I was lazy and did not use a loop, but worked file by file...
		  		   
centrifuge -x /DKHA/swalt/bioDBs/centrifuge/dbs_v2018/nt -1 /DKHB/work/mojcaj/SxP_Centrifuge/WT5_1.fastq -2 /DKHB/work/mojcaj/SxP_Centrifuge/WT5_2.fastq -S /DKHB/work/mojcaj/SxP_Centrifuge/WT5_output_centrifuge.txt --report-file /DKHB/work/mojcaj/SxP_Centrifuge/WT5_output_report.txt -p 30

/usr/lib/centrifuge/centrifuge-kreport -x /DKHA/swalt/bioDBs/centrifuge/dbs_v2018/nt /DKHB/work/mojcaj/SxP_Centrifuge/WT5_output_centrifuge.txt > /DKHB/work/mojcaj/SxP_Centrifuge/WT5_kreport.txt