293 Killed error when running GCTA in WSL

Question

[itsmesmb]

Dear all, I'm running GWAS in GTCA with the parameter shown below. However, I end up having an error, what is the source of this error and how to handle it?

Accepted options:
--mlma-loco
--bfile data_qc_filtered_maf_excluded
--pheno int_phenotype.txt
--covar gender_covariate.txt
--qcovar age_pcs_q_covariate.txt
--out GCTA_results
--thread-num 16

Note: the program will be running on 16 threads.

Reading PLINK FAM file from [data_qc_filtered_maf_excluded.fam].
1890 individuals to be included from [data_qc_filtered_maf_excluded.fam].
Reading PLINK BIM file from [data_qc_filtered_maf_excluded.bim].
14442844 SNPs to be included from [data_qc_filtered_maf_excluded.bim].
gcta_analysis_v2.sh: **line 26:   273 Killed**                  gcta64 --mlma-loco --bfile data_qc_filtered_maf_excluded --pheno int_phenotype.txt --covar gender_covariate.txt --qcovar age_pcs_q_covariate.txt --out GCTA_results --thread-num 16
head: cannot open 'GCTA_results' for reading: No such file or directory
awk: fatal: cannot open file `GCTA_results' for reading: No such file or directory
head: cannot open 'GCTA_results' for reading: No such file or directory
awk: fatal: cannot open file `GCTA_results' for reading: No such file or directory.

Even when I change the number of threads (10 to 8) I still get the same error (below).

Accepted options:
--mlma-loco
--bfile data_qc_filtered_maf_excluded
--pheno int_phenotype.txt
--covar gender_covariate.txt
--qcovar age_pcs_q_covariate.txt
--out GCTA_results
--thread-num 10

Note: the program will be running on 10 threads.

Reading PLINK FAM file from data_qc_filtered_maf_excluded.fam].
1890 individuals to be included from [data_qc_filtered_maf_excluded.fam].
Reading PLINK BIM file from [data_qc_filtered_maf_excluded.bim].
14442844 SNPs to be included from [data_qc_filtered_maf_excluded.bim].
gcta_analysis_v2.sh: **line 26:   293 Killed**                  gcta64 --mlma-loco --bfile data_qc_filtered_maf_excluded --pheno int_phenotype.txt --covar gender_covariate.txt --qcovar age_pcs_q_covariate.txt --out GCTA_results --thread-num 10
head: cannot open 'GCTA_results' for reading: No such file or directory
awk: fatal: cannot open file `GCTA_results' for reading: No such file or directory
head: cannot open 'GCTA_results' for reading: No such file or directory
awk: fatal: cannot open file `GCTA_results' for reading: No such file or directory

Thank you very much in advance

Answer 1

[Mensur Dlakic]

The thing with error messages is to read everything that is on the screen. In your case the error seems to be very clear, and it has nothing to do with a number of threads.

Cannot open 'GCTA_results' for reading: No such file or directory awk: fatal: cannot open file GCTA_results' for reading: No such file or directory head: cannot open 'GCTA_results' for reading: No such file or directory awk: fatal: cannot open file GCTA_results' for reading: No such file or directory

Chances are you are running this in a directory where you don't have writing permissions. Maybe instead of -out GCTA_results try -out $HOME/GCTA_results, or give a full path to a directory where you have reading/writing access.

[itsmesmb]

Thank you very much for your comment. I appreciate your response. I have tried just the way you instructed by specifying the out directory.

OUTPUT_DIR=/mnt/c/Users/main_data/Documents/genome_analyis/scd

end of path specification

gcta64 --mlma-loco --bfile data_qc_filtered_maf_excluded --pheno int_phenotype.txt --covar gender_covariate.txt --qcovar age_pcs_q_covariate.txt --out ${OUT_PUT}/GCTA_results --thread-num 10 ${OUT_PUT>

This is what I get.

Accepted options: --mlma-loco --bfile data_qc_filtered_maf_excluded --pheno int_phenotype.txt --covar gender_covariate.txt --qcovar age_10pcs_q_covariate.txt --out /mnt/c/Users/main_data/Documents/genome_analyis/scd/GCTA_results --thread-num 10

Note: the program will be running on 10 threads.

Reading PLINK FAM file from [data_qc_filtered_maf_excluded.fam]. 1890 individuals to be included from [data_qc_filtered_maf_excluded.fam]. Reading PLINK BIM file from [data_qc_filtered_maf_excluded.bim]. 14442844 SNPs to be included from [data_qc_filtered_maf_excluded.bim]. gcta_analysis_v2.sh: line 30: 1041 Killed gcta64 --mlma-loco --bfile data_qc_filtered_maf_excluded --pheno int_phenotype.txt --covar gender_covariate.txt --qcovar age_10pcs_q_covariate.txt --out ${OUTPUT_DIR}/GCTA_results --thread-num 10 Thank you

[Mensur Dlakic]

What happened to following my advice to read a complete error message that is on the screen? Do you want me to read it for you again and highlight the relevant part?