Error 001

[kit...@gmail.com]

Hi Kyoko,

Thanks so much for sharing this great software. I've tried running FUMA a few times and each time I get Error 001 regarding my input file. In particular it doesn't seem to read my rs# column header. I've tried changing the name of that column a few times (i.e. rsID, SNP) and including this on the input form as well as not indicating this. I get the error each time. My file is a tab delimited .txt file, which looks like the following. The most recent Job IDs were 5317 and 5329.

rsID effect_allele non_effect_allele P

rs11126630 c t 5.295E-008

rs1542678 g t 1.016E-006

rs10192926 t a 1.483E-006

rs2015436 c t 1.574E-006

Thanks!

Kit

[Kyoko Watanabe]

Hi Kit,

Thank you for using FUMA.

There are two possibilities.

1. If the file is created on DOS, the file format might not be readable for linux (due to the difference of the new line). Since the web server is linux, please make sure that the new line is "\n".

2. Is the header also tab delimited? FUMA assume the header and the rest of the file have the same delimiter. So if there is any extra space, that might cause ERROR:001.

If neither is your case, could you please share your file (first 15 lines are enough) since I do not have access to your input file security reason? Please attache to k.wat...@vu.nl. I will investigate further.

Best,

Kyoko

[carolina....@gmail.com]

Dear Kyoko,

I am getting this same error 001 even after running several tests (last one: job ID 26614).

My file was created in Unix, is tab delimited (including the header) and looks like this:

SNP     effect_allele   other_allele    eaf     beta.sd se.sd   pval.sd samplesize

rs7793337       C       T       0.151609        -0.013033       0.017201        0.451545        13526

rs77933378      C       A       0.035775        -0.000315       0.038592        0.99352 13523

rs7793338       C       T       0.127999        0.015053        0.018374        0.415618        13523

rs7793339       T       C       0.188628        0.014113        0.016559        0.397083        13524

rs77933396      A       G       0.149508        -0.014838       0.017437        0.397819        13522

rs779334        A       C       0.364166        0.016915        0.012718        0.186307        13523

rs7793340       T       C       0.181856        0.020144        0.016017        0.211427        13522

rs7793342       A       C       0.040669        0.010814        0.031123        0.72993 13524

rs77933426      A       C       0.009991        -0.058162       0.077521        0.455989        12035

PS: I have compressed it using gzip to be under 600Mb.

I would really appreciate if you could help me find out how to fix the problem. If easier, I am happy to send the file to your personal email.

Thank you.

Best

Carolina

[Kyoko Watanabe]

Hi Carolina,

I checked the error log for jobID 26614.

It seems like you have a float number in one of the allele columns?

In one of the script, alleles are converted to upper case but it failed due to non-string value.

Could you check if you have any non string in your allele columns?

If that is not the case, please let me know, I'll further follow you up.

Best,

Kyoko

[carolina....@gmail.com]

Hi Kyoko,

Thank you for your reply!

I have double checked and the only values in the allele columns (ie effect_allele and other_allele) are "A", "C", "G", "T". So I guess this shouldn't explain the error.

Would you have any additional ideas on what might be going on?

Thanks again!

Best

Carolina

[Kyoko Watanabe]

Hi Carolina,

Thank you for checking!!

Ok, is there any possibility that you have blank in some of the lines?

If you can share your input file with me, I'll have a look what is causing the error.

Best,

Kyoko

[carolina....@gmail.com]

Dear Kyoko,

I've realised I still had some missings in the non effect allele column. I have removed them and it works just fine now.

Thanks a lot for your support!

Best

Carolina