caozilongsuper

HI, tomasnobrega. I get same problem. Have you figured it ou?

I have solved such problem with Kaleido as described in this website [https://search.r-project.org/CRAN/refmans/plotly/html/save_image.html](url)

Thanks for replying,and here is the information. [TCGA@cu03 ~]$ head /share/CZL/pancancer-GWAS/cervix_carcinoma/finngen/finngen_adeno_tomtag.txt chr,bpos,a1,a2,snpid,beta,se,pval,freq,N,z 1,13668,A,G,rs2691328,0.389358,1.61109,0.809033,0.0058238,167301,0.241673649516787 1,14773,T,C,rs878915777,-1.15586,1.008,0.251513,0.0134509,167301,-1.14668650793651 1,15585,A,G,rs533630043,-1.96825,3.15742,0.53304,0.00109271,167301,-0.623372880389685 1,16549,C,T,rs1262014613,-0.318079,4.5183,0.943877,0.000589333,167301,-0.0703979372772946 1,16567,C,G,rs1194064194,1.34032,1.62093,0.408303,0.00422919,167301,0.826883332407939 1,16792,A,G,rs201330479,1.98142,2.53122,0.433749,0.0012803,167301,0.782792487417135 1,16850,C,T,rs1298041101,-0.768738,5.56921,0.890214,0.000259096,167301,-0.13803358106446 1,16869,T,C,rs1201088959,-2.8915,13.1371,0.825792,8.19235e-05,167301,-0.2201018489621 1,17017,G,C,,8.97029,9.22849,0.33104,9.60228e-05,167301,0.972021424956846

Thanks for offering help and first error has been solved. But here comes another problem. Read 20156086 SNPs from --sumstats file. Removed 0 SNPs with missing values. Removed 0 SNPs...

Add it in the code just like this? python /home/CZL/software/MTAG/mtag-master/mtag.py \ --sumstats finngen_adeno_tomtag1.txt,finngen_squam_tomtag1.txt,finngen_uteri_tomtag1.txt \ --median_z_cutoff --out /share/CZL/result/cancer/Cervix/finngen_mtag.1NS \ --n_min 0.0 \ --stream_stdout Thank you in advance!

Hi JonJala, I have fixed SIGNED_SUMSTAT problem using --median_z_cutoff, but here comes another one. Total time elapsed: 3.0m:36.14s 'snpid' Traceback (most recent call last): File "/home/CZL/software/MTAG/mtag-master/mtag.py", line 1577, in mtag(args)...

This is the whole log: MTAG: Multi-trait Analysis of GWAS Version: 1.0.8 (C) 2017 Omeed Maghzian, Raymond Walters, and Patrick Turley Harvard University Department of Economics / Broad Institute of...

There is another question. I have checked my input file data and all pval column is between (0,1]. But I still meet this log: WARNING: 327274 SNPs had P outside...

Dear paturley, Many thanks for your quick response to all my questions, it is very helpful! Best, Zilong Cao

Thanks for quick reply! I am wondering what meaning of "GWAS equiv. (max) N" is. And what's the final sample number I can adapt.The main purpose is combining the two...