Is there a file size or SNP amount limit when using METAL?

[dzimmerman-amc]

Hi there,

I am trying to meta-analyse two summary statistic files together which differ greatly in size (3.2gb, 600mb). The large file contains ~58M SNPs while the small file contains ~7.8M SNPS. METAL is able to process the smaller file, however when I try processing the larger files I get the following error:

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

I have triple checked that the headers are set correctly but it still does not seem to work. Are there limits to to the amount of SNPs metal can process perhaps?

Thanks in advance!

[welchr]

That error looks to only occur in two places in the program:

METAL/metal/Main.cpp

Lines 1807 to 1809 in e2253cc

	if (tokens.Length() == 1) {
	printf("## ERROR: The command you issued could not be processed ...\n");
	continue;

METAL/metal/Main.cpp

Lines 2158 to 2160 in e2253cc

	if (tokens.Length() == 2) {
	printf("## ERROR: The command you issued could not be processed ...\n");
	continue;

Seems to always have something to do with the number of separate tokens it can find on a line in the metal script. It goes through the commands that should only have 1 token (like CLEARFILTERS or ANALYZE), and if it still finds your line only contains 1 token, it returns that error. Same thing for all commands that should have 2 tokens (LOGPVALUE ON). So it could be you've either got a bad command, or maybe there's a strange delimiter causing the actual parsing of the number of tokens to be incorrect. Completely guessing though.

What does your script look like?

[dzimmerman-amc]

Thanks for the reply! My script looks as below:

metal

scheme STDERR
marker SNPID
allele REF ALT
effect log(OR)
pvalue P
stderrlabel LOG(OR)_SE
WEIGHTLABEL OBS_CT
process SCALifeLinesMETALnoSNPFinal.txt

marker SNP
allele A2 A1
effect log(OR)
pvalue P
stderrlabel SE
WEIGHTLABEL N

process AGNES_2738_N_with_header
process GEVAMI_1350_N_with_header
process PREDESTINATION_1256_N_with_header

marker SNPID
allele ALLELE0 ALLELE1
effect BETA
pvalue pvalue
stderrlabel SE
WEIGHTLABEL N

proccess UKBB_SCA_EUR_GWAS__VF_STRICT__sumstats_14032022_MAC3_METALfinal.tsv

analyze heterogeneity

It is only the final file that this error occurs on, just to give you an idea of what the file looks like I will show you a few lines:

GENPOS CHROM SNPID ID ALLELE0 ALLELE1 N BETA SE pvalue
828 17 17:828:C:T rs62053745 C T 457346 0.0916884 0.0621816 0.140340170558253
834 17 17:834:A:G 17:834_G_A A G 457346 0.126658 0.0720196 0.0786339333382236
1389 17 17:1389:A:G rs62053747 A G 457346 0.0500072 0.100815 0.61987339955502
1665 17 17:1665:C:T rs34151105 C T 457346 0.0574858 0.0798451 0.47154592920749
1880 17 17:1880:T:C rs77383171 T C 457346 -0.0343875 0.0774773 0.657158303831746

I still can't seem to resolve the issue who see anything wrong with my script. I could, however, be missing something incredibly obvious! Thanks for helping out!

[welchr]

If you change proccess -> process for the final file, does it work?