Gz file runs slower in make.contigs ? (vs. the non-gz version of the same data)

I happened to run both the compressed version (fastq.gz file) and non-compressed version (fastq file) of the same raw data with make.contigs. Although the results are exactly the same, the compressed gz version takes about 5.5 hrs vs 1.5 hrs of the non-compressed version.

Does anyone have similar experiences? I am running with mothur Linux v1.46

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