-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1162
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE111828
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 12:38:09 EDT 2019
Running on node : scc-kb5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/02_FASTQC
Current job ID : 7046536
Current job name : Step_02_IC57-1162
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046536.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:41 .
drwxrwxrwt. 13 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:41 IC57-1162_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 529M Jun 24 12:39 SRR6833763_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 552M Jun 24 12:41 SRR6833763_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:


Starting FASTQC command


Processing *.fastq

Printing command:
fastqc --outdir *.fastq


Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.1G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:42 .
drwxrwxrwt. 13 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:41 IC57-1162_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 529M Jun 24 12:39 SRR6833763_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 552M Jun 24 12:41 SRR6833763_2.fastq.gz
==========================================================
Finished on : Mon Jun 24 12:43:45 EDT 2019
0 hours, 5 minutes and 46 seconds elapsed.
==========================================================