problems with Meta-analysis in METAL

Question

[ek]

Hi everyone,

I'm trying to run an inverse variance weighted meta-analysis in METAL. I used the below script:

#Metal script for running an inverse SE meta-analysis for PTSD

# === DESCRIBE AND PROCESS THE FIRST INPUT FILE ===
   MARKERLABEL      SNP
   ALLELELABELS     A1 A2
   EFFECTLABEL      Beta
   STDERR           SE
   PROCESS PTSD_Duncan_formatted

# === DESCRIBE AND PROCESS THE SECOND INPUT FILE ===
   MARKERLABEL      SNP
   ALLELELABELS     A1 A2
   EFFECTLABEL      OR
   STDERR           SE
   PROCESS PTSD_Meier_formatted

# Options for inverse variance weighted meta-analysis ...
STDERRLABEL      SE
SCHEME           STDERR

# Options to enable tracking of allele frequencies ...
AVERAGEFREQ      ON
MINMAXFREQ       ON
FREQLABEL        Freq1

# Automatic genomic control correction of input statistics ...
GENOMICCONTROL   ON

# Options for general analysis control ...
EFFECT_PRINT_PRECISION 6
STDERR_PRINT_PRECISION 6
OUTFILE   ptsd_metaanalyzed.tbl
ANALYZE   HETEROGENEITY

QUIT

The meta-analysis doesn't run. I get the following error: Completed meta-analysis for 0 markers!.
Blow is the output. Any idea why that might be?

MetaAnalysis Helper - (c) 2007 - 2009 Goncalo Abecasis
This version released on 2020-05-05

# This program faciliates meta-analysis of genome-wide association studies.
# Commonly used commands are listed below:
#
# Options for describing input files ...
#   SEPARATOR        [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE)
#   COLUMNCOUNTING   [STRICT|LENIENT]            (default = 'STRICT')
#   MARKERLABEL      [LABEL]                     (default = 'MARKER')
#   ALLELELABELS     [LABEL1 LABEL2]             (default = 'ALLELE1','ALLELE2')
#   EFFECTLABEL      [LABEL|log(LABEL)]          (default = 'EFFECT')
#   FLIP
#
# Options for filtering input files ...
#   ADDFILTER        [LABEL CONDITION VALUE]     (example = ADDFILTER N > 10)
#                    (available conditions are <, >, <=, >=, =, !=, IN)
#   REMOVEFILTERS
#
# Options for sample size weighted meta-analysis ...
#   WEIGHTLABEL      [LABEL]                     (default = 'N')
#   PVALUELABEL      [LABEL]                     (default = 'PVALUE')
#   DEFAULTWEIGHT    [NUMBER]                    (default = 1.0)
#   MINWEIGHT        [NUMBER]                    (default = 1.0)
#
# Options for inverse variance weighted meta-analysis ...
#   STDERRLABEL      [LABEL]                     (default = 'STDERR')
#   SCHEME           [SAMPLESIZE|STDERR]         (default = SAMPLESIZE)
#
# Options to enable tracking of allele frequencies ...
#   AVERAGEFREQ      [ON|OFF]                    (default = OFF)
#   MINMAXFREQ       [ON|OFF]                    (default = OFF)
#   FREQLABEL        [LABEL]                     (default = 'FREQ')
#
# Options to enable tracking of user defined variables ...
#   CUSTOMVARIABLE   [VARNAME]
#   LABEL            [VARNAME] AS [HEADER]
#
# Options to enable tracking of chromosomes and positions ...
#   TRACKPOSITIONS   [ON|OFF]                    (default = OFF
#   CHROMOSOMELABEL  [LABEL]                     (default = 'CHROMOSOME')
#   POSITIONLABEL    [LABEL]                     (default = 'POSITION')
#
# Options to enable explicit strand information ...
#   USESTRAND        [ON|OFF]                    (default = OFF)
#   STRANDLABEL      [LABEL]                     (default = 'STRAND')
#
# Automatic genomic control correction of input statistics ...
#   GENOMICCONTROL   [ON|OFF|VALUE|LIST snps.txt](default = OFF)
#
# Options to account for samples overlap ...
#   OVERLAP          [ON|OFF]                    (default = OFF)
#   ZCUTOFF          [NUMBER]                    (default = 1.0)
#
# Options for general analysis control ...
#   PROCESSFILE            [FILENAME]
#   OUTFILE                [PREFIX SUFFIX]       (default = 'METAANALYSIS','.TBL')
#   MAXWARNINGS            [NUMBER]              (default = 20)
#   VERBOSE                [ON|OFF]              (default = 'OFF')
#   LOGPVALUE              [ON|OFF]              (default = 'OFF')
#   EFFECT_PRINT_PRECISION [NUMBER]              (default = '4')
#   STDERR_PRINT_PRECISION [NUMBER]              (default = '4')
#   ANALYZE                [HETEROGENEITY]
#   CLEAR

# Options for general run control ...
#   SOURCE           [SCRIPTFILE]
#   RETURN
#   QUIT

# Processing commands in SE_metal.txt ...
## Set marker header to SNP ...
## Set allele headers to A1 and A2 ...
## Set effect header to Beta ...
## Set standard error header to SE ...
###########################################################################
## Processing file 'PTSD_Duncan_formatted'
## ERROR: No 'PVALUE' column found

## Set marker header to SNP ...
## Set allele headers to A1 and A2 ...
## Set effect header to OR ...
## Set standard error header to SE ...
###########################################################################
## Processing file 'PTSD_Meier_formatted'
## ERROR: No 'PVALUE' column found

## Set standard error header to SE ...
## Meta-analysis will be based on effect sizes and their standard errors ...
## Averaging of allele frequencies enabled
## Tracking of extreme allele frequencies enabled
## Set frequency header to Freq1 ...
## Genomic control correction of input statistics enabled
## Set print pecision for Effect to 6 ...
## Set print pecision for StdErr to 6 ...
## ERROR: The command you issued could not be processed ...
###########################################################################
## Running second pass analysis to evaluate heterogeneity...

###########################################################################
## Executing meta-analysis ...
## Complete results will be stored in file 'METAANALYSIS1.TBL'
## Column descriptions will be stored in file 'METAANALYSIS1.TBL.info'
## Completed meta-analysis for 0 markers!

## Clearing all stored statistics ...
# Clearing user defined filters ...

[Basti]

There is a clear error message regarding your PTSD_Meier_formatted file : "ERROR: No 'PVALUE' column found"