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opain / eQTL_to_TWAS

Methods for converting eQTL summary statistics into TWAS SNP-weights
GNU General Public License v3.0
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Execution Halt Incompatible join types: x.SNP (integer) and i.SNP (character) #17

Closed 1667857557 closed 11 months ago

1667857557 commented 11 months ago

Hi Oliver,

I apologize for reaching out again, but I've encountered an issue with script execution while working on this specific gene. Could you please provide some guidance on how to resolve it? I've included the error information below along with the relevant file:

Thanks in advance!

Huang

ENSG00000154529.txt

_Rscript ./compute_weights.R \ --extract ./ldsc/w_hm3.snplist \ --sumstats ./eQTL_to_TWAS/ENSG00000154529.txt \ --gcta ./gcta/gcta-1.94.1 \ --gctb ./gctb/gctb \ --gctb_ref ./gctb/ukbEURu_hm3_shrunk_sparse/ukbEURu_hm3_chr \ --plink_ref_chr ./Trans-Phar/1000G_EUR_Phase3_plink/1000G.EUR.QC. \ --plink_ref_keep ./EUR_1KG_phase3_samples.tsv \ --ld_b

locks ./ldetect/EUR \ --rscript

Rscript \ --dbslmm ./DBSLMM/software \ --plink ./plink/plink \ --PRScs_path ./PRScs/PRScs.py \ --PRScs_ref_path ./PRScs/ldblk_ukbb_eur \ --ldpred2_ref_dir ./ldref \ --output ./eQTL_to_TWAS/

error report:

Options: -s: ./eQTL_to_TWAS/ENSG00000154529/DBSLMM/s_ENSG00000154529.txt -l: ./eQTL_to_TWAS/ENSG00000154529/DBSLMM/l_ENSG00000154529.txt -r: ./eQTL_to_TWAS/ENSG00000154529/ref/ref_chr9 -nsnp: 2 -n: 192 -mafMax: 0.2 -b: ./ldetect/EUR/fourier_ls-chr9.bed -h: 0.1 -t: 1 -eff: ./eQTL_to_TWAS/ENSG00000154529/DBSLMM/ENSG00000154529.dbslmm Reading PLINK FAM file from [./eQTL_to_TWAS/ENSG00000154529/ref/ref_chr9.fam] 489 individuals to be included from reference FAM file. Reading PLINK BIM file from [./eQTL_to_TWAS/ENSG00000154529/ref/ref_chr9.bim] Calculating MAF of reference panel ... 2 SNPs to be included from reference BIM file. Reading summary data of small effect SNPs from [./eQTL_to_TWAS/ENSG00000154529/DBSLMM/s_ENSG00000154529.txt] Segmentation fault Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult, : Incompatible join types: x.SNP (integer) and i.SNP (character) Calls: merge -> merge.data.table -> [ -> [.data.table -> bmerge Execution halted_

1667857557 commented 11 months ago

It has been solved, it seems due to a system error in my computer