-----------------------
Start of variable list:
-----------------------
Sample_ID:
Con_WT1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Apr 26 13:20:19 EDT 2019
Running on node : scc-kb4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5610220
Current job name : Step_06_Con_WT1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5610220.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 662M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 13:24 .
drwxrwxrwt. 81 root   root      164K Apr 26 13:24 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 13:24 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 654M Apr 26 13:24 Con_WT1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 26 13:24 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 26 13:24 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=Con_WT1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Con_WT1'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 662M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 13:24 .
drwxrwxrwt. 79 root   root      164K Apr 26 13:28 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 13:28 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 654M Apr 26 13:24 Con_WT1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 26 13:24 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 26 13:24 rRNA_intervalList_sorted
==========================================================
Finished on : Fri Apr 26 13:28:49 EDT 2019
0 hours, 8 minutes and 30 seconds elapsed.
==========================================================