-----------------------
Start of variable list:
-----------------------
Sample_ID:
LRH-APAPL2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/Scripts/00_Setup_Pipeline
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Jun 28 12:11:21 EDT 2019
Running on node : scc-tm2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/Scripts/03_Read_Length
Current job ID : 7283218
Current job name : Step_03_LRH-APAPL2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7283218.1.linga

Loading required modules...


List files in scratch directory:

total 4.9G
drwx------  2 varsha97 waxmanlab 4.0K Jun 28 12:12 .
drwxrwxrwt. 6 root     root      4.0K Jun 28 12:11 ..
-rwxr-xr-x  1 varsha97 waxmanlab 2.4G Jun 28 12:12 SRR6080072_1.fastq.gz
-rwxr-xr-x  1 varsha97 waxmanlab 2.6G Jun 28 12:13 SRR6080072_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Starting Read Length


Processing SRR6080072_1.fastq


Processing SRR6080072_2.fastq


Ending Read Length


List files in scratch

total 17G
drwx------  2 varsha97 waxmanlab 4.0K Jun 28 12:16 .
drwxrwxrwt. 7 root     root      4.0K Jun 28 12:13 ..
-rwxr-xr-x  1 varsha97 waxmanlab 8.2G Jun 28 12:12 SRR6080072_1.fastq
-rwxr-xr-x  1 varsha97 waxmanlab 8.2G Jun 28 12:13 SRR6080072_2.fastq
==========================================================
Finished on : Fri Jun 28 12:17:25 EDT 2019
0 hours, 6 minutes and 4 seconds elapsed.
==========================================================