Open wilsonava opened 1 year ago
Input:
genelist=" "
for i in {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,22,X}; do
run_rvtest_wes="wget https://github.com/zhanxw/rvtests/releases/download/v2.1.0/rvtests_linux64.tar.gz; \ tar zxvf rvtests_linux64.tar.gz; \ ./executable/rvtest --inVcf WES_c${i}_qc_pass.vcf.gz --freqUpper 0.05 \ --pheno m2_pheno_bur_ord.txt --pheno-name copd_only --out M2_c${i}_rvtest_gs5 \ --covar m2_cov_bur_ord.txt --covar-name age,sex,py_rec,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 \ --geneFile refFlat_c${i}.txt.gz ${genelist} --burden cmc --kernel skat,skato ; \ rm rvtests_linux64.tar.gz; rm -rf ex*; rm -rf READM* " dx run swiss-army-knife -iin="${data_file_dir}/WES_c${i}_qc_pass.vcf.gz" \ -iin="${data_file_dir}/WES_c${i}_qc_pass.vcf.gz.tbi" \ -iin="${txt_file_dir}/m2_pheno_bur_ord.txt" \ -iin="${txt_file_dir}/m2_cov_bur_ord.txt" \ -iin="${txt_file_dir}/reflat38/refFlat_c${i}.txt.gz" \ -icmd="${run_rvtest_wes}" --tag="Step2-rvt" --instance-type "mem1_ssd1_v2_x36"\ --destination="${project}:/Data/M2_burden/" --brief --yes
done
Below is the output for my log file, I copied the end of the log where all information pertaining to the error is listed:
CPU: 3% (36 cores) Memory: 34825/70235MB Storage: 5/841GB Net: 0↓/0↑MBpsFeb 17, 2023 7:38 PM CPU: 3% (36 cores) Memory: 21833/70235MB Storage: 5/841GB Net: 0↓/0↑MBpsFeb 17, 2023 7:48 PM terminate called after throwing an instance of 'std::bad_alloc'Feb 17, 2023 7:57 PM Thank you for using rvtests (version: 20190205, git: c86e589efef15382603300dc7f4c3394c82d69b8) what(): std::bad_alloc For documentations, refer to http://zhanxw.github.io/rvtests/ For questions and comments, plase send to Xiaowei Zhan zhanxw@umich.edu For bugs and feature requests, please submit at: https://github.com/zhanxw/rvtests/issues /home/dnanexus/job-GPgv8Y0J06vyBqBFqYx97G5J.code.sh: line 69: 7425 Aborted ./executable/rvtest --inVcf WES_c2_qc_pass.vcf.gz --freqUpper 0.05 --pheno m2_pheno_bur_ord.txt --pheno-name copd_only --out M2_c2_rvtest_gs5 --covar m2_cov_bur_ord.txt --covar-name age,sex,py_rec,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 --geneFile refFlat_c2.txt.gz --burden cmc --kernel skat,skato
Input:
genelist=" "
loop over all genes
for i in {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,22,X}; do
done
Below is the output for my log file, I copied the end of the log where all information pertaining to the error is listed:
CPU: 3% (36 cores) Memory: 34825/70235MB Storage: 5/841GB Net: 0↓/0↑MBpsFeb 17, 2023 7:38 PM CPU: 3% (36 cores) Memory: 21833/70235MB Storage: 5/841GB Net: 0↓/0↑MBpsFeb 17, 2023 7:48 PM terminate called after throwing an instance of 'std::bad_alloc'Feb 17, 2023 7:57 PM Thank you for using rvtests (version: 20190205, git: c86e589efef15382603300dc7f4c3394c82d69b8) what(): std::bad_alloc For documentations, refer to http://zhanxw.github.io/rvtests/ For questions and comments, plase send to Xiaowei Zhan zhanxw@umich.edu For bugs and feature requests, please submit at: https://github.com/zhanxw/rvtests/issues /home/dnanexus/job-GPgv8Y0J06vyBqBFqYx97G5J.code.sh: line 69: 7425 Aborted
./executable/rvtest --inVcf WES_c2_qc_pass.vcf.gz --freqUpper 0.05 --pheno m2_pheno_bur_ord.txt --pheno-name copd_only --out M2_c2_rvtest_gs5 --covar m2_cov_bur_ord.txt --covar-name age,sex,py_rec,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 --geneFile refFlat_c2.txt.gz --burden cmc --kernel skat,skato