-----------------------
Start of variable list:
-----------------------
Sample_ID:
C_IP1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
NONE
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 06:17:14 EDT 2017
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/06_CollectRnaSeqMetrics
Current job ID : 9332906
Current job name : Step_06_C_IP1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9332906.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:17 .
drwxrwxrwt. 22 root   root        40K Jun 15 06:17 ..
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:17 C_IP1_primary_unique.bam
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:17 CollectRnaSeqMetrics
-rwxr-xr-x   1 kkarri montilab-p 4.4M Jun 15 06:17 genes_refFlat
-rwx------   1 kkarri montilab-p  55K Jun 15 06:17 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=C_IP1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/C_IP1'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:17 .
drwxrwxrwt. 22 root   root        40K Jun 15 06:17 ..
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:17 C_IP1_primary_unique.bam
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:17 CollectRnaSeqMetrics
-rwxr-xr-x   1 kkarri montilab-p 4.4M Jun 15 06:17 genes_refFlat
-rwx------   1 kkarri montilab-p  55K Jun 15 06:17 rRNA_intervalList_sorted
==========================================================
Finished on : Thu Jun 15 06:17:23 EDT 2017
0 hours, 0 minutes and 9 seconds elapsed.
==========================================================