-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1170
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 12:38:10 EDT 2019
Running on node : scc-ka3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/02_FASTQC
Current job ID : 7046546
Current job name : Step_02_IC57-1170
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046546.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:42 .
drwxrwxrwt. 11 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:42 IC57-1170_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 501M Jun 24 12:39 SRR6833773_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 525M Jun 24 12:42 SRR6833773_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833773_1.fastq <==
@SRR6833773.1 1/1
ACATGNACTGCCAGTGTAATTGGGATAGCATTC
+
AAAAA#EEEEEEEEEAEEAEEEEEEE/EEEEEE
@SRR6833773.2 2/1
CCTGANGACTCTCCAAAGATGGTCACGGAATCCGGG
+
AAAA6#EAEEEEAEEEEEEEE6EEEEEEEEEEEAEE
@SRR6833773.3 3/1
TGCTTNCCAAAAGTGGCCCACTAGGCACTCGCATTC
+
AAAAA#EEEEEEEEEEEAE/EEEEEEEEEEEEEEEE
@SRR6833773.4 4/1
TGCAANAGATATCTCTGGTAGCCACATATGCCAGGC
+
AAAAA#EA/EEEA/EEE/E66EE/EA/E///E/A/E
@SRR6833773.5 5/1
GCTCANAGAGCACACAGGAAGCAACACAAGCTCAAT
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEAE

==> SRR6833773_2.fastq <==
@SRR6833773.1 1/2
NAATTCTGCGNNTNTNATAANNTCNNNNNNNN
+
#/AAAAEEAA##A#E#/EAA##AA########
@SRR6833773.2 2/2
NGAACACAGCCNANGNAACTGNGCNCNNNTNNACCN
+
#AAAAEEEEEE#E#E#EAEEE#EE#E###E##EEE#
@SRR6833773.3 3/2
NGTAAAGCGAANGATTAGAGGTCTNGGGNCCNAAAC
+
#AAAAEEEEEE#EEEEEEEEEEEE#EEE#EE#EEEE
@SRR6833773.4 4/2
NGAGCTCGGAGNACCTCGTCACACNGACACCNTG
+
#//AAA//E/E#//E//E/E/E//#/AEA/E#A/
@SRR6833773.5 5/2
NGGGAAGTCATNCAGCCTGGGCTTNGGCGTGNCCTC
+
#AAAAEEEEEE#EEEEEEEEEEEE#EEEEEE#EEEE

Starting FASTQC command


Processing SRR6833773_1.fastq

Printing command:
fastqc --outdir SRR6833773_1.fastq

Analysis complete for SRR6833773_1.fastq

Processing SRR6833773_2.fastq

Printing command:
fastqc --outdir SRR6833773_2.fastq

Analysis complete for SRR6833773_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.3G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:43 .
drwxrwxrwt. 10 root     root      4.0K Jun 24 12:52 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:52 IC57-1170_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 2.2G Jun 24 12:39 SRR6833773_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 2.2G Jun 24 12:42 SRR6833773_2.fastq
==========================================================
Finished on : Mon Jun 24 12:52:14 EDT 2019
0 hours, 14 minutes and 4 seconds elapsed.
==========================================================