/n34/chr9_first_occurrence_n34_NFE.txt.gz: invalid compressed data--crc error gzip: /hps/nobackup/parkinso/spot/gwas/scratch/goci-1267/aws/gwas_summary_stats/n34/chr9_first_occurrence_n34_NFE.txt.gz: invalid compressed data--length error gzip: /hps/nobackup/parkinso/spot/gwas/scratch/goci-1267/aws/gwas_summary_stats/o35/chr18_first_occurrence_o35_NFE.txt.gz: invalid compressed data--crc error gzip: /hps/nobackup/parkinso/spot/gwas/scratch/goci-1267/aws/gwas_summary_stats/o35/chr18_first_occurrence_o35_NFE.txt.gz:...

submitted format jobs in SLURM using gwas-ssf format command for binary studies. 23949330 short temp_sbatch_script.sh spotbot R 2:30 1 hl-codon-130-01 23949331 short temp_sbatch_script.sh spotbot R 2:30 1 hl-codon-bm-10 23949332 short...

Job codon-slurm.23972158: compare-md5sum-quant-private-ftp Began

Job codon-slurm.23972158: compare-md5sum-quant-private-ftp complete. No issues with md5sum values for Quant files in the private ftp and aws/formatted/gwas_summary_stats_quant.

When unzipped two files appeared. I fixed the header for both but the metadata yaml files are missing. Since the study is old, the data is not available from the...

- [x] Create metadata yaml files that contain GCST ID and genome assembly for the harmonisation. - [x] Submit the harmonisation

Submitted to codon with the submission script `/hps/software/users/parkinso/spot/gwas/prod/scripts/cron/start_harmonisation_pre_standard_goci1226.sh` ``` Job is submitted to default queue . ```

- [x] Compare two studies in FTP ("EduYears" and "College") - [x] If they are the same, replace the zipped file with the correct one - Moved `SSGAC_College_Rietveld2013_publicrelease.txt` to `GCST002001-GCST003000/GCST002047`...