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I have written a bash script with has a python code embedded within it. What I did was read in the file and cut it with the below bash commands and then I exported it so that the python code could use it:

export BWA_compare=$(cut --output-delimiter='' -f1-3 ${BWA_AT}| sed 1d)

The problem is I get 

/bin/cut: Argument list too long
/bin/sed: Argument list too long

It works on smaller files. Is there a limit on how much you can export?

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  • The sed error doesn't make sense to me as the argument list contains just one element. – Hauke Laging Nov 1 '14 at 21:30
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There are limits for both the number of arguments and the combined length of the arguments. These are not uniform values but depend of the system.

Usually such problems are solved with xargs.

But it seems to me that you are using cut wrongly. cut expects only files are arguments. Is ${BWA_AT} a huge list of files? If it is the Python code then you need something like

echo "${BWA_AT}" | cut

If it really is a file list then you need something like

echo "${BWA_AT}" | xargs cut

with the needed xargs options depending on the separator.

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  • 1
    The limit is on the cumulative size of the arguments and environment passed to execve(2). There's also a limit on the size of single argument or env var string. For instance, after export "a=$(yes | head -c129k)", you won't be able to run any command on current versions of Linux. – Stéphane Chazelas Nov 1 '14 at 22:16
  • ${BWA_AT} is just the file location. I was thinking that by exporting all the data that cut has generated I would run into a limit which produced those two errors. – crysis405 Nov 4 '14 at 14:50

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