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: UKB-b-9976
Constructing ScanVcfParam object.
VCF contains: 9,851,866 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:
   - 4,266,841 rows
   - 4,265,955 unique variants
   - 0 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 44 seconds.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 10,000 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 78 seconds.
Inferred genome build: GRCH37
Checking SNP RSIDs.
321 SNP IDs are not correctly formatted. 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/ukb-b-9976/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.
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 4,265,645 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 76 seconds.
21,458 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/ukb-b-9976/logs/snp_not_found_from_chr_bp_2.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 4,245,085 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 93 seconds.
Checking for correct direction of A1 (reference) and A2 (alternative allele).
There are 60 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/ukb-b-9976/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 22 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.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
820 RSIDs are duplicated in the sumstats file. These duplicates will be removed
Sorting coordinates with 'data.table'.
Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ukb-b-9976/logs/dup_snp_id.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 SNPs with duplicated base-pair positions.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Checking for bi-allelic SNPs.
109,647 SNPs are non-biallelic. 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/ukb-b-9976/logs/snp_bi_allelic.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.
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.
1,211,107 SNPs (29.3%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, AF_EFF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
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/ukb-b-9976/ukb-b-9976.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:
   - 4,135,378 rows (96.9% of original 4,266,841 rows)
   - 4,135,378 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 22 chromosomes
Done munging in 14.17 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR     BP A1 A2    END FILTER      FRQ         BETA       LP
1:  rs10399793   1  49298  T  C  49298   PASS 0.623765 -3.72746e-04 0.619789
2:   rs2462492   1  54676  C  T  54676   PASS 0.400401  1.64162e-04 0.221849
3: rs114608975   1  86028  T  C  86028   PASS 0.103556  6.46831e-04 0.698970
4:   rs6702460   1  91536  G  T  91536   PASS 0.456846 -7.05391e-04 1.657580
5:   rs6680723   1 534192  C  T 534192   PASS 0.240959 -4.98627e-05 0.050610
            SE          P          Z
1: 0.000316075 0.23999987 -1.1749871
2: 0.000313133 0.59999965  0.5244010
3: 0.000500634 0.20000000  1.2815516
4: 0.000308316 0.02199986 -2.2903702
5: 0.000352180 0.88999999 -0.1383042