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opain / Predicting-TWAS-features

Tool for predicting TWAS features (e.g. gene expression) in a target sample
GNU General Public License v3.0
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Error in { : task 1 failed - "cannot open the connection" #4

Closed MIAO0916 closed 1 year ago

MIAO0916 commented 1 year ago

Calls: %dopar% -> In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted

Rscript FeaturePred.V2.0.R \ --PLINK_prefix_chr FeaturePred/PLINK_prefix_chr/1000G.EUR. \ --weights FeaturePred/OA_synovium_v1.WH_fusion/OA_synovium_v1.WH_fusion.P01.pos \ --weights_dir FeaturePred/OA_synovium_v1.WH_fusion \ --ref_ld_chr FeaturePred/PLINK_prefix_chr/1000G.EUR. \ --plink plink \ --ref_maf FeaturePred/PLINK_prefix_chr/1000G.EUR. \ --pigz pigz \ --chr 1 \ --output demo

Hi，could you plz tell me how can I solve this problem? where should I adjust?

BEST, miaoz

MIAO0916 commented 1 year ago

I have already solved this problem！ Now I want to share some tips： First, make sure that the content of PANEL is consistent with the path of WGT Then, if your pos file has some genes that don't work, be sure to remove it in the pos file and delete the corresponding rdat file hope you all can apply this package successfully~

opain commented 1 year ago

Thanks for reporting your solution! I will try and improve the error reporting in the future.