-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M14
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA/Scripts/00_Setup_Pipeline
STRAND_SPECIFICITY:
FIRST_READ_TRANSCRIPTION_STRAND
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA/Scripts/06_CollectRnaSeqMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Mar  5 11:44:00 EST 2020
Running on node : scc-ka2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G123_New_Env_PCA/Scripts/06_CollectRnaSeqMetrics
Current job ID : 3671490
Current job name : Step_06_G123_M14
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3671490.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   3 kkarri waxmanlab 4.0K Mar  5 11:47 .
drwxrwxrwt. 49 root   root       12K Mar  5 11:43 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar  5 11:47 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.1G Mar  5 11:47 G123_M14_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Mar  5 11:47 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Mar  5 11:47 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=G123_M14_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G123_M14'_metrics'


Finished CollectRnaSeqMetrics command


Copy output to storage dir


List files in scratch

total 1.1G
drwx------   3 kkarri waxmanlab 4.0K Mar  5 11:47 .
drwxrwxrwt. 49 root   root       12K Mar  5 11:43 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar  5 11:47 CollectRnaSeqMetrics
-rw-r--r--   1 kkarri waxmanlab 1.1G Mar  5 11:47 G123_M14_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab 7.9M Mar  5 11:47 genes_refFlat
-rwxr-xr-x   1 kkarri waxmanlab  52K Mar  5 11:47 rRNA_intervalList_sorted
==========================================================
Finished on : Thu Mar  5 11:47:14 EST 2020
0 hours, 3 minutes and 14 seconds elapsed.
==========================================================