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genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association
https://github.com/genetics-statistics/GEMMA
GNU General Public License v3.0
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error writing file #213

Closed avdanurag closed 4 years ago

avdanurag commented 4 years ago

I am getting error while generating relatedness matrix in GEMMA, which is required for GMMAT. My command is as follows:

dell@dell-Precision-T3610:~/Downloads/software$ ./gemma-0.98.1 --bfile /home/dell/Documents/Rishi/Chickpea_Genome_data/LD_block/Genotype_only_in_chr/GMMAT/GRM_file/Geno2 -gk 1 -o /home/dell/Documents/Rishi/Chickpea_Genome_data/LD_block/Genotype_only_in_chr/GMMAT/GRM_file/Geno2_g.gemma GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 Reading Files ...

number of total individuals = 217

number of analyzed individuals = 217

number of covariates = 1

number of phenotypes = 1

number of total SNPs/var = 431414

number of analyzed SNPs = 292518

Calculating Relatedness Matrix ... ================================================== 100% error writing file: ./output///home/dell/Documents/Rishi/Chickpea_Genome_data/LD_block/Genotype_only_in_chr/GMMAT/GRM_file/Geno2_g.gemma.cXX.txt error writing log file: ./output///home/dell/Documents/Rishi/Chickpea_Genome_data/LD_block/Genotype_only_in_chr/GMMAT/GRM_file/Geno2_g.gemma.log.txt

xiangzhou commented 4 years ago

This is usually a directory permission issue. Make sure you have setup permission to allow you to write files under this directory.

avdanurag commented 4 years ago

Thanks for your reply.

On Thu, Jan 23, 2020 at 8:07 PM xiangzhou notifications@github.com wrote:

This is usually a directory permission issue. Make sure you have setup permission to allow you to write files under this directory.

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