bschilder
commented
1 year ago Hi @PhoebeGuo97
Unfortunately, I need more information to be able to assess the problem. Please submit a new Issue by filling out all fields in the Bugs template provided. https://github.com/RajLabMSSM/echolocatoR/issues/new/choose
I have munged my summary statistics. I ran fine map_loci()and got following errors. Could you please let me know how to fix it? Thanks!
[1] "+ CONDA:: Activating conda env 'echoR'" [1] "Checking for tabix installation..." [1] "Checking for bcftools installation..." [1] "+ Assuming sumstats have already been processed with MungeSumstats"
) ) ) ))))))}}}}}}}} {{{{{{{{{(((((( ( ( ( 1 (1 / 29) ) ) ) ))))))}}}}}}}} {{{{{{{{{(((((( ( ( ( [1] "+ Extracting relevant variants from fullSS..." [1] "+ Query Method: tabix" [1] "+ QUERY: Chromosome = 1 ; Min position = 161145392 ; Max position = 161165392" [1] "TABIX:: Converting full summary stats file to tabix format for fast querying..." [1] "TABIX:: Ensuring file is bgzipped." [1] "TABIX:: Tabix-indexing file." [ti_index_core] the file out of order at line 1253647 Create tabix index failed for [ /var/folders/g9/f5z6vsbx7q3_wmk06jz0j9zm0000gn/T//RtmpUeD8qB/filec8a364f2c78f.tsv.bgz ]! [1] "Determining chrom type from file header" [1] "Chromosome format = 1" [1] "TABIX:: Extracting subset of sum stats" Cannot open specified tabix file: /var/folders/g9/f5z6vsbx7q3_wmk06jz0j9zm0000gn/T//RtmpUeD8qB/filec8a364f2c78f.tsv.bgz Cannot open specified tabix file: /var/folders/g9/f5z6vsbx7q3_wmk06jz0j9zm0000gn/T//RtmpUeD8qB/filec8a364f2c78f.tsv.bgz Error in strsplit(body, "\t") : non-character argument Fine-mapping complete in: Time difference of 1.9 mins
) ) ) ))))))}}}}}}}} {{{{{{{{{(((((( ( ( ( 10 (2 / 29) ) ) ) ))))))}}}}}}}} {{{{{{{{{(((((( ( ( ( [1] "+ Extracting relevant variants from fullSS..." [1] "+ Query Method: tabix" [1] "+ QUERY: Chromosome = 7 ; Min position = 99961834 ; Max position = 99981834" [1] "TABIX:: Converting full summary stats file to tabix format for fast querying..." [1] "TABIX:: Ensuring file is bgzipped." [1] "TABIX:: Tabix-indexing file." [ti_index_core] the file out of order at line 1253647 Create tabix index failed for [ /var/folders/g9/f5z6vsbx7q3_wmk06jz0j9zm0000gn/T//RtmpUeD8qB/filec8a364f2c78f.tsv.bgz ]!