METAL ERROR: The command you issued could not be processed ...

Question

[JJ]

Hello,

the meta-analysis seems to work in metal but I keep seeing this error which the log file does not indicate what the error is about. Also, the outfile flag does not seem to work, I always get the METAANALYSIS1.TBL rather than the denoted outfile in the output directory. Please let me know if you have any ideas. Thanks in advance.

SEPARATOR WHITESPACE
MARKER SNP_37
ALLELE A1 A2
EFFECT Effect
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 1000
SCHEME STDERR
STDERR SD
PVALUE Wald_P
USESTRAND OFF
MAXWARNINGS 100000
PROCESS .../metalInput_ITA_YAOSPsqrt_YOBAAO_locoAll_240612.txt
PROCESS .../metalInput_US_YAOSPsqrt_YOBAAO_locoAll_240612.txt
PROCESS .../metalInput_SWE_GSA_YAOSPsqrt_YOBAAO_locoAll_240612.assoc
PROCESS .../metalInput_SWE_OE_YAOSPsqrt_YOBAAO_locoAll_240612.assoc

OUTFILE .../meta_SWEUSITA_YAOSP_YOBAAO_loco_240612.TBL
ANALYZE HETEROGENEITY

QUIT

  ./generic-metal/metal script/metal_YAOSP.par
MetaAnalysis Helper - (c) 2007 - 2009 Goncalo Abecasis
This version released on 2011-03-25

# 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 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 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')
#   ANALYZE          [HETEROGENEITY]
#   CLEAR

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

# Processing commands in script/metal_YAOSP.par ...
## Set column separator to WHITESPACE ...
## Set marker header to SNP_37 ...
## Set allele headers to A1 and A2 ...
## Set effect header to Effect ...
## Set weight header to DONTUSECOLUMN ...
## Set default weight to 1000.00 ...
## Meta-analysis will be based on effect sizes and their standard errors ...
## Set standard error header to SD ...
## Set p-value header to Wald_P ...
## Strand flipping according to strand column disabled
## Set the maximum number of warnings per file to 100000 ...
###########################################################################
## Processing file '.../metalInput_ITA_YAOSPsqrt_YOBAAO_locoAll_240612.txt'
## Processed 7017277 markers ...

###########################################################################
## Processing file '.../metalInput_US_YAOSPsqrt_YOBAAO_locoAll_240612.txt'
## WARNING: Marker '4:12091706:C:T' duplicated in input, first instance used, others skipped
## Processed 7059759 markers ...

###########################################################################
## Processing file '.../mm_timeP_GSA_240429/metalInput_SWE_GSA_YAOSPsqrt_YOBAAO_locoAll_240612.assoc'
## Processed 7615254 markers ...

###########################################################################
## Processing file '.../mm_timeP_OE_240429/metalInput_SWE_OE_YAOSPsqrt_YOBAAO_locoAll_240612.assoc'
## Processed 7659130 markers ...

## ERROR: The command you issued could not be processed ...
###########################################################################
## Running second pass analysis to evaluate heterogeneity...
## Processing file '.../metalInput_SWE_OE_YAOSPsqrt_YOBAAO_locoAll_240612.assoc'
## Processing file '.../metalInput_SWE_GSA_YAOSPsqrt_YOBAAO_locoAll_240612.assoc'
## Processing file '.../metalInput_US_YAOSPsqrt_YOBAAO_locoAll_240612.txt'
## Processing file '.../metalInput_ITA_YAOSPsqrt_YOBAAO_locoAll_240612.txt'

###########################################################################
## 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 7895492 markers!
## Smallest p-value is xxxx at marker 'xxxx'

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

[bk11]

Why do you have 3 dots (.../) before your input files? Where are your input files located? Are they a directory back from your working directory or somewhere else?

[Ram]

JJ Why did you delete this post?

[Ram]

JJ Please answer the question if you want this post to stay closed. Closing the post again without explaining why will get your account suspended.

[JJ]

I just closed because i got the issue resolved that was pretty much it. Are you an admin here? didn't know

[Ram]

I am a moderator but that does not matter.

I just closed because I got the issue resolved

That's not how forums work. You asked a question in a knowledgebase and got feedback, so the right thing to do is to add an answer with information on how you resolved the issue and accept that answer so people in the future with the same issue (and that could be you in the future too) will know how to solve the issue or at least one of the possible avenues to pursue.

[JJ]

sounds good, can do in that way in the future