-----------------------
Start of variable list:
-----------------------
Sample_ID:
AB1_M1
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 00:31:32 EDT 2017
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/CMC/Scripts/06_CollectRnaSeqMetrics
Current job ID : 9288043
Current job name : Step_06_AB1_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9288043.1.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 13 00:33 .
drwxrwxrwt. 174 root   root       108K Jun 13 00:31 ..
-rw-r--r--    1 kkarri montilab-p 2.3G Jun 13 00:32 AB1_M1_primary_unique.bam
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 13 00:33 CollectRnaSeqMetrics
-rwxr-xr-x    1 kkarri montilab-p 4.4M Jun 13 00:33 genes_refFlat
-rwx------    1 kkarri montilab-p  55K Jun 13 00:33 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_M1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/AB1_M1'_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 13 00:33 .
drwxrwxrwt. 174 root   root       108K Jun 13 00:31 ..
-rw-r--r--    1 kkarri montilab-p 2.3G Jun 13 00:32 AB1_M1_primary_unique.bam
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 13 00:33 CollectRnaSeqMetrics
-rwxr-xr-x    1 kkarri montilab-p 4.4M Jun 13 00:33 genes_refFlat
-rwx------    1 kkarri montilab-p  55K Jun 13 00:33 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Jun 13 00:33:26 EDT 2017
0 hours, 1 minutes and 55 seconds elapsed.
==========================================================