gene-covar error

[Miguel Martin Alvarez]

Hi, 

I'm getting this error when running --gene-covar on magma results:

```

Welcome to MAGMA v1.10 (linux)
Using flags:
        --gene-results magma.genes.raw
        --gene-covar gtex_v8_ts_avg_log2TPM.txt
        --out results

Reading file magma.genes.raw...
        6 genes read from file
Loading gene-level covariates...
Reading file gtex_v8_ts_avg_log2TPM.txt
        detected 55 variables in file (using all)

        WARNING: discarding variable 'Adipose_Subcutaneous', missing value rate exceeds missingness threshold (0.05)

...

(... all variables same error...)

...
        WARNING: discarding variable 'Average', missing value rate exceeds missingness threshold (0.05)
        found 0 valid gene covariates, for 5 genes defined in genotype data

ERROR - loading gene-level data: no valid gene sets or covariates found in input files

Terminating program.

```

gtex_v8_ts_avg_log2TPM.txt is from https://fuma.ctglab.nl/downloadPage, and it looks like this:

```

$ head gtex_v8_ts_avg_log2TPM.txt | cut -f1-5
GENE Adipose_Subcutaneous Adipose_Visceral_Omentum Adrenal_Gland Artery_Aorta
ENSG00000227232 2.35002617075486 2.13054647427272 1.90824187657363 2.33594758753967
ENSG00000233750 0.0379849325530441 0.0810158914406306 0.0337631588942668 0.0515874667806995
ENSG00000268903 2.13752186374553 2.69603741249722 2.34662004249861 2.29653547887999
ENSG00000269981 2.64642789167158 3.13510979660103 2.93051136911785 2.86748484707175
ENSG00000239906 0.269285264183931 0.310227668182762 0.234724538841685 0.297607879879638
ENSG00000279928 0.127102156369897 0.157884398554057 0.233038842696312 0.169981082019149
ENSG00000279457 3.05147966920867 2.70500635960052 2.68645543792496 3.05877001774473
ENSG00000228463 1.00496845013067 0.733334439984681 0.655331831104215 0.349202975139979

```

and magma.genes.raw contains

```

# VERSION = 110

# COVAR = NSAMP MAC

ENSG00000215018 1 3404506 3528059 1 1 9244 47 5.65833

ENSG00000042088 14 157710054 15774525 1 1 9247 53 4.61435

ENSG00000267583 10 88695297 88717425 1 1 9239 73 5.01396

ENSG00000449212 14 10603246 10728805 1 1 9271 86 14.9343

ENSG00000275945 15 23684535 23692390 1 1 9245 77 6.71979

ENSG00000102290 17 78518625 78940173 1 1 9272 70 4.94746

```

i.e. only 6 genes.

Thanks,

Miguel

[Miguel Martin Alvarez]

EDIT: 

Forgot to add that there are no NA, na, NaN, etc... in the gtex_v8_ts_avg_log2TPM.txt file