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This page was generated on 2022-01-21 11:08:06 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MungeSumstats on riesling1


To the developers/maintainers of the MungeSumstats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MungeSumstats.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1246/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MungeSumstats 1.3.1  (landing page)
Alan Murphy
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/MungeSumstats
git_branch: master
git_last_commit: feb8c98
git_last_commit_date: 2021-12-19 12:11:43 -0500 (Sun, 19 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MungeSumstats
Version: 1.3.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MungeSumstats.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MungeSumstats_1.3.1.tar.gz
StartedAt: 2022-01-20 19:30:06 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:36:24 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 378.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MungeSumstats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MungeSumstats.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MungeSumstats_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MungeSumstats.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MungeSumstats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MungeSumstats' version '1.3.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MungeSumstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
get_genome_builds 57.75   7.13   71.22
format_sumstats   34.37   4.62   41.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MungeSumstats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MungeSumstats
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MungeSumstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MungeSumstats'
    finding HTML links ... done
    api_query                               html  
    axel                                    html  
    check_access_token                      html  
    check_allele_flip                       html  
    check_allele_merge                      html  
    check_bi_allelic                        html  
    check_chr                               html  
    check_col_order                         html  
    check_dup_bp                            html  
    check_dup_col                           html  
    check_dup_snp                           html  
    check_effect_columns_nonzero            html  
    check_empty_cols                        html  
    check_four_step_col                     html  
    check_frq                               html  
    check_frq_maf                           html  
    check_info_score                        html  
    check_ldsc_format                       html  
    check_miss_data                         html  
    check_multi_gwas                        html  
    check_multi_rs_snp                      html  
    check_n_int                             html  
    check_n_num                             html  
    check_no_allele                         html  
    check_no_chr_bp                         html  
    check_no_rs_snp                         html  
    check_no_snp                            html  
    check_on_ref_genome                     html  
    check_pos_se                            html  
    check_range_p_val                       html  
    check_row_snp                           html  
    check_save_path                         html  
    check_signed_col                        html  
    check_small_p_val                       html  
    check_strand_ambiguous                  html  
    check_tabular                           html  
    check_two_step_col                      html  
    check_vcf                               html  
    check_vital_col                         html  
    check_zscore                            html  
    column_dictionary                       html  
    compute_nsize                           html  
    compute_sample_size                     html  
    compute_sample_size_n                   html  
    compute_sample_size_neff                html  
    convert_sumstats                        html  
    download_vcf                            html  
    downloader                              html  
    dt_to_granges                           html  
    find_sumstats                           html  
    format_sumstats                         html  
    get_access_token                        html  
    get_chain_file                          html  
    get_genome_build                        html  
    get_genome_builds                       html  
    get_query_content                       html  
    get_unique_name_log_file                html  
    get_vcf_sample_ids                      html  
    gwasinfo                                html  
    hg19ToHg38                              html  
    hg38ToHg19                              html  
    ieu-a-298                               html  
    import_sumstats                         html  
    index_tabular                           html  
    infer_vcf_sample_ids                    html  
    legacy_ids                              html  
    liftover                                html  
    list_sumstats                           html  
    load_ref_genome_data                    html  
    load_snp_loc_data                       html  
    logs_example                            html  
    message_parallel                        html  
    messager                                html  
    parse_dropped_INFO                      html  
    parse_dropped_chrom                     html  
    parse_dropped_duplicates                html  
    parse_dropped_nonA1A2                   html  
    parse_dropped_nonBiallelic              html  
    parse_dropped_nonRef                    html  
    parse_flipped                           html  
    parse_genome_build                      html  
    parse_idStandard                        html  
    parse_logs                              html  
    parse_pval_large                        html  
    parse_pval_neg                          html  
    parse_pval_small                        html  
    parse_report                            html  
    preview_sumstats                        html  
    raw_ALSvcf                              html  
    raw_eduAttainOkbay                      html  
    read_header                             html  
    read_sumstats                           html  
    read_vcf                                html  
    remove_nonstandard_vcf_cols             html  
    report_summary                          html  
    select_api                              html  
    sort_coords                             html  
    standardise_sumstats_column_headers_crossplatform
                                            html  
    sumstatsColHeaders                      html  
    supported_suffixes                      html  
    to_GRanges                              html  
    to_VRanges                              html  
    validate_parameters                     html  
    vcf2df                                  html  
    write_sumstats                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MungeSumstats)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'methylKit' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OMICsPCA' is missing or broken
 done

Tests output

MungeSumstats.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MungeSumstats)
> 
> test_check("MungeSumstats")
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07cad38e0.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf067ff1d8
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A0	A1	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07cad38e0.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf047c13066.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf067ff1d8
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf047c13066.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Sorting coordinates.
3 p-values are >1 which LDSC/MAGMA may not be able to handle. These will be converted to 1.
5 p-values are <0 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Sorting coordinates.
8 p-values are <=5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
Reading header.
Tabular format detected.
Importing tabular file: D:/biocbuild/bbs-3.15-bioc/R/library/MungeSumstats/extdata/eduAttainOkbay.txt
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)`
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf042a14401.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02e5c4825
Standardising column headers.
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP_A2_A1 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file: 
SNP	FRQ	BETA	SE	P	CHR	BP	A2	A1	
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.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf042a14401.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0a2a19f3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02e5c4825
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0a2a19f3.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0620368c3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf029144e3c
Standardising column headers.
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	CHR_BP_A2_A1_2	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position:A2:A1.
The column CHR_BP_A2_A1_2 will be kept whereas the column(s) CHR_BP_A2_A1 will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column CHR_BP_A2_A1_2 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file: 
SNP	FRQ	BETA	SE	P	CHR	BP	A2	A1	
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.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0620368c3.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01f5a539a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf029144e3c
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01f5a539a.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf065284b50.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06c841dfb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	EAF	Beta	SE	Pval	alleles	allele	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Warning: Multiple columns in the sumstats file seem to relate to alleles A1>A2.
The column ALLELES will be kept whereas the column(s) ALLELE will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column ALLELES has been separated into the columns A1, A2
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.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf065284b50.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0c4d5854.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06c841dfb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0c4d5854.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf065c61ece.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02bb73972
Standardising column headers.
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	CHR	BP	
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.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf065c61ece.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03bafd7d.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02bb73972
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03bafd7d.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf022836d1a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf038411a0a
Standardising column headers.
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	CHR_BP_2	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position.
The column CHR_BP_2 will be kept whereas the column(s) CHR_BP will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column CHR_BP_2 has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	CHR	BP	
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.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf022836d1a.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02054333f.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf038411a0a
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02054333f.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02b0e5e96.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04d7759f0
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02b0e5e96.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04a18322e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07c2e5a11
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04a18322e.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf085b6663.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf018ca29bf
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf085b6663.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf078721263.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Saving output messages to:
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/MungeSumstats_log_msg.txt
Any runtime errors will be saved to:
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/MungeSumstats_log_output.txt
Messages will not be printed to terminal.
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf066f83548.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01f8173c5
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf066f83548.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07c15335.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d686cbb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 186 rows
   - 93 unique variants
   - 140 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
93 RSIDs are duplicated in the sumstats file. These duplicates will be removed
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07c15335.tsv.gz
Summary statistics report:
   - 93 rows (50% of original 186 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02d717f75.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d686cbb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02d717f75.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf05106969.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d686cbb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 94 rows
   - 94 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
1 base-pair positions are duplicated in the sumstats file. These duplicates will be removed.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf05106969.tsv.gz
Summary statistics report:
   - 93 rows (98.9% of original 94 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf067e54c00.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02a1d6988
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Filtering effect columns, ensuring none equal 0.
5 SNPs have effect values = 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf067e54c00.tsv.gz
Summary statistics report:
   - 88 rows (94.6% of original 93 rows)
   - 88 unique variants
   - 65 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0164b7c05.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf073477233
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	FRQ	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0164b7c05.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P      FRQ
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1.863269
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1.169733
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01e044b1.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf073477233
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	FRQ	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
As frq_is_maf=FALSE, the FRQ column will be renamed MAJOR_ALLELE_FRQ to differentiate the values from 
minor/effect allele frequency.
Sorting coordinates.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01e044b1.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08
   MAJOR_ALLELE_FRQ
1:         1.863269
2:         1.169733
3:         1.401423
4:         1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07f5d1602.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf025e06274
Standardising column headers.
First line of summary statistics file: 
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07f5d1602.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d9a1560.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf05b0c6b30
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	INFO	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs based on INFO score.
38 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/info_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
28 SNPs (50.9%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d9a1560.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P     INFO
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1.863269
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1.169733
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf020443c4b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf031cf3594
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf020443c4b.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0488c7539.tsv.gz
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0488c7539.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file1\\file9cf074ca2027.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file2\\file9cf075171bf9.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file3\\file9cf0365c3ea.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file4\\file9cf0774539f6.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file5\\file9cf0373f5c34.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file6\\file9cf037aa2746.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file7\\file9cf05f837947.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file8\\file9cf05d776149.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file9\\file9cf0383479d.tsv.gz"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpwtYLYU/data/file10\\file9cf070835d7c.tsv.gz"
10 file(s) found.
Parsing info from 10 log file(s).
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf070ee46f1.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07f6a36c5
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
WARNING: 1 rows in sumstats file are missing data and will be removed.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
46 SNPs (50%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf070ee46f1.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:  rs12646808   4  3249828  T  C 0.64180  0.016 0.003 4.002e-08
2:    rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
3: rs117468730  16 10205467  A  G 0.02425 -0.049 0.009 1.242e-07
4:  rs76076331   2 10977585  T  C 0.09328  0.020 0.004 3.632e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0107a11c2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07f6a36c5
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0107a11c2.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:  rs12646808   4  3249828  T  C 0.64180  0.016 0.003 4.002e-08
2:    rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
3: rs117468730  16 10205467  A  G 0.02425 -0.049 0.009 1.242e-07
4:  rs76076331   2 10977585  T  C 0.09328  0.020 0.004 3.632e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04092291d.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03b61689
Standardising column headers.
First line of summary statistics file: 
chromosome	rs_id	markername	position_hg18	Effect_allele	Other_allele	EAF_HapMapCEU	N_SMK	Effect_SMK	StdErr_SMK	P_value_SMK	N_NONSMK	Effect_NonSMK	StdErr_NonSMK	P_value_NonSMK	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 1 chromosomes
Checking for multi-GWAS.
WARNING: Multiple traits found in sumstats file only one of which can be analysed: 
SMK, NONSMK
Standardising column headers.
First line of summary statistics file: 
CHR	SNP	MARKERNAME	POSITION_HG18	A2	A1	EAF_HAPMAPCEU	N	EFFECT	STDERR	P_VALUE	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK	
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
1 SNP IDs are not correctly formatted and will be removed.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column MARKERNAME has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
CHR	SNP	POSITION_HG18	A2	A1	EAF_HAPMAPCEU	N	BETA	STDERR	P	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK	BP	
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.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Ensuring all SNPs have N<5 std dev above mean.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04092291d.tsv.gz
Summary statistics report:
   - 4 rows (80% of original 5 rows)
   - 4 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
         SNP  CHR        BP A1 A2 POSITION_HG18 EAF_HAPMAPCEU     N    BETA
1: rs1000085 chr1  66630503  G  C      66630503        0.1667 38761  0.0053
2: rs1000075 chr1  94939420  C  T      94939420        0.3583 38959 -0.0013
3: rs1000073 chr1 155522020  G  A     155522020        0.3136 36335  0.0046
4: rs1000050 chr1 161003087  C  T     161003087        0.9000 36257  0.0001
   STDERR      P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
1: 0.0095 0.5746   147259       -0.0034        0.0052         0.5157
2: 0.0082 0.8687   147567       -0.0043        0.0044         0.3259
3: 0.0083 0.5812   126780        0.0038        0.0045         0.3979
4: 0.0109 0.9931   127514        0.0058        0.0059         0.3307
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06d833bbb.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf071231cb
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	N_fixed	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06d833bbb.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N N_FIXED
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 5       5
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1       1
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1       1
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 7       7
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf040016569.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf011a2480
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf040016569.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf015587e28.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf011a2480
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf015587e28.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06316731d.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf011a2480
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/n_large.tsv.gz
Removing rows where is.na(N)
0 SNPs have N values that are NA and will be removed.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/n_null.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06316731d.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06aa74653.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf039b42c53
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 23 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
3 SNPs are on chromosomes X, Y, MT and will be removed
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU/chr_excl.tsv.gz
Warning: When method is an integer, must be >0.
45 SNPs (50%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf06aa74653.tsv.gz
Summary statistics report:
   - 90 rows (96.8% of original 93 rows)
   - 90 unique variants
   - 67 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf050073901.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf039b42c53
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf050073901.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07d0fcbc
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf015ca5ade
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Writing in VCF format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf041d92e0b.vcf.gz
Reading header.
Importing VCF file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf041d92e0b.vcf.gz
Reading VCF file.
Standardising column headers.
First line of summary statistics file: 
CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GWAS	
Removing non-standard columns: QUAL, FILTER, FORMAT
Parsing 'GWAS' data column.
1 empty column(s) detected.
Formatting INFO column.
NOTE: All INFO scores are empty. Replacing all with 1.
Standardising column headers.
First line of summary statistics file: 
CHR	BP	SNP	A1	A2	INFO	FRQ	BETA	SE	P	
0 empty column(s) detected.
Reading VCF file.
Standardising column headers.
First line of summary statistics file: 
CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	EBI-a-GCST005647	
Removing non-standard columns: QUAL, FILTER, FORMAT
Parsing 'EBI-A-GCST005647' data column.
0 empty column(s) detected.
VCF file has -log10 P-values, these will be converted to unadjusted p-values in the 'P' column.
Formatting INFO column.
INFO column is actually AF, it will be converted.
Standardising column headers.
First line of summary statistics file: 
CHR	BP	SNP	A1	A2	INFO	ES	SE	LP	AF	ID	P	
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Writing in VCF format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf045ec2897.vcf.gz
Reading VCF file.
Standardising column headers.
First line of summary statistics file: 
CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GWAS	
Removing non-standard columns: QUAL, FILTER, FORMAT
Parsing 'GWAS' data column.
0 empty column(s) detected.
VCF file has -log10 P-values, these will be converted to unadjusted p-values in the 'P' column.
Formatting INFO column.
Standardising column headers.
First line of summary statistics file: 
CHR	BP	SNP	A1	A2	INFO	BETA	SE	LP	FRQ	ID	P	
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07b057d4a.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Standardising column headers.
First line of summary statistics file: 
SNP	P	FRQ	BETA	CHR	BP	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
5 SNP IDs contain other information in the same column. These will be separated.
Checking for merged allele column.
Column SNP_INFO has been separated into the columns A1, A2
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.
Checking for SNPs with duplicated base-pair positions.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07b057d4a.tsv.gz
Summary statistics report:
   - 5 rows (100% of original 5 rows)
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR    BP A1 A2           P       FRQ      BETA
1: rs140052487   1 54353  C  A 0.037219838 0.3000548 0.8797957
2: rs558796213   1 54564  G  T 0.004382482 0.5848666 0.7068747
3: rs561234294   1 54591  A  G 0.070968402 0.3334671 0.7319726
4:   rs2462492   1 54676  C  T 0.065769040 0.6220120 0.9316344
Returning data directly.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************

Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0201c183a.tsv.gz
Log data to be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU
Standardising column headers.
First line of summary statistics file: 
SNP	P	FRQ	BETA	CHR	BP	A1	A2	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
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.
Checking for SNPs with duplicated base-pair positions.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0201c183a.tsv.gz
Summary statistics report:
   - 5 rows (100% of original 5 rows)
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR    BP A1 A2           P       FRQ      BETA
1: rs140052487   1 54353  C  A 0.037219838 0.3000548 0.8797957
2: rs558796213   1 54564  G  T 0.004382482 0.5848666 0.7068747
3: rs561234294   1 54591  A  G 0.070968402 0.3334671 0.7319726
4:   rs2462492   1 54676  C  T 0.065769040 0.6220120 0.9316344
Returning data directly.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf040395455.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02853ff0
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf079703ffd.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf018137a2f
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf079703ffd.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf040081cac.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf018137a2f
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf040081cac.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03be71bd2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07c9fc45
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03be71bd2.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0425147c7.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0740c2be1
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0425147c7.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf060433315.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf07ea16975
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
5 SNPs have SE values <= 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) 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, MAF, FRQ_U, F_U, FREQUENCY, 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
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.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf060433315.tsv.gz
Summary statistics report:
   - 88 rows (94.6% of original 93 rows)
   - 88 unique variants
   - 65 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf02dee4700.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0678d7d85.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04546735e
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
Sorting coordinates.
Writing in tabular format ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf0678d7d85.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Converting summary statistics to Genomic Ranges.
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04f0825b7.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf01a266a39.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf036c2710d.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04fad4b17.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03169675c.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf050d05ba0.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04fe22ef3.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03a331dba.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf03d884af9.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf08a930e4.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf09717301.tsv.gz
Formatted summary statistics will be saved to ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf014f28de.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpwtYLYU\file9cf04c9c669
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 10 | SKIP 1 | PASS 98 ]
> 
> proc.time()
   user  system elapsed 
  16.25    8.56   47.84 

Example timings

MungeSumstats.Rcheck/MungeSumstats-Ex.timings

nameusersystemelapsed
download_vcf000
find_sumstats000
format_sumstats34.37 4.6241.41
get_genome_builds57.75 7.1371.22
import_sumstats000
index_tabular0.030.000.04
list_sumstats000
load_snp_loc_data000
parse_logs000
read_sumstats0.000.000.01
write_sumstats0.020.000.02