Update kaiju

kaiju

 conda activate kaiju-1.7.3
-##TBD
+##for multiple files
+conda activate kaiju-1.7.2
+for i in {1..10}
+do
+kaiju -i *"$i"*R1*.fastq.gz -j *"$i"*R2*.fastq.gz -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -f /db/outils/kaiju-1.7.0/nr/kaiju_db_nr.fmi  -z 6 -o fraggenescan_"$i"_kaijuNR
+
+#add Taxon names
+addTaxonNames -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan_"$i"_kaijuNR -r superkingdom,genus,species -o kaiju_"$i"_names.out
+kaijuReport -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan_"$i"_kaijuNR -l superkingdom,phylum,class,family,genus -r genus -o kaiju.out.summary_"$i"_3.txt
+kaijuReport -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan.kaijuNR -p -r genus -o kaiju.out.summary_"$i"_4.txt
+done