-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M8
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Mar 12 12:07:11 EDT 2019
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/06_CollectRnaSeqMetrics
Current job ID : 3529886
Current job name : Step_06_G168_G169_M8
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3529886.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   3 kkarri waxmanlab 4.0K Mar 12 12:07 .
drwxrwxrwt. 25 root   root      268K Mar 12 12:07 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 12 12:07 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.9G Mar 12 12:07 G168_G169_M8_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Mar 12 12:07 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Mar 12 12:07 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=G168_G169_M8_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G168_G169_M8'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 2.0G
drwx------   3 kkarri waxmanlab 4.0K Mar 12 12:07 .
drwxrwxrwt. 25 root   root      268K Mar 12 12:07 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 12 12:07 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.9G Mar 12 12:07 G168_G169_M8_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Mar 12 12:07 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Mar 12 12:07 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Mar 12 12:07:35 EDT 2019
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================