-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M12
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Dec 20 16:43:26 EST 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/06_CollectRnaSeqMetrics
Current job ID : 422884
Current job name : Step_06_G123_M12
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/422884.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Dec 20 16:43 .
drwxrwxrwt. 12 root   root       20K Dec 20 16:43 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 20 16:43 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 20 16:43 G123_M12_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Dec 20 16:43 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Dec 20 16:43 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_M12_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G123_M12'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Dec 20 16:43 .
drwxrwxrwt. 10 root   root       20K Dec 20 16:45 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 20 16:45 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 20 16:43 G123_M12_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Dec 20 16:43 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Dec 20 16:43 rRNA_intervalList_sorted
==========================================================
Finished on : Thu Dec 20 16:45:52 EST 2018
0 hours, 2 minutes and 26 seconds elapsed.
==========================================================