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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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Error: invalid sample size in line #70

Open anafyp opened 5 months ago

anafyp commented 5 months ago

Hi all,

I want to run a post-GWAS analysis using COJO and keep getting the error: Error: invalid sample size in line: "22 rs62224609 16051249 C T 0.0971188 -6.35821 8.84771 0.47237 24990"

The command I run is : gcta64 --bfile chr_22 --cojo-file chr_22.mlma --cojo-slct --out output --thread-num 5

I am running GCTA version v1.94.1 Linux but have also tried with version v1.92.1 Linux My summary statistics have been generated by gcta64 --mlma.

head chr_22.mlma Chr SNP bp A1 A2 Freq b se p N
22 rs62224609 16051249 C T 0.0971188 -6.35821 8.84771 0.47237 24990
22 rs62224614 16053862 T C 0.0976277 -5.92364 8.84895 0.503229 24870
22 rs7286962 16054454 T C 0.09796 -7.09463 8.85563 0.423048 24755
22 rs62224618 16057417 T C 0.099153 -6.87479 8.74109 0.43158 25148
22 rs3949130 16488635 A C 0.0750821 -1.38239 9.92712 0.889249 24653
22 rs200167968 16488702 C G 0.0744487 0.241026 9.9621 0.980698 24668
22 rs79847867 16495833 A C 0.0767854 -3.00421 9.74897 0.757963 25148
22 rs131523 16869223 A G 0.304698 -6.47315 5.69416 0.25562 24736
22 rs131525 16869511 A G 0.308689 -5.69452 5.67245 0.315431 24766
22 rs131526 16869617 A G 0.0495893 -5.74799 12.0954 0.634629 24834

I tried running the same command with my fastgwa output but getting the same error. Am I missing something here? I don't know if it changes anything but I also tried giving the discovery subject list as input.

Thanks in advance for the help. Arya.

anglixue commented 5 months ago

Hi Arya,

Please remove the Chr column and rerun COJO.

The input format for COJO analysis can be found here https://yanglab.westlake.edu.cn/software/gcta/index.html#COJO

SNP A1 A2 freq b se p N rs1001 A G 0.8493 0.0024 0.0055 0.6653 129850 rs1002 C G 0.0306 0.0034 0.0115 0.7659 129799 rs1003 A C 0.5128 0.0045 0.0038 0.2319 129830 ...

Cheers Angli