-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE77729_PB_ENV
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 10:59:35 EDT 2019
Running on node : scc-kb6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/02_FASTQC
Current job ID : 5784542
Current job name : Step_02_WT2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5784542.1.linga

Loading required modules...


List files in scratch directory:

total 4.4G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 11:04 .
drwxrwxrwt. 58 root   root       84K Apr 30 10:59 ..
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 30 11:02 SRR3157437_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 30 11:04 SRR3157437_R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 11:04 WT2_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR3157437_R1.fastq <==
@SRR3157437.1 1/1
GCCTCTGATACGGNTTCGACAAGGCAGGCAGGCAGATATGATTTGGAAACA
+
@?@FDFFFHHHHG#2AE@;EGHGIIIIIIGGGIII;BDEE@BCEGIHGIII
@SRR3157437.2 2/1
CTACAAACTTCTCNTCTGTGGTGAGCCCGTGCAGCTCTCCAGACTCCGCGG
+
CCCFFFFFFHGHH#2AFGHIJHIIIIIGIFGGGIIIGJIIIIBHJIIJJJJ
@SRR3157437.3 3/1
GTCTCCCTTGCAGCTCCTGCAGCTTCTGGCGCGCGCTCTCCTGCAGCTCGG
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJGEFE0@@FGF>DGAE;C''
@SRR3157437.4 4/1
GTGAGCTTTAGGTCTACTTGGGGTTATTGACTTTGGCCATAAAGAGGATAC
+
CBCFFFFFHHHHHIJJJJJJJJJHIJJJJJIJJJJFIJJJJJIJJJJIJHI
@SRR3157437.5 5/1
CCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAATGAGATGAGCCATA
+
@@@DBDDFGHHFFH<=FGICFHGHCGFH@GIIIDEGIGGGGEHGGI<@GGH

==> SRR3157437_R2.fastq <==
@SRR3157437.55653576 55653576/2
CACGCTCCTTTGACTTGTGGTCTTTCCCTTCCCTGATGGGCTTCCGGCGTC
+
CCCFFFFFHHGHHJIJJEHIEGHIIIIGIJJJJJJJGIIJJIIJGIIIJGE
@SRR3157437.55653577 55653577/2
GTCCGAGGCAGCCCTGCTGTAGACGTGGCTGTAAAAGNGTTCAAAAAGACC
+
@@@FFFFDGHHHHJIIJIJGIIJJJBGHIGI;GFEF>#07BCHHJJG@GII
@SRR3157437.55653578 55653578/2
GGACGAATTCCAGAAGAAATGGAAAGAGGATGTGGAGCTCTACCGCCAGAA
+
C@CFFFFFHHHFHHIIIJJJJJJJJJJJIIIJHHJIJJIJIIIHJJJIJHG
@SRR3157437.55653579 55653579/2
CCAGCTGTGTGTTTCAACAGGCCATTCCTGATTGTTATCTATCACACAAGT
+
CCCFFFFEHFHHHIJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJ
@SRR3157437.55653580 55653580/2
TGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTAT
+
@@@DDABDH?FH4AGFBGEHG9IEH@EFEHBFEFCH@BFECBFGGDDGHCF

Starting FASTQC command


Processing SRR3157437_R1.fastq

Printing command:
fastqc --outdir SRR3157437_R1.fastq

Analysis complete for SRR3157437_R1.fastq

Processing SRR3157437_R2.fastq

Printing command:
fastqc --outdir SRR3157437_R2.fastq

Analysis complete for SRR3157437_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 15G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 11:07 .
drwxrwxrwt. 49 root   root       84K Apr 30 11:31 ..
-rw-r--r--   1 kkarri waxmanlab 7.2G Apr 30 11:02 SRR3157437_R1.fastq
-rw-r--r--   1 kkarri waxmanlab 7.2G Apr 30 11:04 SRR3157437_R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 11:32 WT2_FASTQC
==========================================================
Finished on : Tue Apr 30 11:32:01 EDT 2019
0 hours, 32 minutes and 26 seconds elapsed.
==========================================================