Post by forevertl on Oct 17, 2019 14:54:26 GMT
Hi
I am running GCTA code as below and it seems the mlma model can be run but when it write results to output, it failed. I am very confused because I run the code for each chromosome and all chromosomes work except this one. Is there any suggestion on how to fix it? Thanks a lot in advance!
code:
for chr in $(seq 4 4); do gcta64 --mlma --bfile chr${chr}_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip --grm ../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet --pheno ../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt --mpheno 1 --qcovar ../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt --thread-num 15 --out chr${chr}_PC1& done;
log information:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.25.2
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Wed Oct 16 23:45:54 2019
Options:
--mlma
--bfile chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip
--grm ../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet
--pheno ../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt
--mpheno 1
--qcovar ../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt
--thread-num 15
--out chr4_PC1
Note: the program will be running on 15 threads.
Reading PLINK FAM file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.fam].
3968 individuals to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.fam].
Reading PLINK BIM file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bim].
657004 SNPs to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bim].
Reading PLINK BED file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bed] in SNP-major format ...
Genotype data for 3968 individuals and 657004 SNPs to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bed].
Reading phenotypes from [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
There are 3 traits specified in the file [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
The 1th trait is included for analysis.
Non-missing phenotypes of 3968 individuals are included from [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
Reading quantitative covariates from [../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt].
3 quantitative covariate(s) of 3968 individuals read from [../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt].
Reading IDs of the GRM from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.id].
3968 IDs read from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.id].
Reading the GRM from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.bin].
Pairwise genetic relationships between 3968 individuals are included from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.bin].
3968 individuals are in common in these files.
3 quantitative variable(s) included as covariate(s).
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
3968 observations, 4 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 1.0252 1.05112
logL: -3378.29
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 -3377.32 0.83601 1.20658
2 -3370.02 0.44238 1.54363
3 -3363.86 0.44867 1.54174
4 -3363.82 0.45301 1.54044
5 -3363.81 0.46242 1.53763
6 -3363.80 0.46240 1.53768
7 -3363.80 0.46240 1.53768
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 657004 SNPs ...
Saving the results of the mixed linear model association analyses of 657004 SNPs to [chr4_PC1.mlma] ...
Can not open the file [chr4_PC1.mlma] to write.
Analysis finished: Thu Oct 17 01:29:02 2019
Computational time: 1:43:8
thanks,
Lin
I am running GCTA code as below and it seems the mlma model can be run but when it write results to output, it failed. I am very confused because I run the code for each chromosome and all chromosomes work except this one. Is there any suggestion on how to fix it? Thanks a lot in advance!
code:
for chr in $(seq 4 4); do gcta64 --mlma --bfile chr${chr}_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip --grm ../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet --pheno ../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt --mpheno 1 --qcovar ../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt --thread-num 15 --out chr${chr}_PC1& done;
log information:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.25.2
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Wed Oct 16 23:45:54 2019
Options:
--mlma
--bfile chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip
--grm ../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet
--pheno ../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt
--mpheno 1
--qcovar ../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt
--thread-num 15
--out chr4_PC1
Note: the program will be running on 15 threads.
Reading PLINK FAM file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.fam].
3968 individuals to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.fam].
Reading PLINK BIM file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bim].
657004 SNPs to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bim].
Reading PLINK BED file from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bed] in SNP-major format ...
Genotype data for 3968 individuals and 657004 SNPs to be included from [chr4_prev_cust_r2gtp3_mafp005_w_asmet_wodupsflip.bed].
Reading phenotypes from [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
There are 3 traits specified in the file [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
The 1th trait is included for analysis.
Non-missing phenotypes of 3968 individuals are included from [../../../previous_genome/geno_data/asmet_gwas_genodata/asmet_pc1pc2pc3.txt].
Reading quantitative covariates from [../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt].
3 quantitative covariate(s) of 3968 individuals read from [../../../previous_genome/geno_data/asmet_gwas_genodata/sexage_batch.txt].
Reading IDs of the GRM from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.id].
3968 IDs read from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.id].
Reading the GRM from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.bin].
Pairwise genetic relationships between 3968 individuals are included from [../../../previous_genome/geno_data/asmet_gwas_genodata/samples_w_asmet.grm.bin].
3968 individuals are in common in these files.
3 quantitative variable(s) included as covariate(s).
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
3968 observations, 4 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 1.0252 1.05112
logL: -3378.29
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 -3377.32 0.83601 1.20658
2 -3370.02 0.44238 1.54363
3 -3363.86 0.44867 1.54174
4 -3363.82 0.45301 1.54044
5 -3363.81 0.46242 1.53763
6 -3363.80 0.46240 1.53768
7 -3363.80 0.46240 1.53768
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 657004 SNPs ...
Saving the results of the mixed linear model association analyses of 657004 SNPs to [chr4_PC1.mlma] ...
Can not open the file [chr4_PC1.mlma] to write.
Analysis finished: Thu Oct 17 01:29:02 2019
Computational time: 1:43:8
thanks,
Lin