So, I can't manually handle them.

So, add 

system qq[ 
cat $outputdir/$date_seq_comparison_summary.csv 
    >> $outputdir/$date_seq_comparison_log.log 
];
system qq[ rm $outputdir/$date_seq_comparison_summary.csv ];

[download]

or the equivalent formulation for your OS, to the end of the script, or to the command file you submit to cron.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

In reply to Re^3: Changing the order of printing by BrowserUk
in thread Changing the order of printing by Anonymous Monk

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