-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1160
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 : 7046534
Current job name : Step_02_IC57-1160
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046534.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
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 IC57-1160_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 512M Jun 24 12:40 SRR6833761_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 540M Jun 24 12:42 SRR6833761_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833761_1.fastq <==
@SRR6833761.1 1/1
CTGTGNGCCACGCACTCCGGTCAAGTCTGCTTG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR6833761.2 2/1
CCTCANGCCCCCAGCACAACCTACTGAGCTAAT
+
/AAAA#EEEEEEEEEEEEEEEEEEEEEEEEEE/
@SRR6833761.3 3/1
GTATGNGCTGAGCAGGGCTGCGATGGTGTAGTGGCG
+
AAAAA#AEEAEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR6833761.4 4/1
GATGGNAGCATGGAAGCTGTGGGCGCCAAAGGTCTC
+
AAAAA#AEEEE6EEEEEEEEEEEA/AEEEE/AEEAA
@SRR6833761.5 5/1
GCAGGNTAGCTTGACACAAATGCTGTATATTATTCC
+
AAAA/#EEEEEEEEEEAEEEEEAAEEEEAEEEEEEE

==> SRR6833761_2.fastq <==
@SRR6833761.1 1/2
NGAATACTGCNNNNNNNNNNNNNNNNNNNNNN
+
#AAAAEEEEE######################
@SRR6833761.2 2/2
NCTGACCAGGANGNCNACAGNNATNGNNNCNNNGGN
+
#AAAAEEEEEE#E#E#EEEE##EE#E###E###EE#
@SRR6833761.3 3/2
NTGGCATTTCCNCGTTCCATGAATNCGCNGANGTGG
+
#AAAAEEEEEE#EEEEEEEEEE6E#AEE#EE#EEEE
@SRR6833761.4 4/2
NGGGGGGGGGGNGGGGGGGGGGGGNGGGNGGNGGGG
+
#AAAAEEE6EE#AEE6E66EEEEE#//E#E/#EA6A
@SRR6833761.5 5/2
NGTCAAATATGNCACAAAGGCTGGGAAGTTCNAAGT
+
#A6AAEEEEE6#AEEEEEEEEAEEEE6EEEE#EE/E

Starting FASTQC command


Processing SRR6833761_1.fastq

Printing command:
fastqc --outdir SRR6833761_1.fastq

Analysis complete for SRR6833761_1.fastq

Processing SRR6833761_2.fastq

Printing command:
fastqc --outdir SRR6833761_2.fastq

Analysis complete for SRR6833761_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.4G
drwx------  3 varsha97 waxmanlab 4.0K Jun 24 12:43 .
drwxrwxrwt. 9 root     root      4.0K Jun 24 12:53 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 12:53 IC57-1160_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 2.2G Jun 24 12:40 SRR6833761_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 2.2G Jun 24 12:42 SRR6833761_2.fastq
==========================================================
Finished on : Mon Jun 24 12:53:57 EDT 2019
0 hours, 15 minutes and 47 seconds elapsed.
==========================================================