-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT12
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE96650_LxRKo_ENV
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 29 14:25:26 EDT 2019
Running on node : scc-kb8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/02_FASTQC
Current job ID : 5758540
Current job name : Step_02_WT12
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5758540.1.linga

Loading required modules...


List files in scratch directory:

total 299M
drwx------   3 kkarri waxmanlab 4.0K Apr 29 14:25 .
drwxrwxrwt. 43 root   root      112K Apr 29 14:25 ..
-rw-r--r--   1 kkarri waxmanlab 147M Apr 29 14:25 SRR5345543_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 153M Apr 29 14:25 SRR5345543_2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 14:25 WT12_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR5345543_1.fastq <==
@SRR5345543.1 1/1
CTATAGAGGAGTCCTGATCAGCCAGCCGTTCCCATTTGTCT
+
AAAAAEEEEEEEEE/EEEA/EEAEEEEEEEEEAEEEAEEEE
@SRR5345543.2 2/1
GCATCACTTTCACAGGACTTAACAGACAGCTCTGAGGTCCTGG
+
AAAAAEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEAE<E
@SRR5345543.3 3/1
TATCAGCTTGTCCATCAGGACGGGGAAGTCATAGTGACAAAC
+
AAAAAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@SRR5345543.4 4/1
TTGAAGCACCTGGAATTCAATCTTGCAGCCAAAGGCACATTT
+
AAAAAEAEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEE
@SRR5345543.5 5/1
CTTCAGTTGCTCCGCTGTAGCCTTGGGCTTGTGCTTCACCAGC
+
AAAA/EEEEAE6EEEE/EEEAEEAEAE/EEEEEAEAAAEEEEE

==> SRR5345543_2.fastq <==
@SRR5345543.1 1/2
TTCCAGCACAGGAGGATGCTAACCCCAGCCTTCCACTATGAC
+
AAAAAEEEEEEEEEEAEAAEEEEAAAEEEEEEEEEEEAEAAE
@SRR5345543.2 2/2
GGTCAACCAGCTTGTGAAGGAAGTTGTCTCCTTGACTGAGG
+
A6AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEE<EE
@SRR5345543.3 3/2
GAGGATTTCAAACCTCAAACCTTTGACAGAGAAAAAGTCCTGC
+
AAAAAAEEEEEEEEEEEE6EEEEEE/EEEEAEEEEEEEEEEEE
@SRR5345543.4 4/2
GTCGATAGCTCCATCTTCCTGCTTGTCTTATCGATGATCCTTT
+
AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEE
@SRR5345543.5 5/2
CATGTTACCAAGTGCTGTAGTGGATCCCTGGTGGAAAGGCGGC
+
AA/AAEE<E<EAEEEE//EEEEEAEEAE6AEEEEE/AAEEEEE

Starting FASTQC command


Processing SRR5345543_1.fastq

Printing command:
fastqc --outdir SRR5345543_1.fastq

Analysis complete for SRR5345543_1.fastq

Processing SRR5345543_2.fastq

Printing command:
fastqc --outdir SRR5345543_2.fastq

Analysis complete for SRR5345543_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 14:26 .
drwxrwxrwt. 27 root   root      112K Apr 29 14:27 ..
-rw-r--r--   1 kkarri waxmanlab 578M Apr 29 14:25 SRR5345543_1.fastq
-rw-r--r--   1 kkarri waxmanlab 577M Apr 29 14:25 SRR5345543_2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 14:27 WT12_FASTQC
==========================================================
Finished on : Mon Apr 29 14:27:28 EDT 2019
0 hours, 2 minutes and 2 seconds elapsed.
==========================================================