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Meta-analysis of genomewide association scans
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## ERROR: The command you issued could not be processed ... #17

Closed AMCalejandro closed 2 years ago

AMCalejandro commented 2 years ago

Hi,

I am falling within the following error for one of my input GWAS files, and I cannot figure out what may be causing the issue.

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

The commands applied to run metal for that specific file are:

SCHEME STDERR AVERAGEFREQ ON MINMAXFREQ ON CUSTOMVARIABLE TotalSampleSize LABEL TotalSampleSize as Nsample

......

=== DESCRIBE AND PROCESS PDSTAT ===

MARKER SNP ALLELE A1 A2 FREQ MAF EFFECT Coeff STDERR se

PVALUE p.value

WEIGHT N

PROCESS ../PDSTAT/RESULTS_TIDY/modelbasic/PDSTAT_modelBasic_total.txt

OUTFILE metal_pdstat.ppmi.proband.opdc_totalOutcome.tbl ANALYZE HETEROGENEITY

QUIT

The header of the file....

SNP    CHR BP  A1  A2  Coeff   se  tVal    pVal    BIC MargR2  CondR2  N   OutcomeVar  MAF Nsample
rs3131972   1   752721  A   G   0.0973184269099255  2.67166182127882    0.036426177196088   0.971001390250452   2825.86652627283    0.0500525556109709  0.727862513155491   359 modelBasic_total    0.125   124
rs11240777  1   798959  A   G   -2.14252697297112   2.3854162409976 -0.898177406587578  0.370844019013569   2825.06389682483    0.0551317431253653  0.727815810596432   359 modelBasic_total    0.1452  124
rs149737509 1   837657  C   G   6.60417605349683    7.71465092921372    0.856056367824529   0.393608058617525   2777.63173570397    0.0534888264358287  0.726936500207331   353 modelBasic_total    0.0123  124
rs4970383   1   838555  A   C   -2.70012794265555   2.17867195354516    -1.23934580342023   0.217566025004361   2824.34196413237    0.0594708696112736  0.727699345499498   359 modelBasic_total    0.2339  124
rs4475691   1   846808  T   C   -1.47328548866513   2.33944711207393    -0.629757980448236  0.530014360388402   2825.47189275845    0.052632200446018   0.727888577432786   359 modelBasic_total    0.1694  124
rs142336952 1   853394  A   G   6.60417605349683    7.71465092921372    0.856056367824529   0.393608058617525   2777.63173570397    0.0534888264358287  0.726936500207331   353 modelBasic_total    0.0123  124
rs2341354   1   918573  A   G   -0.72996695315949   1.83703377666599    -0.397361748287664  0.691786177551442   2825.71004960227    0.0510635406241033  0.727883044919168   359 modelBasic_total    0.3911  124
rs1891910   1   932457  A   G   -2.10424347088426   2.03991795500077    -1.03153338384311   0.304336295809023   2802.41346678747    0.0566960400606542  0.729877648923114   356 modelBasic_total    0.2439  124
rs3128117   1   944564  C   T   -1.76744223187919   1.79856880696992    -0.98269369791686   0.327687448531142   2824.90585265697    0.056144250493417   0.727907813743213   359 modelBasic_total    0.4113  124

Best, Alejandro.

welchr commented 2 years ago

Can you attach your full metal script and error log here?

AMCalejandro commented 2 years ago

Sorry,

Apparently my meta file had a bug. I wrote it and ran it again. It seems that everything went fine. Apologies.