geno_prep erro protection

jiang548 · May 11, 2022 · e877fa0 · e877fa0
1 parent f190fe2
commit e877fa0
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diff --git a/script/geno_prep/geno_prep.sh b/script/geno_prep/geno_prep.sh
@@ -1,3 +1,5 @@
+trap "exit -1" 10
+export job_id="$$"
 $SIGNET_SCRIPT_ROOT/geno_prep/plink.sh  && 
 $SIGNET_SCRIPT_ROOT/geno_prep/imputation.sh  
 $SIGNET_SCRIPT_ROOT/geno_prep/combine_geno.sh 
diff --git a/script/geno_prep/imputation.sh b/script/geno_prep/imputation.sh
@@ -83,3 +83,8 @@ done
 
 ## employ parallel computing for imputation 
 time ParaFly -c impute_params.txt -CPU $ncores
+if [[ $(wc -l < impute_params.txt) -ne $(wc -l < impute_params.txt.completed) ]];then
+echo -e "\nPlease note that some of the jobs are not finished !!! This could be a memeory allocation issue\n"
+kill -10 $job_id
+fi
+