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我将一个批处理文件发送到一个 slurm 集群，该集群 awks 相同 infile 的字段并附加到输出。前几行有效，但随后突然死亡。它在第二次回响之前就死了。如果有人会调试或向我展示更好的脚本会很好，但我想知道为什么（或是否）bash 文件在一遍又一遍地执行相同的工作时会崩溃。

#!/bin/bash
#SBATCH -A b2014091
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 23:00:00
#SBATCH -J sbatch

#input was MK...vcf

input=$1

output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="1/1") && (substr($15,1,3)=="1/1") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="0/0") && (substr($15,1,3)=="0/0") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="1/1") && (substr($15,1,3)=="./.") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="./.") && (substr($15,1,3)=="1/1") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="0/0") && (substr($15,1,3)=="./.") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="./.") && (substr($15,1,3)=="0/0") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt

错误信息：

slurmstepd：get_exit_code 任务 0 因信号而死

字段 12-15 的示例：

1/1:0,38:38:99:1149,114,0       1/1:0,39:39:99:1161,117,0       1/1:0,46:46:99:1383,138,0       0/1:21,18:39:99:413,0,524
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1 回答 1

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也许你可以改变这一切：

input=$1

output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="1/1") && (substr($15,1,3)=="1/1") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="0/0") && (substr($15,1,3)=="0/0") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="1/1") && (substr($15,1,3)=="./.") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="./.") && (substr($15,1,3)=="1/1") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="0/0") && (substr($15,1,3)=="./.") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt
output=$(grep -v '^#' ${input} | awk '(substr($12,1,3)=="./.") && (substr($15,1,3)=="0/0") {print $0}')
echo "$output\n" >> /proj/b2014091/nobackup/potHomoF1.txt

为此？

awk '!/^#/ && substr($12,1,3)~/[01.]\/[01.]/ && substr($15,1,3)~/[01.]\/[01.]/' <<< $1 > /proj/b2014091/nobackup/potHomoF1.txt

试试这两个：

awk '{a=substr($12,1,3);b=substr($15,1,3)} !/^#/ && ((a=="1/1" && b=="1/1") || (a=="0/0" && b=="0/0") || (a=="1/1" && b=="./.") || (a=="./." && b=="1/1") || (a=="0/0" && b=="./.") || (a=="./." && b=="0/0"))' $1 > /proj/b2014091/nobackup/potHomoF1.txt

或者

input=$1
awk '{a=substr($12,1,3);b=substr($15,1,3)} !/^#/ && ((a=="1/1" && b=="1/1") || (a=="0/0" && b=="0/0") || (a=="1/1" && b=="./.") || (a=="./." && b=="1/1") || (a=="0/0" && b=="./.") || (a=="./." && b=="0/0"))' ${input} > /proj/b2014091/nobackup/potHomoF1.txt
于 2014-09-08T10:36:42.497 回答