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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MungeSumstats.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MungeSumstats_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MungeSumstats.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MungeSumstats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MungeSumstats’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... 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
format_sumstats 32.863  3.689  36.749
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MungeSumstats
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
** 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)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
First line of summary statistics file: 
MarkerName	CHR	POS	A2	A1	EAF	Beta	SE	Pval	
There are more matches to the reference genome found when the alleles are flipped.
These will be flipped along with the effect column.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
1 SNPs are non-biallelic.  These will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs10061788	5	87934707	A	G	0.2164	0.021	0.004	2.464e-09
rs1007883	16	51163406	T	C	0.3713	-0.015	0.003	5.326e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	
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
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.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	FRQ	BETA	SE	P	A2	A1
rs13402908	2	100333377	0.5056	-0.018	0.003	1.695e-11	C	T
rs113081851	13	100664477	0.3265	-0.015	0.003	9.829e-08	C	T
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	CHR_BP_A2_A1_2	
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
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.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	FRQ	BETA	SE	P	A2	A1
rs13402908	2	100333377	0.5056	-0.018	0.003	1.695e-11	C	T
rs113081851	13	100664477	0.3265	-0.015	0.003	9.829e-08	C	T
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	EAF	Beta	SE	Pval	alleles	allele	
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
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	FRQ	BETA	SE	P	A1	A2
rs12646808	4	3249828	0.6418	0.016	0.003	4.002e-08	T 	 C
rs301800	1	8490603	0.1791	0.019	0.003	1.794e-08	T 	 C
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	
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
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.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs13402908	2	100333377	T	C	0.5056	-0.018	0.003	1.695e-11
rs113081851	13	100664477	T	C	0.3265	-0.015	0.003	9.829e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	CHR_BP_2	
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
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.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs13402908	2	100333377	T	C	0.5056	-0.018	0.003	1.695e-11
rs113081851	13	100664477	T	C	0.3265	-0.015	0.003	9.829e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
WARNING: GWAS sumstat file has comma field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
93 RS IDs are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
1 base-pair Positions are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	INFO	
38 SNPs are below the INFO threshold of 0.9 and will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	INFO
rs76076331	2	10977585	T	C	0.09328	0.02	0.004	3.632e-08	1.21987180458382
rs7945718	11	12748819	A	G	0.5951	0.015	0.003	1.54e-08	1.52137891063467
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
WARNING: 1 rows in sumstats file are missing data and will be removed.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
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	
WARNING: Multiple traits found in sumstats file only one of which can be analysed: 
SMK, NONSMK
First line of summary statistics file: 
CHR	SNP	MARKERNAME	POSITION_HG18	A1	A2	EAF_HAPMAPCEU	N	EFFECT	STDERR	P_VALUE	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK	
1 SNP IDs are not correctly formatted and will be removed
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
First line of summary statistics file: 
CHR	SNP	POSITION_HG18	A1	A2	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.
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	POSITION_HG18	A1	A2	EAF_HAPMAPCEU	N	BETA	STDERR	P	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK
rs1000073	chr1	155522020	155522020	A	G	0.3136	36335	0.0046	0.0083	0.5812	126780	0.0038	0.0045	0.3979
rs1000050	chr1	161003087	161003087	T	C	0.9	36257	1e-04	0.0109	0.9931	127514	0.0058	0.0059	0.3307
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	N_fixed	
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	N	N_FIXED
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08	9	9
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08	5	5
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	N
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08	2
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08	3
First line of summary statistics file: 
MarkerName	CHR	POS	EAF	Beta	SE	Pval	
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving both A1 and A2 from reference genome
WARNING: Inferring the alternative allele (A2) from the reference genome. In some instances, there are more than one
alternative allele. Arbitrarily, only the first will be kept. See column `alt_alleles` in your returned sumstats file
for all alternative alleles.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	alt_alleles
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08	C
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08	C
First line of summary statistics file: 
MarkerName	CHR	POS	A2	EAF	Beta	SE	Pval	
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving A1 from reference genome
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	EAF	Beta	SE	Pval	
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving A2 from reference genome
WARNING: Inferring the alternative allele (A2) from the reference genome. In some instances, there are more than one
alternative allele. Arbitrarily, only the first will be kept. See column `alt_alleles` in your returned sumstats file
for all alternative alleles.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	alt_alleles
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08	C
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08	C
First line of summary statistics file: 
MarkerName	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file: 
SNP	BP	A1	A2	FRQ	BETA	SE	P	
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
1 SNP IDs are not correctly formatted. These will be corrected from the reference genome.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	
1 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome
1 SNP IDs are not correctly formatted and will be removed
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
1 SNP IDs are not correctly formatted. These will be corrected from the reference genome.
1 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
CHR	POS	A1	A2	EAF	Beta	SE	Pval	
There is no SNP column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
1 SNPs are not on the reference genome.  These will be corrected from the reference genome.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
3 SNPs are on chromosomes X, Y, MT and will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	SE	Pval	
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
There are existing p-values as low as 5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
WARNING: GWAS sumstat file has space field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs12646808	4	3249828	T	C	0.6418	0.016	0.003	4.002e-08
rs301800	1	8490603	T	C	0.1791	0.019	0.003	1.794e-08
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
8 SNPs are strand-ambiguous alleles including 4 A/T and 4 C/G ambiguous SNPs. These will be removed
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P
rs10061788	5	87934707	A	G	0.2164	0.021	0.004	2.464e-09
rs1007883	16	51163406	T	C	0.3713	-0.015	0.003	5.326e-08
VCF format detected, this will be converted to a standard summary statistics file format.
Inputted VCF format has -log10 P-values, these will be converted to unadjusted p-values in the 'P' column.
First line of summary statistics file: 
CHROM	POS	REF	ALT	INFO	ES	SE	LP	AF	ID	P	
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP	CHR	BP	A1	A2	INFO	BETA	SE	LP	AF	P
rs58108140	1	10583	G	A	0.1589	0.0312	0.0393	0.369267	0.1589	0.427300105456596
rs806731	1	30923	G	T	0.7843	-0.0114	0.0353	0.126854	0.7843	0.746699739815279
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
199.365  21.946 221.304