-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 29 09:55:58 EDT 2019
Running on node : scc-kb3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5739034
Current job name : Step_06_WT2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5739034.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.5G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 09:58 .
drwxrwxrwt. 54 root   root      112K Apr 29 09:56 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 09:58 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 2.5G Apr 29 09:58 WT2_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 29 09:58 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 29 09:58 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=WT2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WT2'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 2.5G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 09:58 .
drwxrwxrwt. 54 root   root      112K Apr 29 09:56 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 10:06 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 2.5G Apr 29 09:58 WT2_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 29 09:58 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 29 09:58 rRNA_intervalList_sorted
==========================================================
Finished on : Mon Apr 29 10:06:13 EDT 2019
0 hours, 10 minutes and 15 seconds elapsed.
==========================================================