-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M10
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
SECOND_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Jul 15 18:08:36 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/06_CollectRnaSeqMetrics
Current job ID : 6944797
Current job name : Step_06_G167_M10
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944797.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 726M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:08 .
drwxrwxrwt. 116 root   root      116K Jul 15 18:08 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:08 CollectRnaSeqMetrics
-rw-r--r--    1 kkarri waxmanlab 718M Jul 15 18:08 G167_M10_primary_unique.bam
-rwxr-xr-x    1 kkarri waxmanlab 7.9M Jul 15 18:08 genes_refFlat
-rwxr-xr-x    1 kkarri waxmanlab  52K Jul 15 18:08 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=G167_M10_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G167_M10'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 726M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:08 .
drwxrwxrwt. 114 root   root      116K Jul 15 18:13 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:13 CollectRnaSeqMetrics
-rw-r--r--    1 kkarri waxmanlab 718M Jul 15 18:08 G167_M10_primary_unique.bam
-rwxr-xr-x    1 kkarri waxmanlab 7.9M Jul 15 18:08 genes_refFlat
-rwxr-xr-x    1 kkarri waxmanlab  52K Jul 15 18:08 rRNA_intervalList_sorted
==========================================================
Finished on : Sun Jul 15 18:13:22 EDT 2018
0 hours, 4 minutes and 46 seconds elapsed.
==========================================================