-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 04:24:36 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5781705
Current job name : Step_06_WT1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5781705.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 262M
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:27 .
drwxrwxrwt. 55 root   root       84K Apr 30 04:24 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:27 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 254M Apr 30 04:26 WT1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 30 04:27 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 30 04:27 rRNA_intervalList_sorted

Starting to run my commands


Starting CollectRnaSeqMetrics command

Printing command:
CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND=FIRST_READ_TRANSCRIPTION_STRAND INPUT=WT1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WT1'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 262M
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:27 .
drwxrwxrwt. 54 root   root       84K Apr 30 04:27 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:28 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 254M Apr 30 04:26 WT1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 30 04:27 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 30 04:27 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Apr 30 04:28:08 EDT 2019
0 hours, 3 minutes and 32 seconds elapsed.
==========================================================