-----------------------
Start of variable list:
-----------------------
Sample_ID:
Con_WT3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE111828_Aceto_Env
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Apr 24 13:57:25 EDT 2019
Running on node : scc-ka1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/02_FASTQC
Current job ID : 5554904
Current job name : Step_02_Con_WT3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5554904.1.linga

Loading required modules...


List files in scratch directory:

total 755M
drwx------   3 kkarri waxmanlab 4.0K Apr 24 13:59 .
drwxrwxrwt. 63 root   root      124K Apr 24 13:57 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 24 13:59 Con_WT3_FASTQC
-rw-r--r--   1 kkarri waxmanlab 368M Apr 24 13:58 SRR6833754_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 388M Apr 24 13:59 SRR6833754_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833754_R1.fastq <==
@SRR6833754.1 1/1
ATTCTNCTTAACAAAGACATCTGATTTNTCTTG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEE#EEEEE
@SRR6833754.2 2/1
TGACANTCTCACATTTTACACTAAGCAATATGT
+
/AAA6#E/EEEEEEEEEEEEAEEEAEEEEEEEE
@SRR6833754.3 3/1
GTGCANATTTCAAGGAACATGGTATTCTTGGCTTNN
+
AAAA6#EE/EEEEAEEEEEEEE<EEEEEEEEEE/##
@SRR6833754.4 4/1
CCTGGNCAGACAGCGTCTGCACCCAGCGCAGGTAAT
+
AAAAA#EEEEEEEEEEAEEEEEEE/EEEEEEEEEAA
@SRR6833754.5 5/1
CAAGCNGATTGCTAGGAGCACCCAGGTTTCCAGTG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEE

==> SRR6833754_R2.fastq <==
@SRR6833754.1 1/2
NAATAGCATTNNNNNNNNNNNNNNNNNNNNNN
+
#AAAAEE6EE######################
@SRR6833754.2 2/2
NAAAATGATCNNANNNNTGANNAANNNNNNNN
+
#//A/E66/A##E####/A/##/E########
@SRR6833754.3 3/2
NCCAAACTCANNANCNNAGTNNCCNNNNNNNN
+
#AAAAEEEEE##6#E##/EE##EA########
@SRR6833754.4 4/2
NCTGTTGGTCANATTGCTGACAGGNTGCNTANCCG
+
#AAAAEE6EEA#/EEEEAE6AEEE#EEE#E/#EEE
@SRR6833754.5 5/2
NATTGAGGAGGNTCACACACACAGNTGTNGGNAGA
+
#AAAAEEEEEE#EEEEEEEEEEEE#EEE#EE#EEE

Starting FASTQC command


Processing SRR6833754_R1.fastq

Printing command:
fastqc --outdir SRR6833754_R1.fastq

Analysis complete for SRR6833754_R1.fastq

Processing SRR6833754_R2.fastq

Printing command:
fastqc --outdir SRR6833754_R2.fastq

Analysis complete for SRR6833754_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.1G
drwx------   3 kkarri waxmanlab 4.0K Apr 24 14:00 .
drwxrwxrwt. 59 root   root      124K Apr 24 14:03 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 24 14:04 Con_WT3_FASTQC
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 24 13:58 SRR6833754_R1.fastq
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 24 13:59 SRR6833754_R2.fastq
==========================================================
Finished on : Wed Apr 24 14:04:15 EDT 2019
0 hours, 6 minutes and 50 seconds elapsed.
==========================================================