Open espenhgn opened 4 months ago
Problem reported by Siim, similar to #51, except that the order of `chr` <integer> and `chr` <character> is reverted.
`chr` <integer> and `chr` <character>
I need to run the LDPred2 separately on all chromosomes (can add all the sumstats as final step manually) but get the following error:
8,358,512 variants to be matched. Error in `vctrs::vec_in()`: ! Can't combine `chr` <integer> and `chr` <character>. Backtrace: x 1. +-bigsnpr::snp_match(...) 2. | +-...[] 3. | +-base::`[.data.frame`(...) 4. | \-vctrs::vec_in(sumstats[, join_by[1:2]], info_snp[, join_by[1:2]]) 5. \-vctrs (local) `<fn>`() 6. \-vctrs::vec_default_ptype2(...) 7. +-base::withRestarts(...) 8. | \-base (local) withOneRestart(expr, restarts[[1L]]) 9. | \-base (local) doWithOneRestart(return(expr), restart) 10. \-vctrs::stop_incompatible_type(...) 11. \-vctrs:::stop_incompatible(...) 12. \-vctrs:::stop_vctrs(...) 13. \-rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call)) Execution halted
Has anyone reported this on the updated version while using the .bgen files? Maybe I missed some instructions?
For clartity the run.sh has following content:
#!/bin/bash #SBATCH --job-name=chr21 # job name #SBATCH --output=SCF1_chr21_LDpred2.txt # output #SBATCH --error=SCF1_chr21.txt # errors #SBATCH --mail-type=END #SBATCH --mail-type=FAIL #SBATCH --[mail-user=user@domain.edu](mailto:mail-user=user@domain.edu) #SBATCH --time=48:00:00 # walltime #SBATCH --cpus-per-task=2 # number of CPUS for task #SBATCH --mem-per-cpu=30GB #SBATCH --partition=amd module load any/singularity/3.7.3 # point to input/output files export fileGeno=/GEN/4_latest_freeze/imputation_EstRef/hg38/EstBB_chr21.bgen export fileGenoRDS=chr21.nomiss.rds export fileSNPList=/COMOR/containers/scripts/pgs/LDpred2/Chr21_for_LDPred2.csv export fileSumstats=/COMOR/containers/scripts/pgs/LDpred2/SCF_sumstats/SCF1_allBMI_regenie_forPRS.txt export fileOut=SCF1_chr21 export colPheno=SCF1 # set environmental variables. Replace "<path/to/comorment>" with # the full path to the folder containing cloned "containers" and "ldpred2_ref" repositories export GENOMICS=/gpfs/space/GI/GV/EGCUT_data/genotype_data/GSA_arrays export COMORMENT=/gpfs/space/GI/GV/Projects/PsychGen/CoMorMent export SIF=$COMORMENT/containers/singularity export REFERENCE=$COMORMENT/containers/reference export LDPRED2_REF=$COMORMENT/ldpred2_ref export SINGULARITY_BIND=$REFERENCE:/REF,${LDPRED2_REF}:/ldpred2_ref,$COMORMENT:/COMOR,$GENOMICS:/GEN export RSCRIPT="singularity exec --home=$PWD:/home $SIF/r.sif Rscript" # convert genotype to LDpred2 format $RSCRIPT createBackingFile.R --file-input $fileGeno --file-output $fileGenoRDS --file-snp-list $fileSNPList # Generate PGS usign LDPRED-inf $RSCRIPT ldpred2.R \ --genomic-build hg38 \ --ldpred-mode inf \ --col-stat BETA \ --col-stat-se SE \ --col-A1 EFFECT_ALLELE \ --col-A2 OTHER_ALLELE \ --col-chr CHR \ --col-bp POS \ --col-snp-id RSID \ --stat-type BETA \ --geno-file-rds $fileGenoRDS \ --sumstats $fileSumstats \ --out $fileOut.inf
This issue appears to be stale due to non-activity
Problem reported by Siim, similar to #51, except that the order of
`chr` <integer> and `chr` <character>
is reverted.I need to run the LDPred2 separately on all chromosomes (can add all the sumstats as final step manually) but get the following error:
Has anyone reported this on the updated version while using the .bgen files? Maybe I missed some instructions?
For clartity the run.sh has following content: