-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1169
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-kb1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/02_FASTQC
Current job ID : 7046545
Current job name : Step_02_IC57-1169
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046545.1.linga

Loading required modules...


List files in scratch directory:

total 808M
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:41 .
drwxrwxrwt. 12 root     root      4.0K Jun 24 12:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:41 IC57-1169_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 393M Jun 24 12:39 SRR6833772_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 416M Jun 24 12:41 SRR6833772_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833772_1.fastq <==
@SRR6833772.1 1/1
GTAGANCTAGCTTCTTCTGCATGGACACAGACT
+
AAAAA#EEEEAEEEEEEEEEEEEEEEEEEEEEE
@SRR6833772.2 2/1
GCGCANGTAATCCCAGAAGCGGTTCAGGGCCTGCTC
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR6833772.3 3/1
GGGGANAGGAGCTGGTCTGACCCTCCGCCCCATGC
+
AAAA6#AEE/EEEEEEA/E/EEEEE/EEE<E//AE
@SRR6833772.4 4/1
CTTTGNGTCTACTTGGGGTTATTGACTTTGGCCAT
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR6833772.5 5/1
CCAGGNGCCTCAGGCCCAGAACCCGGAAGAGCTTG
+
AAAAA#EEEEEEEEEEEEEE6EEEEEEEEEEEEEE

==> SRR6833772_2.fastq <==
@SRR6833772.1 1/2
NGACAATCCTNNNNNNNACCNNNNNNNNNNNN
+
#AAAA6EEEE#######EEE############
@SRR6833772.2 2/2
NGAGAGCCGGANGNGACAGATNAGNTCNNGNNGC
+
#AAAAEEEEEE#E#EEEEEEE#EE#EE##E##EE
@SRR6833772.3 3/2
NCACAGTTGGANCCCAAACTCCTGCAGCTGCATGGG
+
#AAA/EEEEE/#EAE//EEAEEE/EAEE//E/EAEE
@SRR6833772.4 4/2
NGCACAGAAGCAGCTGCTGCCACAGGGGTTATTGGT
+
#AAAAEEAEEEEEEEEEEEEEEEEEEEEEE6EEEEE
@SRR6833772.5 5/2
NAGGATGAGCGTGAATGCACCATGGACCTTTCTGA
+
#AAAAEE6EEEEEEEEAAEEEEEEEEEEEEEEEEE

Starting FASTQC command


Processing SRR6833772_1.fastq

Printing command:
fastqc --outdir SRR6833772_1.fastq

Analysis complete for SRR6833772_1.fastq

Processing SRR6833772_2.fastq

Printing command:
fastqc --outdir SRR6833772_2.fastq

Analysis complete for SRR6833772_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.4G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 12:41 .
drwxrwxrwt. 11 root     root      4.0K Jun 24 12:41 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:49 IC57-1169_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.7G Jun 24 12:39 SRR6833772_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.7G Jun 24 12:41 SRR6833772_2.fastq
==========================================================
Finished on : Mon Jun 24 12:51:14 EDT 2019
0 hours, 13 minutes and 8 seconds elapsed.
==========================================================