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POCommand arguments being interpreted as command file name
 

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  1. POCommand arguments being interpreted as command file name
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    <p>I'm trying to create a bash script that builds up a command to execute (that includes arguments). The name of the command executable is ms (which lives in the ms directory) and it takes a bunch of parameters that I compute and store in a string. When it comes time to execute the command, I try:</p> <pre><code>GENETREES=$(../ms/${x:1}) </code></pre> <p>but am getting the error message:</p> <pre><code>./simulate.sh: line 21: ../ms/ms 6 1 -T -I 6 1 1 1 1 1 1 -ej 0.059851352500000010170566611122922040522098541259765625 1 4 -es 0.059851352500000010170566611122922040522098541259765625 4 0.3457841801761454281205487859551794826984405517578125 -ej 0.059851352500000010170566611122922040522098541259765625 2 3 -es 0.059851352500000010170566611122922040522098541259765625 3 0.54870128110803395582451003065216355025768280029296875 -ej 0.0897770262499999471828004971030168235301971435546875 7 9 -es 0.089777026250000002693951728360843844711780548095703125 3 0.8097582153199012200417428175569511950016021728515625 -ej 0.119702699999999995217336845598765648901462554931640625 3 4 -ej 0.125827642499999947656164067666395567357540130615234375 9 10 -es 0.1258276425000000031673152989242225885391235351562500 4 0.28069295861466903030390085405088029801845550537109375 -ej 0.13195258499999995560614252099185250699520111083984375 8 10 -ej 0.1817980399999999663318561715641408227384090423583984375 6 5 -ej 0.2525933399999999717788767839010688476264476776123046875 10 4 -ej 0.41145434999999996872332985731191001832485198974609375 4 5 : File name too long </code></pre> <p>I think bash thinks that I intended all those command parameters to be a part of the executable name. But this is not my intent.</p> <p>What am I doing wrong?</p> <p>Thanks.</p> <p><em>Update - More info requested on how x is constructed</em></p> <pre><code>MSOUT=$(java -jar ./NetworkSearchGen.jar ms $3 $TRUENETWORK $4) OIFS=$IFS IFS='}' first="true" for x in $MSOUT do if [ $first = "true" ]; then echo "$x" else GENETREES=$(../ms/${x:1}) fi first="false" done </code></pre>
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    1. USDejas
    1. USDejas
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    1. COCan you show how you populate `$x`?
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      1. USchoroba
    2. COIt mostly comes from the output of a java command. I'll make an edit to update and show more.
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      1. USDejas
 

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