-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M5
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:46:48 EST 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/06_CollectRnaSeqMetrics
Current job ID : 364966
Current job name : Step_06_G123_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/364966.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec 18 18:47 .
drwxrwxrwt. 11 root   root       40K Dec 18 18:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 18 18:47 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec 18 18:47 G123_M5_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Dec 18 18:47 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Dec 18 18:47 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=G123_M5_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G123_M5'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec 18 18:47 .
drwxrwxrwt. 11 root   root       40K Dec 18 18:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 18 18:47 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec 18 18:47 G123_M5_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Dec 18 18:47 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Dec 18 18:47 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Dec 18 18:47:35 EST 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================