Loading required namespace: GenomicFiles Using local VCF. File already tabix-indexed. Finding empty VCF columns based on first 10,000 rows. Dropping 1 duplicate column(s). 1 sample detected: EBI-a-GCST004885 Constructing ScanVcfParam object. VCF contains: 504,798 variant(s) x 1 sample(s) Reading VCF file: multi-threaded (4 threads) Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Dropping 1 duplicate column(s). Renaming ID as SNP. VCF file has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column. No INFO (SI) column detected. Standardising column headers. First line of summary statistics file: SNP chr BP end REF ALT FILTER AF ES LP SE P Summary statistics report: - 491,603 rows - 491,603 unique variants - 12 genome-wide significant variants (P<5e-8) - 22 chromosomes Checking for multi-GWAS. Checking for multiple RSIDs on one row. Inferring genome build. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 10,000 SNPs using BSgenome::snpsById... Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: expand.grid, I, unname BSgenome::snpsById done in 81 seconds. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 10,000 SNPs using BSgenome::snpsById... BSgenome::snpsById done in 63 seconds. Inferred genome build: GRCH37 Checking SNP RSIDs. Checking for merged allele column. Checking A1 is uppercase Checking A2 is uppercase Checking for incorrect base-pair positions Ensuring all SNPs are on the reference genome. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 491,603 SNPs using BSgenome::snpsById... BSgenome::snpsById done in 49 seconds. 1,535 SNPs are not on the reference genome. These will be corrected from the reference genome. Loading SNPlocs data. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ebi-a-GCST004885/logs/snp_not_found_from_chr_bp.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Loading SNPlocs data. Loading reference genome data. Preprocessing RSIDs. Validating RSIDs of 490,074 SNPs using BSgenome::snpsById... BSgenome::snpsById done in 19 seconds. Checking for correct direction of A1 (reference) and A2 (alternative allele). There are 1 SNPs where neither A1 nor A2 match the reference genome. These will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ebi-a-GCST004885/logs/alleles_dont_match_ref_gen.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. There are 2 SNPs where A1 doesn't match the reference genome. These will be flipped with their effect columns. Reordering so first three column headers are SNP, CHR and BP in this order. Reordering so the fourth and fifth columns are A1 and A2. Checking for missing data. WARNING: 12 rows in sumstats file are missing data and will be removed. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ebi-a-GCST004885/logs/missing_data.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Checking for duplicate columns. Checking for duplicate SNPs from SNP ID. Checking for SNPs with duplicated base-pair positions. INFO column not available. Skipping INFO score filtering step. Filtering SNPs, ensuring SE>0. 490,061 SNPs have SE values <= 0 and will be removed Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ebi-a-GCST004885/logs/se_neg.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Ensuring all SNPs have N<5 std dev above mean. Checking for bi-allelic SNPs. Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)` Warning: When method is an integer, must be >0. Sorting coordinates with 'data.table'. Sorting coordinates with 'data.table'. Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ebi-a-GCST004885/ebi-a-GCST004885.tsv Writing uncompressed instead of gzipped to enable tabix indexing. Converting full summary stats file to tabix format for fast querying... Reading header. Ensuring file is bgzipped. Tabix-indexing file. Removing temporary .tsv file. Summary statistics report: - 0 rows (0% of original 491,603 rows) - 0 unique variants - 0 genome-wide significant variants (P<5e-8) - 0 chromosomes Done munging in 4.162 minutes. Successfully finished preparing sumstats file, preview: Reading header. file not found: SNP CHR BP A1 A2 END FILTER FRQ BETA LP SE P Z Done with all processing in 4.19 minutes. Warning messages: 1: In max(score) : no non-missing arguments to max; returning -Inf 2: In lapply(.SD, as.numeric) : NAs introduced by coercion 3: In lapply(.SD, as.numeric) : NAs introduced by coercion 4: In lapply(.SD, as.numeric) : NAs introduced by coercion 5: In lapply(.SD, as.numeric) : NAs introduced by coercion ===================== 🦠🌋🦠 Welcome to MAGMA.Celltyping 🦠🌋🦠 ===================== This package uses MAGMA: https://ctg.cncr.nl/software/magma To cite MAGMA.Celltyping, please use: * Skene, N.G., Bryois, J., Bakken, T.E. et al. Genetic identification of brain cell types underlying schizophrenia. Nat Genet 50, 825-833 (2018). https://doi.org/10.1038/s41588-018-0129-5 * de Leeuw CA, Mooij JM, Heskes T, Posthuma D (2015) MAGMA: Generalized Gene-Set Analysis of GWAS Data. PLOS Computational Biology 11(4): e1004219. https://doi.org/10.1371/journal.pcbi.1004219 Please report any bugs or feature requests by filling out an Issues template: https://github.com/neurogenomics/MAGMA_Celltyping/issues ===================== 🦠🌋🦠 =========================== 🦠🌋🦠 ===================== Installed MAGMA version: v1.10 Skipping MAGMA installation. The desired_version of MAGMA is currently installed: v1.10 Using: magma_v1.10 Using existing genome_ref found in storage_dir. Error in path.expand(x) : invalid 'path' argument Calls: lapply ... lapply -> FUN -> -> fix_path -> path.expand Execution halted