-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1151
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 : 7046527
Current job name : Step_02_IC57-1151
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7046527.1.linga

Loading required modules...


List files in scratch directory:

total 755M
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 IC57-1151_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 368M Jun 24 12:40 SRR6833754_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 388M Jun 24 12:42 SRR6833754_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6833754_1.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_2.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_1.fastq

Printing command:
fastqc --outdir SRR6833754_1.fastq

Analysis complete for SRR6833754_1.fastq

Processing SRR6833754_2.fastq

Printing command:
fastqc --outdir SRR6833754_2.fastq

Analysis complete for SRR6833754_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 3.1G
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 12:52 IC57-1151_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.6G Jun 24 12:40 SRR6833754_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.6G Jun 24 12:42 SRR6833754_2.fastq
==========================================================
Finished on : Mon Jun 24 12:53:17 EDT 2019
0 hours, 15 minutes and 8 seconds elapsed.
==========================================================