-----------------------
Start of variable list:
-----------------------
Sample_ID:
LERKO_male1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 04:22:44 EDT 2019
Running on node : scc-ka2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5781714
Current job name : Step_06_LERKO_male1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5781714.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.1G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:27 .
drwxrwxrwt. 60 root   root      116K Apr 30 04:26 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:27 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 2.1G Apr 30 04:26 LERKO_male1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 30 04:26 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=LERKO_male1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LERKO_male1'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 2.1G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:27 .
drwxrwxrwt. 58 root   root      116K Apr 30 04:33 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:37 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 2.1G Apr 30 04:26 LERKO_male1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 30 04:26 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 30 04:27 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Apr 30 04:37:07 EDT 2019
0 hours, 14 minutes and 23 seconds elapsed.
==========================================================