Runtime Bug Chromosome 2 UKB WES

[wilsonava]

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

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: c86e589)
what(): std::bad_alloc
For documentations, refer to http://zhanxw.github.io/rvtests/
For questions and comments, plase send to Xiaowei Zhan [email protected]
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