-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1167
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 : 7046544
Current job name : Step_02_IC57-1167
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046544.1.linga

Loading required modules...


List files in scratch directory:

total 732M
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 IC57-1167_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 354M Jun 24 12:39 SRR6833771_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 379M Jun 24 12:41 SRR6833771_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR6833771.1 1/1
GTGGANGGACGAGGAGCAAACACGCCAGTCAACTNN
+
AAAAA#EEEEEEEEEEEEAAEEEEEEEEEEEEEE##
@SRR6833771.2 2/1
CCGCTNTTAACATGGAAAGTCTTAGAGAAGGTCCNN
+
AAAAA#EAAEEEE/EEEEEEEEE/E/E/E/EEEE##
@SRR6833771.3 3/1
GCTGANTAAGGATCTATGGCAGGAGACACTCAGCC
+
/AAAA#EEEAAEEEEEEAAEEEEEEEEEEEEEEEE
@SRR6833771.4 4/1
GCCATNCTTCAGCTCTCGGGAAGCTACTTTGAAGGC
+
/AAAA#EEEAEEAEEE/EEEE/EEEEEEEEEEEE/E
@SRR6833771.5 5/1
GTGGANACTCCTGGAAGGCTCCCATAGCTTCTTGAT
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

Starting FASTQC command


Processing SRR6833771_1.fastq

Printing command:
fastqc --outdir SRR6833771_1.fastq

Analysis complete for SRR6833771_1.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.9G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:42 .
drwxrwxrwt. 10 root     root      4.0K Jun 24 12:47 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:46 IC57-1167_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.6G Jun 24 12:39 SRR6833771_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 379M Jun 24 12:41 SRR6833771_2.fastq.gz
==========================================================
Finished on : Mon Jun 24 12:47:43 EDT 2019
0 hours, 9 minutes and 34 seconds elapsed.
==========================================================