-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
NONE
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jun 17 04:53:48 EDT 2017
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/06_CollectRnaSeqMetrics
Current job ID : 9394855
Current job name : Step_06_PB_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9394855.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.5G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 17 04:54 .
drwxrwxrwt. 135 root   root       268K Jun 17 04:54 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 04:54 CollectRnaSeqMetrics
-rw-r--r--    1 kkarri montilab-p 2.4G Jun 17 04:54 PB_M3_primary_unique.bam
-rwxr-xr-x    1 kkarri montilab-p 4.4M Jun 17 04:54 genes_refFlat
-rwx------    1 kkarri montilab-p  55K Jun 17 04:54 rRNA_intervalList_sorted

Starting to run my commands


Starting CollectRnaSeqMetrics command

Printing command:
CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND=NONE INPUT=PB_M3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/PB_M3'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 2.5G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 17 04:54 .
drwxrwxrwt. 135 root   root       268K Jun 17 04:54 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 04:54 CollectRnaSeqMetrics
-rw-r--r--    1 kkarri montilab-p 2.4G Jun 17 04:54 PB_M3_primary_unique.bam
-rwxr-xr-x    1 kkarri montilab-p 4.4M Jun 17 04:54 genes_refFlat
-rwx------    1 kkarri montilab-p  55K Jun 17 04:54 rRNA_intervalList_sorted
==========================================================
Finished on : Sat Jun 17 04:54:13 EDT 2017
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================