ERROR:001 for hg38

[Maxim Freydin]

Hi,

Job ID: 748922

I follow the guidance to upload hg38 data, but I got ERROR:001

Here is the log

2026-06-26 17:24:12,516 [INFO] __main__: You indicated that your input gwas sumstat is in GRCh38. FUMA will look up rsid using dbSNP v157
2026-06-26 17:24:15,741 [INFO] __main__: Input file header: ['chromosome base_pair_location effect_allele other_allele beta p_value']
2026-06-26 17:24:15,742 [ERROR] __main__: Columns chromosome and base_pair_location are required in the input file.

And here are a few lines from the file I upload:

chromosome base_pair_location effect_allele other_allele beta p_value
1 817341 G A 0.0213125 0.447552
1 858952 A G -0.063105 0.0957919
1 866156 G T 0.00574367 0.942594

As you can see, both chromosome and base_pair_location columns are present in the file.

Please can you advise on how to proceed.

Thanks in anticipation.

Maxim

[Tanya Phung]

Hi Maxim, 

This log message Input file header: ['chromosome base_pair_location effect_allele other_allele beta p_value'] indicates that the delimiter is not detected correctly and FUMA failed to parse the header. 
If all goes well, it should read:  ['chromosome', 'base_pair_location', 'effect_allele', 'other_allele', 'beta', 'p_value']

How did you generate the file? 
If you look at this issue from another user: https://groups.google.com/g/fuma-gwas-users/c/S4MvlgWgzW0, their snippet of R code looks correct, so you can do something similar: 

Full R code being run:

```

library(tidyverse)
library(data.table)

bellenguez_prev <- fread("~/Dropbox/GWAS/GWAS Summary Stats/Bellenguez_filtered.tsv.gz", data.table = F)

bellenguez_reorder <- bellenguez_prev %>%
  select(chromosome, base_pair_location, effect_allele, other_allele, beta, p_value)

write.table(bellenguez_reorder, file = "~/Downloads/bellenguez_grch38_reordered.tsv", quote = FALSE)

```

Best,
Tanya

[Maxim Freydin]

Hi Tanya,

Thanks for your reply. It is just a standard text file I saved using write.table in R.

Might be a separator issue. I will try again.

Kind regards

Max