-----------------------
Start of variable list:
-----------------------
Sample_ID:
AB1_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
NONE
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Jun 13 00:31:18 EDT 2017
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/06_CollectRnaSeqMetrics
Current job ID : 9288045
Current job name : Step_06_AB1_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9288045.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.7G
drwxr-xr-x  3 kkarri montilab-p 4.0K Jun 13 00:31 .
drwxrwxrwt. 5 root   root        36K Jun 13 00:31 ..
-rw-r--r--  1 kkarri montilab-p 1.7G Jun 13 00:31 AB1_M3_primary_unique.bam
drwxr-xr-x  2 kkarri montilab-p 4.0K Jun 13 00:31 CollectRnaSeqMetrics
-rwxr-xr-x  1 kkarri montilab-p 4.4M Jun 13 00:31 genes_refFlat
-rwx------  1 kkarri montilab-p  55K Jun 13 00:31 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=AB1_M3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/AB1_M3'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 1.7G
drwxr-xr-x  3 kkarri montilab-p 4.0K Jun 13 00:31 .
drwxrwxrwt. 5 root   root        36K Jun 13 00:31 ..
-rw-r--r--  1 kkarri montilab-p 1.7G Jun 13 00:31 AB1_M3_primary_unique.bam
drwxr-xr-x  2 kkarri montilab-p 4.0K Jun 13 00:31 CollectRnaSeqMetrics
-rwxr-xr-x  1 kkarri montilab-p 4.4M Jun 13 00:31 genes_refFlat
-rwx------  1 kkarri montilab-p  55K Jun 13 00:31 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Jun 13 00:31:44 EDT 2017
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================