使用EagleC处理.mcool文件时遇/dev/tty设备错误求助

当前目录下存在多个多分辨率.mcool文件，使用以下EagleC脚本批量处理，计划将输出（含.stderr和.log文件）保存至./../EagleC_output目录，但执行时出现/dev/tty: No such device or address错误。

执行脚本 #

for mcool_file in *.mcool; do

  OUTPUT=$(echo $mcool_file | grep -oE "[A-Z0-9]*\.hg38" | cut -d '.' -f 1)

  cooler ls $mcool_file | grep -E '\/[1][0]{4}$|\/[5][0]{3,4}$' \
  | tr '\n' '\t' \
  | parallel --colsep '\t' --link -j16 \
  --eta --progress --bar --joblog $mcool_file'_parallel.log' \
  predictSV --hic-5k {1} --hic-10k {2} --hic-50k {3} \
  -O './../EagleC_output/'$OUTPUT -g hg38 --balance-type ICE --output-format full \
  --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999 2> $mcool_file'.stderr'
  # | tr -d "'"

done

错误回溯 #

sh: /dev/tty: No such device or address
0% 0:1=0s A001C007.hg38.nodups.pairs.mcool::/resolutions/5000 A001C007.hg38.nodush: /dev/tty: No such device or address
0% 0:1=0s A001C007.hg38.nodups.pairs.mcool::/resolutions/5000 A001C007.hg38.nodush: /dev/tty: No such device or address

单个.mcool文件的cooler ls结果 #

执行命令：

cooler ls ./../input/A001C007.hg38.nodups.pairs.mcool

输出：

./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/200
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/500
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/1000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/2000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/5000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/10000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/20000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/50000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/100000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/250000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/500000
./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/1000000
(EagleC) 

解决方案 #

1. 移除parallel的终端依赖参数 #

错误核心是parallel的--eta、--progress、--bar参数需要访问终端输出进度，但当前运行环境（如后台执行、非交互式shell）无可用终端。移除这些参数即可解决，同时优化脚本的可靠性：

for mcool_file in *.mcool; do
  # 确保输出目录存在，避免写入失败
  mkdir -p ./../EagleC_output

  # 更可靠地提取输出前缀，避免依赖grep正则的兼容性问题
  OUTPUT=$(basename "$mcool_file" .mcool | cut -d '.' -f 1)

  cooler ls "$mcool_file" | grep -E '\/(5000|10000|50000)$' \
  | tr '\n' '\t' \
  | parallel --colsep '\t' --link -j16 \
  --joblog "$mcool_file"_parallel.log \
  predictSV --hic-5k {1} --hic-10k {2} --hic-50k {3} \
  -O "./../EagleC_output/$OUTPUT" -g hg38 --balance-type ICE --output-format full \
  --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999 2> "$mcool_file".stderr
done

2. 强制parallel不使用终端（如需保留进度） #

如果需要保留进度显示，给parallel添加--no-tty参数，强制其不尝试访问终端设备：

for mcool_file in *.mcool; do
  mkdir -p ./../EagleC_output
  OUTPUT=$(basename "$mcool_file" .mcool | cut -d '.' -f 1)

  cooler ls "$mcool_file" | grep -E '\/(5000|10000|50000)$' \
  | tr '\n' '\t' \
  | parallel --colsep '\t' --link -j16 --no-tty \
  --eta --progress --bar --joblog "$mcool_file"_parallel.log \
  predictSV --hic-5k {1} --hic-10k {2} --hic-50k {3} \
  -O "./../EagleC_output/$OUTPUT" -g hg38 --balance-type ICE --output-format full \
  --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999 2> "$mcool_file".stderr
done

3. 排查predictSV的终端依赖 #

如果上述方法无效，检查predictSV是否存在未指定的交互式参数，确保所有必要参数都已明确设置，避免其尝试读取终端输入。

内容的提问来源于stack exchange，提问作者Anon