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    <p>Quote your arguments to <code>grep</code>:</p> <pre><code>grep "${trackid}" "${file}" &gt;&gt; "${outfile}" </code></pre> <p>This way if either <code>$trackid</code> or <code>$file</code> contains whitespace, it will be treated as one argument to <code>grep</code> rather than multiple arguments. Note that <a href="http://www.gnu.org/software/bash/manual/bashref.html#Appending-Redirected-Output" rel="nofollow"><code>&gt;&gt;</code> <em>appends</em></a> to the file "<code>${outfile}</code>" (rather than <a href="http://www.gnu.org/software/bash/manual/bashref.html#Redirecting-Output" rel="nofollow"><code>&gt;</code>, which would <em>truncate</em></a>).</p> <hr> <p>To remove the errant <code>\r</code>s from your input file, use <a href="http://www.manpagez.com/man/1/tr/" rel="nofollow"><strong>tr(1)</strong></a>:</p> <pre><code>tr -d '\r' &lt; "${track_path}" | while read trackid fileid # [...] done </code></pre> <p>I also recommend some sanity checking, such as:</p> <pre><code>if [[ -f "${file}" ]] ; then grep "${trackid}" "${file}" &gt; "${outfile}" else echo "Could not find file [${file}]. Skipping." fi </code></pre> <p>So your finished script <em>may</em> look like this:</p> <pre><code>#!/bin/bash #set -x track_list=Top95_HSI_forGrep.txt track_path="${1-/mnt/gpfs/backup/jpty_surge/kimberly/Launch_multiple_storms/input}/${track_list}" outname="${track_list}" output_directory="output" outfile="${output_directory}/${outname}" if [[ ! -f "${track_path}" ]]; then echo "Could not find track_path input [${track_path}]. Exiting" exit fi if [[ ! -d "${output_directory}" ]] ; then echo "Creating output directory [${output_directory}]..." mkdir -p "${output_directory}" fi IFS=$"," tr -d '\r' &lt; "${track_path}" | while read trackid fileid do file="input/track_param_${fileid}" if [[ -f "${file}" ]]; then grep "${trackid}" "${file}" &gt;&gt; "${outfile}" else echo "Could not find file [${file}]. Skipping." fi done </code></pre>
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    1. POusing grep in bash shell
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    1. COI tried this, and it says: `line 23: {output/Top95_HSI_forGrep.txt}: no such file or directory`
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    2. COExists and is writable. Can you think of anything else that might be going wrong here? Thanks!
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    3. COgrep "${trackid}" "${fileid}" >> "${outname}"
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