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jianyangqt / gcta

GCTA software
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Error: the format of file [gsmr_exposure.txt] is incorrect, line 1. #61

Open umbrellaling opened 10 months ago

umbrellaling commented 10 months ago

Hi all, I have been trying to run GSMR on two traits, here are my command line: ./gcta64 \

--bfile g1000_eur \ --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt \ --gsmr-direction 2 \ --out A2_AD_gsmr_result

log file showed: Analysis started at 20:34:09 CST on Thu Dec 07 2023. Hostname: vm-87fa-8d7bb241113e

Accepted options: --bfile g1000_eur --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt --gsmr-direction 2 --out A2_AD_gsmr_result

Reading PLINK FAM file from [g1000_eur.fam]. 503 individuals to be included from [g1000_eur.fam]. Reading PLINK BIM file from [g1000_eur.bim]. 22665064 SNPs to be included from [g1000_eur.bim].

Reading GWAS summary data for exposure(s) from [A2_eur_gsmr.txt]. Error: the format of file [A2_eur_gsmr.txt] is incorrect, line 1. An error occurs, please check the options or data my inputfiles are two .txt file, SNP A1 A2 freq b se p N rs12238997 A G 0.1376 -0.076145 0.043735 0.081673 17810.9957384644 rs201234755 GAATA G 0.07145 -0.036143 0.03711 0.33009 31580.3769007307 rs72631875 G A 0.0349 0.059381 0.03662 0.1049 32660.9874529816 rs138660747 C A 0.007337 0.24607 0.09936 0.013267 28103.0501930502 rs116030099 T C 0.0872 -0.027646 0.030339 0.36216 32436.1767971955 rs148120343 T C 0.0573 -0.032283 0.036339 0.37433 41409.3605273293 rs58276399 T C 0.1427 -0.069503 0.041037 0.090324 18280.5334706142 rs61770163 A C 0.143 -0.028167 0.027007 0.29697 37641.0769200797 rs12131618 T C 0.08621 0.0035268 0.030258 0.90721 40845.7243413453 rs369030935 C T 0.009339 -0.072416 0.05677 0.20209 32436.1767971955 rs539235603 A C 0.03728 -0.055158 0.065242 0.39786 32436.1767971955 rs141242758 T C 0.1419 -0.069816 0.041104 0.089411 18280.5334706142 rs181876450 T C 0.01552 -0.017158 0.080181 0.83055 40396.604343302 rs140206562 G A 0.005789 -0.052814 0.074122 0.47614 25334.831992145 rs61770167 C T 0.01905 -0.0077167 0.1568 0.96075 21081.335538456 rs552659822 AC A 0.01335 0.096366 0.069976 0.16847 31580.3769007307

I do not know how would this happen and how to solve this!! hope someone can help me ,thank you so much!!

zhzhu083 commented 10 months ago

Hi,

Thanks for your email! The A2_eur_gsmr.txt looks good. While GCTA-GSMR can perform GSMR analysis with multiple exposures and multiple outcomes. Therefore, the input is a list of exposures/outcomes. You may create a new list which includes the A2 GWAS data.

If it does not solve your problem, please feel free to email me.

Best regards, Zhihong Zhu

On Fri, 8 Dec 2023 at 11:27, umbrellaling @.***> wrote:

Hi all, I have been trying to run GSMR on two traits, here are my command line: ./gcta64 \

--bfile g1000_eur --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt --gsmr-direction 2 --out A2_AD_gsmr_result

log file showed: Analysis started at 20:34:09 CST on Thu Dec 07 2023. Hostname: vm-87fa-8d7bb241113e

Accepted options: --bfile g1000_eur --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt --gsmr-direction 2 --out A2_AD_gsmr_result

Reading PLINK FAM file from [g1000_eur.fam]. 503 individuals to be included from [g1000_eur.fam]. Reading PLINK BIM file from [g1000_eur.bim]. 22665064 SNPs to be included from [g1000_eur.bim].

Reading GWAS summary data for exposure(s) from [A2_eur_gsmr.txt].

Error: the format of file [A2_eur_gsmr.txt] is incorrect, line 1. An error occurs, please check the options or data my inputfiles are two .txt file, SNP A1 A2 freq b se p N rs12238997 A G 0.1376 -0.076145 0.043735 0.081673 17810.9957384644 rs201234755 GAATA G 0.07145 -0.036143 0.03711 0.33009 31580.3769007307 rs72631875 G A 0.0349 0.059381 0.03662 0.1049 32660.9874529816 rs138660747 C A 0.007337 0.24607 0.09936 0.013267 28103.0501930502 rs116030099 T C 0.0872 -0.027646 0.030339 0.36216 32436.1767971955 rs148120343 T C 0.0573 -0.032283 0.036339 0.37433 41409.3605273293 rs58276399 T C 0.1427 -0.069503 0.041037 0.090324 18280.5334706142 rs61770163 A C 0.143 -0.028167 0.027007 0.29697 37641.0769200797 rs12131618 T C 0.08621 0.0035268 0.030258 0.90721 40845.7243413453 rs369030935 C T 0.009339 -0.072416 0.05677 0.20209 32436.1767971955 rs539235603 A C 0.03728 -0.055158 0.065242 0.39786 32436.1767971955 rs141242758 T C 0.1419 -0.069816 0.041104 0.089411 18280.5334706142 rs181876450 T C 0.01552 -0.017158 0.080181 0.83055 40396.604343302 rs140206562 G A 0.005789 -0.052814 0.074122 0.47614 25334.831992145 rs61770167 C T 0.01905 -0.0077167 0.1568 0.96075 21081.335538456 rs552659822 AC A 0.01335 0.096366 0.069976 0.16847 31580.3769007307

I do not know how would this happen and how to solve this!! hope someone can help me ,thank you so much!!

— Reply to this email directly, view it on GitHub https://github.com/jianyangqt/gcta/issues/61, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACAVLS6GNGMSHGWOYGMM7L3YIJUHZAVCNFSM6AAAAABAL6LLOOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTCNZXHE2TENY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

ehdhssh commented 2 days ago

Hi, Thanks for your email! The A2_eur_gsmr.txt looks good. While GCTA-GSMR can perform GSMR analysis with multiple exposures and multiple outcomes. Therefore, the input is a list of exposures/outcomes. You may create a new list which includes the A2 GWAS data. If it does not solve your problem, please feel free to email me. Best regards, Zhihong Zhu … On Fri, 8 Dec 2023 at 11:27, umbrellaling @.> wrote: Hi all, I have been trying to run GSMR on two traits, here are my command line: ./gcta64 \ --bfile g1000_eur --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt --gsmr-direction 2 --out A2_AD_gsmr_result log file showed: Analysis started at 20:34:09 CST on Thu Dec 07 2023. Hostname: vm-87fa-8d7bb241113e Accepted options: --bfile g1000_eur --gsmr-file A2_eur_gsmr.txt AD_gsmr.txt --gsmr-direction 2 --out A2_AD_gsmr_result Reading PLINK FAM file from [g1000_eur.fam]. 503 individuals to be included from [g1000_eur.fam]. Reading PLINK BIM file from [g1000_eur.bim]. 22665064 SNPs to be included from [g1000_eur.bim]. Reading GWAS summary data for exposure(s) from [A2_eur_gsmr.txt]. Error: the format of file [A2_eur_gsmr.txt] is incorrect, line 1. An error occurs, please check the options or data my inputfiles are two .txt file, SNP A1 A2 freq b se p N rs12238997 A G 0.1376 -0.076145 0.043735 0.081673 17810.9957384644 rs201234755 GAATA G 0.07145 -0.036143 0.03711 0.33009 31580.3769007307 rs72631875 G A 0.0349 0.059381 0.03662 0.1049 32660.9874529816 rs138660747 C A 0.007337 0.24607 0.09936 0.013267 28103.0501930502 rs116030099 T C 0.0872 -0.027646 0.030339 0.36216 32436.1767971955 rs148120343 T C 0.0573 -0.032283 0.036339 0.37433 41409.3605273293 rs58276399 T C 0.1427 -0.069503 0.041037 0.090324 18280.5334706142 rs61770163 A C 0.143 -0.028167 0.027007 0.29697 37641.0769200797 rs12131618 T C 0.08621 0.0035268 0.030258 0.90721 40845.7243413453 rs369030935 C T 0.009339 -0.072416 0.05677 0.20209 32436.1767971955 rs539235603 A C 0.03728 -0.055158 0.065242 0.39786 32436.1767971955 rs141242758 T C 0.1419 -0.069816 0.041104 0.089411 18280.5334706142 rs181876450 T C 0.01552 -0.017158 0.080181 0.83055 40396.604343302 rs140206562 G A 0.005789 -0.052814 0.074122 0.47614 25334.831992145 rs61770167 C T 0.01905 -0.0077167 0.1568 0.96075 21081.335538456 rs552659822 AC A 0.01335 0.096366 0.069976 0.16847 31580.3769007307 I do not know how would this happen and how to solve this!! hope someone can help me ,thank you so much!! — Reply to this email directly, view it on GitHub <#61>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACAVLS6GNGMSHGWOYGMM7L3YIJUHZAVCNFSM6AAAAABAL6LLOOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTCNZXHE2TENY . You are receiving this because you are subscribed to this thread.Message ID: @.>

When I use GCTA for GSMR, I encountered an error. Below is the complete error message.How can I deal with this problem?Thanks!

Reading PLINK FAM file from [./g1000eur/g1000eur.fam]. 503 individuals to be included from [./g1000eur/g1000eur.fam]. Reading PLINK BIM file from [./g1000eur/g1000eur.bim]. 8550156 SNPs to be included from [./g1000eur/g1000eur.bim].

Reading GWAS summary data for exposure(s) from [exposer.txt]. Reading GWAS summary data for outcome(s) from [outcome.txt]. 118829 genome-wide significant SNPs in common between the exposure(s) and the outcome(s). Error: negative phenotypic variance of trait inflamation. An error occurs, please check the options or data