-----------------------
Start of variable list:
-----------------------
Sample_ID:
Con_WT4
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 13:20:18 EDT 2019
Running on node : scc-kb7
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5610223
Current job name : Step_06_Con_WT4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5610223.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 613M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 13:20 .
drwxrwxrwt. 79 root   root      168K Apr 26 13:20 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 13:20 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 605M Apr 26 13:20 Con_WT4_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 26 13:20 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 26 13:20 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_WT4_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Con_WT4'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 613M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 13:20 .
drwxrwxrwt. 82 root   root      168K Apr 26 13:22 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 13:26 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 605M Apr 26 13:20 Con_WT4_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 26 13:20 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 26 13:20 rRNA_intervalList_sorted
==========================================================
Finished on : Fri Apr 26 13:26:41 EDT 2019
0 hours, 6 minutes and 23 seconds elapsed.
==========================================================