-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1150
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-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/02_FASTQC
Current job ID : 7046526
Current job name : Step_02_IC57-1150
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046526.1.linga

Loading required modules...


List files in scratch directory:

total 780M
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:42 .
drwxrwxrwt. 12 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:42 IC57-1150_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 380M Jun 24 12:39 SRR6833753_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 401M Jun 24 12:42 SRR6833753_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833753_1.fastq <==
@SRR6833753.1 1/1
TGAAGNGAATATCCGCAATGACATTGCAGGGTGCNN
+
/A/AA#6EEEEEEEEAEEEEEEEEEEEEEEEEEE##
@SRR6833753.2 2/1
CGGGGNTTCTGTGGGTTAGAGATGTCATACTGCCNN
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEE##
@SRR6833753.3 3/1
CTCAANGGTGACTTTGCTGCCTGCAGCCACGTTGAC
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR6833753.4 4/1
GGAATNGTAGCGGGCCTGCAGCCTCGGCAGGAGCT
+
AAAAA#EEAEAEA6EAEAE6EAEEEE//AEEEEE/
@SRR6833753.5 5/1
CATCTNGCAGGGCCAGGATGCCTGGGGGACCCGCCG
+
AAAAA#EEEEEEEEEEEA/EEEE/E6E//AEAEAEE

==> SRR6833753_2.fastq <==
@SRR6833753.1 1/2
NCGTGACTGGNNNNNNNGGANNNANNNNNNNN
+
#6AAAAAEEE#######EEE###E########
@SRR6833753.2 2/2
NCTGGATGTTGNCNGNAATGNNTGNTNNNANNACCN
+
#AAAAEEEEEE#E#E#EEEE##EE#E###/##EEE#
@SRR6833753.3 3/2
NGAAAAGGCTGNGTCCCAGGGCAANACANCCNGTTT
+
#AAAAEEEEEE#EEEEEEEEEEEE#EEE#EE#EEEE
@SRR6833753.4 4/2
NCTGGGTGGTGNAGGCCCGGAGGCACATCCTAGCC
+
#A/AAE66E6E#/EAE6EEE/E/EEE/E/AEEEEE
@SRR6833753.5 5/2
NCCCAATGGCCCAGGAAGAGCAGGAGTCCAGTGGCC
+
#AAAAEEEEEEE/EEE/AA/EEEEEEEEEEEEEEEE

Starting FASTQC command


Processing SRR6833753_1.fastq

Printing command:
fastqc --outdir SRR6833753_1.fastq

Analysis complete for SRR6833753_1.fastq

Processing SRR6833753_2.fastq

Printing command:
fastqc --outdir SRR6833753_2.fastq

Analysis complete for SRR6833753_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.3G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:43 .
drwxrwxrwt. 12 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:53 IC57-1150_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.7G Jun 24 12:39 SRR6833753_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.7G Jun 24 12:42 SRR6833753_2.fastq
==========================================================
Finished on : Mon Jun 24 12:53:18 EDT 2019
0 hours, 15 minutes and 8 seconds elapsed.
==========================================================