Error 1 &5 with verified input format

[Siyue WANG]

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: 127216, job title: Toy_folate).
ERROR: 1 (Input file format was not correct / There was no SNPs remained after formatting the input summary statistics.)

My input file looks like this (head):

all rows are Tab delimited (and for all rows with single space did not work still).

I can confirm all rows are separated with the same Tab delimiter (though it appeared to be strange in certain rows)

However, after so many times uploading the same file, it came as a surprise that Error 5 instead of Error 1 appeared :)

job ID: 127217,  ERROR: 5 (Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified)

Could you please give any suggestions to what the issue actually is and how to get it fixed? 

Thanks a lot,

Siyue

[d.p.wi...@vu.nl]

Hi Siyue, 

I had a look at job 127216 and 127217. It looks like in 127216 no snps are being extracted from your file and in 127217 only one variant is being identified (1 11768839 8.14E-11). If you can share your full sumstats with me, can you email me them (d.p.wi...@vu.nl)? If you can't share the full sumstats, can you send me the rows you shared the screenshot of? I will use them to test what is going wrong with your jobs. 

Cheers,

Doug

[Siyue WANG]

Hi Doug,

My summary statistics have been attached and emailed (from siyue...@pku.edu.cn). 

I really appreciate your help!

Best,

Siyue

[d.p.wi...@vu.nl]

Hi Siyue,

I think there are 2 problems:

1) It looks like your data is not on build GRCh37 and currently FUMA only accepts GRCh37. Since you have the rsid, you can exclude/rename the chromosome and base pair columns. If you exclude the chromosome and base pair columns, they will be inferred from the rsID.

2) It also looks like your new lines are from windows and not unix, so FUMA does not recognise them. This thread might be helpful https://stackoverflow.com/questions/20368781/anything-like-dos2unix-for-windows.

Cheers,

Doug