There is a very useful post to find and overcome the line length limitations. As written there are two solutions:

• using the find or xargs command
• using a loop

For instance I have >10000 files to concatenate and I cannot use

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cat Smp*counts.txt > bigFile.txt
rm -f Smp*counts.txt

Instead I can use

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find . -name "Smp*-bTcounts.txt" -exec cat '{}' ';'|sort >bT-colCounts.txt
find . -name "Smp*-bTcounts.txt" -delete
# or 
echo Smp*-bTcounts.txt | xargs /bin/rm -f