If you have enough memory on your computer (> 250MB), try pre-allocating enough room in $_ to stop perl from reallocating the buffer and copying its content back and forward as it reads from the file: 
perl -ne 'BEGIN { $_ = '-' x (260 * 1024 * 1024 )} print and next if l
+ength($_)==1001; print STDERR $_' suspect.txt > goodrecs.txt 2> badre
+cs.txt

[download]
update: see my other comment below in this thread

In reply to Re: Thrashing on very large lines by salva
in thread Thrashing on very large lines by chr1so

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