ERROR:001 with previously accepted files

[Serafi Cambray]

 Hello,

After a year of not using it, I returned to FUMA and was surprised to find that it no longer recognises the pipelines I had previously used. After multiple unsuccessful efforts with tasks that I had previously removed, today I decided to perform some in order to find what's wrong with m files.  

Job 676799 is a duplicate (same file and settings) of 555885 (previously accepted), and it did not work. After reading the suggestions, I attempted "adapting" my old pipeline. 676799 is the same as the previously allowed 555885, however the conversion from.txt to.zip failed as well. 676803 is the same as 676799, but switching browsers (from Chrome to Edge) didn't help either. 676807 is the same as 676799, but with the scientific-formatted p-values changed, it likewise fails.

If you could tell me what is wrong with my pipelines, I would be grateful.  

[Brandon Sanzo]

Hi!

Error 001 means that the input file was not correct. If the files worked before most likely the discontinuation of grch38 played a role and it may be helpful to ensure your files are in hg19. Here is a quote from the trouble shooting guide:

“Make sure that your data is correctly formatted for FUMA

1. Make sure that there is a header (column name) in your input file.

   1. The header should not start with a comment character (#). Any lines that starts with # will be ignored.

   2. The number of column names should be equal to the number of columns in your input file.

      1. sometimes the input file has a row index which means that there is one fewer column name in the header as compared to when the actual data starts.

2. rsID if exists has to be in rsID format. See tutorial.

3. Use gzip software to compress with .gzextension or ZIP software with .zip extension. Make sure you haven't renamed the file manually. Use the proper compression software instead.

4. The chromosome has to be numbers between 1 and 23 or X. 

5. Position values have to be integer (not in scientific notation) (see previous thread: )

6. If your file contains chromosome and position, these have to be in hg19 coordinates.

7. Make sure that there is no missing data for the columns that are mandatory such as p-values (see previous thread:  or  or )

8. If you specify the name of chromosome, position, etc… during submission, make sure that these names exist in your input file (see previous thread: )

9. Make sure that the delimiter is consistent. In addition, Delimiter can be any of white space including single space, multiple space and tab. Because of this, each element including column names must not include any space (see previous thread: ) 

10. Check your file to make sure that there is no quotation around each value. It should be for example 1 instead of "1". This is usually caused when you save a file in R. To avoid this, one needs to set quote=F when saving a file in R (see previous thread: ) 

“

Trouble shooting guide:
https://groups.google.com/g/fuma-gwas-users/c/N3HCEXBJ8Iw 

https://fuma.ctglab.nl/tutorial#prepare-input-files

Hope this helps!

-Brandon