try to fix run kaiju

scripts/run_all_part2.sh

@@ -11,7 +11,9 @@
 ## Skipping this script
 #./compare_components.sh
 
-./unpack_run_kaiju.sh
+./unpack_kaiju.sh
+
+./run_kaiju.sh
 
 ./kaiju_to_korona.sh
 

scripts/run_kaiju.sh

@@ -6,19 +6,20 @@ do
     base=$(basename $filename _1.trim2.fq.gz)
     echo $base
 
-    echo "I'm gonna run Docker now: ${base}"
-    #docker run -v ${PWD}:/data quay.io/biocontainers/kaiju:1.5.0--pl5.22.0_0 kaiju \ 
-    #    -x \
-    #    -v \
-    #    -t \
-    #    /data/kaijudb/nodes.dmp \ 
-    #    -f /data/kaijudb/kaiju_db_nr_euk.fmi \
-    #    -i /data/${base}_1.trim2.fq.gz \ 
-    #    -j /data/${base}_2.trim2.fq.gz \
-    #    -o /data/${base}.kaiju_output.trim2.out \ 
-    #    -z 4
-done
+    docker run -v ${PWD}:/data quay.io/biocontainers/kaiju:1.5.0--pl5.22.0_0 kaiju \
+        -x \
+        -v \
+        -t /data/kaijudb/nodes.dmp \
+        -f /data/kaijudb/kaiju_db_nr_euk.fmi \
+        -i /data/${base}_1.trim2.fq.gz \
+        -j /data/${base}_2.trim2.fq.gz \
+        -z 4
+
+        #-o /data/${base}.kaiju_output.trim2.out \
 
+    exit 1;
+
+done
 
 for filename in *1.trim30.fq.gz
 do
@@ -26,16 +27,14 @@ do
     base=$(basename $filename _1.trim30.fq.gz)
     echo $base
 
-    echo "I'm gonna run Docker now: ${base}"
-    #docker run -v ${PWD}:/data quay.io/biocontainers/kaiju:1.5.0--pl5.22.0_0 kaiju \
-    #    -x \
-    #    -v \
-    #    -t \
-    #        /data/kaijudb/nodes.dmp \
-    #    -f data/kaijudb/kaiju_db_nr_euk.fmi \ 
-    #    -i /data/${base}_1.trim30.fq.gz -j \
-    #        /data/${base}_2.trim30.fq.gz \
-    #    -o /data/${base}.kaiju_output.trim30.out \
-    #    -z 4
+    docker run -v ${PWD}:/data quay.io/biocontainers/kaiju:1.5.0--pl5.22.0_0 kaiju \
+        -x \
+        -v \
+        -t /data/kaijudb/nodes.dmp \
+        -f data/kaijudb/kaiju_db_nr_euk.fmi \
+        -i /data/${base}_1.trim30.fq.gz \
+        -j /data/${base}_2.trim30.fq.gz \
+        -o /data/${base}.kaiju_output.trim30.out \
+        -z 4
 done