-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M19
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
SECOND_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 14:05:39 EDT 2018
Running on node : scc-ka7
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/06_CollectRnaSeqMetrics
Current job ID : 6184418
Current job name : Step_06_LZ_M19
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184418.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 303M
drwx------   3 kkarri waxmanlab 4.0K May 13 14:05 .
drwxrwxrwt. 47 root   root      340K May 13 14:05 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:05 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 295M May 13 14:05 LZ_M19_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M May 13 14:05 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K May 13 14:05 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=LZ_M19_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M19'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 303M
drwx------   3 kkarri waxmanlab 4.0K May 13 14:05 .
drwxrwxrwt. 48 root   root      340K May 13 14:06 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:06 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 295M May 13 14:05 LZ_M19_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M May 13 14:05 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K May 13 14:05 rRNA_intervalList_sorted
==========================================================
Finished on : Sun May 13 14:06:59 EDT 2018
0 hours, 1 minutes and 20 seconds elapsed.
==========================================================