-----------------------
Start of variable list:
-----------------------
Sample_ID:
MANFHet_2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/GSE123116_fullpipeline_run
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/GSE123116_fullpipeline_run/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/GSE123116_fullpipeline_run/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Aug  1 06:13:15 EDT 2019
Running on node : scc-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/GSE123116_fullpipeline_run/Scripts/06_CollectRnaSeqMetrics
Current job ID : 8162078
Current job name : Step_06_MANFHet_2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8162078.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 3.3G
drwx------   3 kkarri waxmanlab 4.0K Aug  1 06:18 .
drwxrwxrwt. 27 root   root      4.0K Aug  1 06:14 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Aug  1 06:18 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 3.3G Aug  1 06:18 MANFHet_2_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Aug  1 06:18 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Aug  1 06:18 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=MANFHet_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/MANFHet_2'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 3.3G
drwx------   3 kkarri waxmanlab 4.0K Aug  1 06:18 .
drwxrwxrwt. 27 root   root      4.0K Aug  1 06:14 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Aug  1 06:18 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 3.3G Aug  1 06:18 MANFHet_2_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Aug  1 06:18 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Aug  1 06:18 rRNA_intervalList_sorted
==========================================================
Finished on : Thu Aug  1 06:19:53 EDT 2019
0 hours, 6 minutes and 40 seconds elapsed.
==========================================================