Metal - the commnad you issued could not be processed
1
0
Entering edit mode
4.3 years ago

Hello. When running METAL software I get the following message:

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

On the guide METAL "quick start" I found: For convenience, many commands can be shortened. For example, instead of writing MARKERLABEL SNP, you could write MARKER SNP. If you make a mistake and METAL doesn't understand your command, it will usually say:

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

My infoconfig file is:

MARKERLABEL SNP
ALLELELABEL EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ FREQ_EFFECT
EFFECTLABEL BETA
PVALUELABEL PVALUE
STDERR SE
WEIGHTLABEL N
PROCESS file.txt

Why do I still get this message? Does it affect my results? Please let me know.

Meta-alanysis METAL GWAS • 1.4k views
ADD COMMENT
0
Entering edit mode

what is "metal" ?

ADD REPLY
2
Entering edit mode
ADD REPLY
0
Entering edit mode

METAL: fast and efficient meta-analysis of genomewide association scans (2010) Cristen J. Willer, Yun Li and Gonçalo R. Abecasis

ADD REPLY
0
Entering edit mode
4.0 years ago
ShirleyDai ▴ 40

I guess you would like to run ./metal first. Then here's my script, and it worked.

MARKER   name
ALLELE   A1      A2
EFFECT   beta_SNP_add
STDERR   sebeta_SNP_add
PVAL     p.val
WEIGHTLABEL  n
FREQLABEL Freq1
MINMAXFREQ ON
AVERAGEFREQ ON

PROCESS file1.txt
PROCESS file2.txt
ADD COMMENT

Login before adding your answer.

Traffic: 1257 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6