Post by mcanive on Mar 9, 2021 13:33:26 GMT
I´m trying to run a mlma analysis with gcta with the following command:
gcta64 --mlma --dosage-mach Chr1.mach.dose Chr1.mach.info --grm GRMcows_HD099 --pheno traitelisa_pcr_cultivo.phen --reml-no-lrt --out epc_chr1.gwas --thread-num 5
But I get the following "Segmentation fault" 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 14:24:54 CET on Tue Mar 09 2021.
Hostname: gt4.i2basque.es
Accepted options:
--mlma
--dosage-mach Chr1.mach.dose Chr1.mach.info
--grm GRMcows_HD099
--pheno traitelisa_pcr_cultivo.phen
--reml-no-lrt
--out epc_chr1.gwas
--thread-num 5
Note: the program will be running on 5 threads.
Reading map file of the imputed dosage data from [Chr1.mach.info].
2335707 SNPs to be included from [Chr1.mach.info].
Reading dosage data from [Chr1.mach.dose] in individual-major format (Note: may use huge RAM).
(Imputed dosage data for 984 individuals detected).
Imputed dosage data for 984 individuals are included from [Chr1.mach.dose].
Reading phenotypes from [traitelisa_pcr_cultivo.phen].
Non-missing phenotypes of 984 individuals are included from [traitelisa_pcr_cultivo.phen].
Reading IDs of the GRM from [GRMcows_HD099.grm.id].
984 IDs read from [GRMcows_HD099.grm.id].
Reading the GRM from [GRMcows_HD099.grm.bin].
GRM for 984 individuals are included from [GRMcows_HD099.grm.bin].
983 individuals are in common in these files.
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
983 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.0261599 0.0285509
logL: 939.559
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 942.80 0.01740 0.03515
2 951.27 0.01254 0.03935
3 954.76 0.00979 0.04197
4 956.15 0.00820 0.04361
5 956.71 0.00724 0.04466
6 956.94 0.00538 0.04678
7 957.10 0.00566 0.04656
8 957.11 0.00563 0.04658
9 957.11 0.00563 0.04658
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 2335707 SNPs ...
Segmentation fault (core dumped)
Any help is welcome!!!!
gcta64 --mlma --dosage-mach Chr1.mach.dose Chr1.mach.info --grm GRMcows_HD099 --pheno traitelisa_pcr_cultivo.phen --reml-no-lrt --out epc_chr1.gwas --thread-num 5
But I get the following "Segmentation fault" 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 14:24:54 CET on Tue Mar 09 2021.
Hostname: gt4.i2basque.es
Accepted options:
--mlma
--dosage-mach Chr1.mach.dose Chr1.mach.info
--grm GRMcows_HD099
--pheno traitelisa_pcr_cultivo.phen
--reml-no-lrt
--out epc_chr1.gwas
--thread-num 5
Note: the program will be running on 5 threads.
Reading map file of the imputed dosage data from [Chr1.mach.info].
2335707 SNPs to be included from [Chr1.mach.info].
Reading dosage data from [Chr1.mach.dose] in individual-major format (Note: may use huge RAM).
(Imputed dosage data for 984 individuals detected).
Imputed dosage data for 984 individuals are included from [Chr1.mach.dose].
Reading phenotypes from [traitelisa_pcr_cultivo.phen].
Non-missing phenotypes of 984 individuals are included from [traitelisa_pcr_cultivo.phen].
Reading IDs of the GRM from [GRMcows_HD099.grm.id].
984 IDs read from [GRMcows_HD099.grm.id].
Reading the GRM from [GRMcows_HD099.grm.bin].
GRM for 984 individuals are included from [GRMcows_HD099.grm.bin].
983 individuals are in common in these files.
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
983 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.0261599 0.0285509
logL: 939.559
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 942.80 0.01740 0.03515
2 951.27 0.01254 0.03935
3 954.76 0.00979 0.04197
4 956.15 0.00820 0.04361
5 956.71 0.00724 0.04466
6 956.94 0.00538 0.04678
7 957.10 0.00566 0.04656
8 957.11 0.00563 0.04658
9 957.11 0.00563 0.04658
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 2335707 SNPs ...
Segmentation fault (core dumped)
Any help is welcome!!!!