jonic
New Member
Posts: 7 
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Post by jonic on May 21, 2020 11:12:55 GMT
Hi,
When I specify e.g. --gsmr-ld-fdr 0.05, GCTA returns "--gsmr-ld-fdr 0" as the accepted option. This seems to be consistent for multiple specified values from 0.01-0.99, although --gsmr-ld-fdr 1 returns "--gsmr-ld-fdr 1".
I do not know if this is a bug just in the accepted option or whether this is altering the analysis at this point.
Thanks,
Joni
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ax
New Member
Posts: 27
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Post by ax on Jun 22, 2020 5:41:40 GMT
Hi Jonic,
Could you show the full log history and also your gsmr command line?
Cheers,
Angli
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jonic
New Member
Posts: 7
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Post by jonic on Jul 1, 2020 8:26:57 GMT
Command line:
./gcta_1.93.2beta/gcta64 \
--bfile Imputed_Genotypes/Whole_Genome_Clean \
--gsmr-file BMI2018.gsmr MD.gsmr \
--gsmr-direction 2 \
--effect-plot \
--ref-ld-chr ldscore/eur_w_ld_chr/ \
--w-ld-chr ldscore/eur_w_ld_chr/ \
--out MD_BMI_Result \
--clump-r2 0.05 \
--gwas-thresh 5e-8 \
--heidi-thresh 0.01 \
--gsmr-snp 10 \
--gsmr-ld-fdr 0.05 \
--thread-num 2
Header of log file, showing reported error:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.93.2 beta Linux
* (C) 2010-present, Jian Yang, The University of Queensland
* Please report bugs to Jian Yang <jian.yang.qt@gmail.com>
*******************************************************************
Analysis started at 09:23:14 BST on Wed Jul 01 2020.
Hostname: login3.pri.rosalind2.alces.network
Accepted options:
--bfile Imputed_Genotypes/Whole_Genome_Clean
--gsmr-file BMI2018.gsmr MD.gsmr
--gsmr-direction 2
--effect-plot
--ref-ld-chr ldscore/eur_w_ld_chr/
--w-ld-chr ldscore/eur_w_ld_chr/
--out MD_BMI_Result
--clump-r2 0.05
--gwas-thresh 5e-08
--heidi-thresh 0.01
--gsmr-snp-min 10
--gsmr-ld-fdr 0
--thread-num 2
Warning: --gsmr-snp has been superseded by --gsmr-snp-min.
Note the reported --gsmr-ld-fdr in the log file
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