Hi John,

thank you for advise, you are right. The tool was using

<command interpreter="bash">
seqclust-main.sh -s $input -m $mvstup -o $ovstup -d $repeatmasker -v
$archive -w $contigs -y $log -x pdffile.pdf -z RMSKtable -r $__root_dir__
-t $summary -u '$summary.extra_files_path' -p $paired -f $prefix -a
$sq_rename -l $overlap

I have removed extra_ and it starts to work.

Regards, Pavel
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