fixing some mistakes

src/batch_processor.py

@@ -23,15 +23,19 @@ def process_file(accession, region):
         print("region - " + region)
         startTime = datetime.now()
 
+        os.system(' '.join(["df", "-T"]))
+        os.system(' '.join(["cat","/dfT.txt"]))
+        os.system(' '.join(["lsblk"]))
+        os.system(' '.join(["cat","/lsblk.txt"]))
+
+
         # go to /tmp (that's where local storage / nvme is)
         # go to /data instead (EBS)
         os.chdir("/mnt/serratus-data")
         os.system(' '.join(["pwd"]))
         
         # check free space
-        os.system(' '.join(["df", "-T"]))
         os.system(' '.join(["df", "-h","."]))
-        os.system(' '.join(["lsblk"]))
 
         # download reads from accession
         os.system('mkdir -p out/')

template/template.yaml

@@ -112,13 +112,13 @@ Resources:
         Vcpus: 4 
         Memory: 8000 # seems that 4000 wasn't enough for parallel-fastq-dump, 4 threads
         MountPoints:
-          - ContainerPath: "/serratus-data"
+          - ContainerPath: "/mnt/serratus-data"
             ReadOnly: false
             SourceVolume: serratus-data
         Volumes:
           - Name: serratus-data
             Host:
-              SourcePath: "/serratus-data"
+              SourcePath: "/mnt/serratus-data"
       RetryStrategy:
         Attempts: 1
   RayanSerratusDlBatchProcessingJobQueue:
@@ -182,7 +182,9 @@ Resources:
             mkdir /mnt/serratus-data
             echo -e "/dev/xvdh\t/mnt/serratus-data\text4\tdefaults\t0\t0" >> /etc/fstab
             mount -a
-            chmod 777 /serratus-data
+            lsblk > /lsblk.txt
+            df -T > /dfT.txt
+            chmod 777 /mnt/serratus-data
             service docker restart 
 
             --==MYBOUNDARY==--