-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M12
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 04:52:32 EDT 2019
Running on node : scc-ka2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/06_CollectRnaSeqMetrics
Current job ID : 5533269
Current job name : Step_06_G166_M12
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5533269.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 794M
drwx------   3 kkarri waxmanlab 4.0K Apr 23 04:53 .
drwxrwxrwt. 65 root   root      116K Apr 23 04:52 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 04:53 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 786M Apr 23 04:53 G166_M12_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 23 04:53 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 23 04:53 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=G166_M12_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G166_M12'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 794M
drwx------   3 kkarri waxmanlab 4.0K Apr 23 04:53 .
drwxrwxrwt. 65 root   root      116K Apr 23 04:52 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 04:53 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 786M Apr 23 04:53 G166_M12_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Apr 23 04:53 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Apr 23 04:53 rRNA_intervalList_sorted
==========================================================
Finished on : Tue Apr 23 04:53:02 EDT 2019
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================