-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
SECOND_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:25:43 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/06_CollectRnaSeqMetrics
Current job ID : 473667
Current job name : Step_06_G160_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473667.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.1G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:25 .
drwxrwxrwt. 54 root   root    164K Aug 30 20:25 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:25 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 20:25 G160_M11_primary_unique.bam
-rwxr-xr-x   1 kkarri pulmseq 7.9M Aug 30 20:25 genes_refFlat
-rwxr-xr-x   1 kkarri pulmseq  52K Aug 30 20:25 rRNA_intervalList_sorted

Starting to run my commands


Starting CollectRnaSeqMetrics command

Printing command:
CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G160_M11_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G160_M11'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 1.1G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:25 .
drwxrwxrwt. 56 root   root    164K Aug 30 20:29 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:31 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 20:25 G160_M11_primary_unique.bam
-rwxr-xr-x   1 kkarri pulmseq 7.9M Aug 30 20:25 genes_refFlat
-rwxr-xr-x   1 kkarri pulmseq  52K Aug 30 20:25 rRNA_intervalList_sorted
==========================================================
Finished on : Wed Aug 30 20:31:13 EDT 2017
0 hours, 5 minutes and 30 seconds elapsed.
==========================================================