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RajLabMSSM / echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
https://rajlabmssm.github.io/echolocatoR
MIT License
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PolyFun: `x Column `SNP_x` doesn't exist.` #80

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

After updating PolyFun, ran into this error. Will check internal code.

+++ Multi-finemap:: POLYFUN_SUSIE +++
[1] "PolyFun:: Preparing SNP input file..."
[1] "+ PolyFun:: 113 SNPs identified."
[1] "+ PolyFun:: Writing SNP file ==> /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpQKRSVA/results/GWAS/Nalls23andMe_2019/BST1/PolyFun/snps_to_finemap.txt.gz"
[1] "/opt/anaconda3/envs/echoR/bin/python /Library/Frameworks/R.framework/Versions/4.1/Resources/library/echolocatoR/tools/polyfun//extract_snpvar.py --sumstats /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpQKRSVA/results/GWAS/Nalls23andMe_2019/BST1/PolyFun/snps_to_finemap.txt.gz --out /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpQKRSVA/results/GWAS/Nalls23andMe_2019/BST1/PolyFun/snps_with_priors.snpvar.tsv.gz"
[INFO]  Loading sumstats files...
[INFO]  Done in 0.67 seconds
[INFO]  Loading meta-analyzed per-SNP-h2 files...
[INFO]  Done in 77.59 seconds
[INFO]  Merging sumstats with per-SNP h2 data...
[INFO]  Done in 1.85 seconds
[INFO]  Writing output file to /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpQKRSVA/results/GWAS/Nalls23andMe_2019/BST1/PolyFun/snps_with_priors.snpvar.tsv.gz
[1] "++ Remove tmp file."
Error in stop_subscript(class = "vctrs_error_subscript_oob", i = i, subscript_type = subscript_type,  : 
  Can't rename columns that don't exist.
x Column `SNP_x` doesn't exist.
bschilder commented 2 years ago

SNP_x and SNP_y columns no longer exist in PolyFun's merged sumstats/h2 files (just "SNP").

Will add a conditional to handle both scenarios.