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iotop let you monitor the I/O consumption of each running process : sudo apt-get install iotop sudo iotop -a (-a option is to display accumulated I/O instead of bandwidth) For example, if I want to monitor Firefox I will run : sudo iotop -ap 3120 (Where 3120 is the PID of Firefox)


I think you are looking for a simple iterative solution like this: #!/bin/sh ( tmpfile=/tmp/result read firstfilename cat "$firstfilename" >$tmpfile.in while read filename do cgatools join \ --beta \ --input $tmpfile.in "$filename" \ --match <specification> \ --overlap <overlap_spec> \ ...


Assuming that your file contains a single file per line, you can do this ugly thing: tool="cgatools join --beta --match <specification> --overlap <overlap_spec> --select <output_fields> --always-dump --output-mode compact --input" { read -r filename cmd="cat \"$filename\"" while read -r filename; do cmd+=" | $tool ...

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