-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M21
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/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 15:06:49 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/06_CollectRnaSeqMetrics
Current job ID : 6178424
Current job name : Step_06_LZ_M21
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178424.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 348M
drwx------   3 kkarri waxmanlab 4.0K May 11 15:06 .
drwxrwxrwt. 36 root   root      168K May 11 15:06 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:06 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 339M May 11 15:06 LZ_M21_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M May 11 15:06 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K May 11 15:06 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_M21_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M21'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 348M
drwx------   3 kkarri waxmanlab 4.0K May 11 15:06 .
drwxrwxrwt. 37 root   root      168K May 11 15:06 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:08 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 339M May 11 15:06 LZ_M21_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M May 11 15:06 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K May 11 15:06 rRNA_intervalList_sorted
==========================================================
Finished on : Fri May 11 15:08:44 EDT 2018
0 hours, 1 minutes and 55 seconds elapsed.
==========================================================