Error 1

[Varun Warrier]

Hi Fuma Team,

I'm trying to upload a file and run FUMA, but I keep getting the following error message:

FUMA an error occurred

This is unfortunate! An error occurred during the process of your job (job ID: 84149, job title: ).
ERROR: 1 (Input file format was not correct / There was no SNPs remained after formatting the input summary statistics.)
Please make sure your input file has sufficient column names. Please refer Tutorial for details.

You can post questions, suggestions and bug reports on Google Forum: FUMA GWAS users

My input file looks like this (head):

                    SNP CHR        BP   A1    A2         BETA          SE      P
1:   10:100010430_CAG_C  10 100010430  CAG     C  0.038684639 0.041373946 0.3500
2:    10:100014847_CT_C  10 100014847   CT     C  0.002678710 0.003882189 0.4900
3: 10:100017008_TTCAC_T  10 100017008    T TTCAC -0.061356192 0.021430734 0.0042
4:  10:10001753_TAAAG_T  10  10001753    T TAAAG  0.001722551 0.008527480 0.8400
5:    10:100019492_GC_G  10 100019492    G    GC -0.011111539 0.027848468 0.6900
6:  10:100025128_CTAT_C  10 100025128 CTAT     C  0.005299800 0.003772100 0.1600

And tail:
         SNP CHR        BP A1 A2          BETA          SE       P
1: rs9999992   4 122902084  A  G -6.389953e-05 0.005324961 0.99040
2: rs9999993   4  98562671  A  T -5.929140e-03 0.003427248 0.08366
3: rs9999995   4 185171608  A  G  1.899263e-03 0.006166437 0.75820
4: rs9999996   4  69782467  A  C -1.244735e-03 0.005080551 0.80660
5: rs9999997   4 163870478  A  G -2.027825e-03 0.003454557 0.55740
6: rs9999998   4 117161848  T  C  5.033015e-03 0.004673180 0.28140

I can confirm that there are no quotes in the uploaded file. 

Any suggestion as to what the issue is and how I can resolve it, please?

Thanks,
Varun

[DP Wightman]

Hi Varun,

From the looks of your file it could be that the row numbers are being interpreted as a column causing your p-value column to shift to an empty column. It could also be that there are no significant variants in your dataset.

Cheers,

Doug

[pyrot...@gmail.com]

Thanks Doug. I think, in the end, the issue was that the columns were not in the same order as that on the FUMA website. When I re-ordered it, it worked!

Cheers

Varun