-----------------------
Start of variable list:
-----------------------
Sample_ID:
TA_IP3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/home/waxmanlab/public_html/FASTQC/IP_Saline
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jun 14 17:16:07 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/02_FASTQC
Current job ID : 9321127
Current job name : Step_02_TA_IP3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9321127.1.linga

Loading required modules...


List files in scratch directory:

total 3.6G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 14 17:17 .
drwxrwxrwt. 58 root   root       164K Jun 14 17:16 ..
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 14 17:16 SRR1177970_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 14 17:17 SRR1177970_R2.fastq.gz
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 14 17:17 TA_IP3_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR1177970_R1.fastq <==
@SRR1177970.1 1 length=101
TCAGTCTTCACTTGGGTGCTATAAACAGATGCCACCAGAAATCCCTTGGGAGGACAGAGTACATGTCTGAGGAGTTATCACTGTGTCCCTCCCTGTCTTGT
+SRR1177970.1 1 length=101
@<@B1?DBHHFFDHD9<1+<ACHHHBHG9B4*?CFC;?;FEGH*:BB39BDF?(=CDCGG4=@@@CECD=A7A1;@CE:;6>C>;>C:>3;=85>@@####
@SRR1177970.2 2 length=101
CTCATGAGTGCAGGACGTCTTCGGATGAGATTAGTATACGAATTGGAAGTTCTATTGGTAAGACTACCCGATTATCAACTTCTAATAGACGAAGTTCACCT
+SRR1177970.2 2 length=101
@@@DDFFFADDHDGGEHIGGEHAF1CGHC@DDDE?DEGEEDCDGFF<?FABFHIIEGC7CF:@@EH=AEHBBEDC3@CE(5;;CD@CCCA=B?7<C::@:A
@SRR1177970.3 3 length=101
AAATCAAATTCTCAGTTTTCCCTTGGCTTGCCTTTATTCTGGTTTCATACTGCACTTCCCATGTCACATGACTGGAAGGAAAACATGTTCGCTGAGGTGCC
+SRR1177970.3 3 length=101
@??=DDD?<=2AFHGFGH9F>E<:AC93<<<3C@C*@FD<?CC<B>@E9D@GGGGHII<D?<8CE88=;=F>FA;C@3(27?)7?;@##############
@SRR1177970.4 4 length=101
GTAGTCAATGCTAGAAGCAAAATGAGGATGTCCGAGAGGCCCAGGAGGTCCAGGAAGTCCAGGAGGTCCAGGAAGTCCAGGAGGAGTCACGTATTGTCTAC
+SRR1177970.4 4 length=101
?88B4=BDF4DFB<BE4CC;ABHEEHGII<2AC8??D):68)?2?;?F(88CC3@CE==DD:A=E8B3)6;@BC2(5@@C39(388,54+0<C@#######
@SRR1177970.5 5 length=101
CTGACTTTCACGTAGACAAGTCCACCACAGTGAAGGTGCCCATGATGAACCGCCTGGGCATGTTTGACATGCACTATTGCAGCACACTGTCCAGCTGGGTG
+SRR1177970.5 5 length=101
@@@F?DDDBDAFAF;EGGIHEHCHIIJJJJEFH@EH;GGGEHEHHJJIIDFGGII@GEHHGIHHHFHHFFFFFFEEDDEDEDABACACD>::ACA>:??35

==> SRR1177970_R2.fastq <==
@SRR1177970.1 1 length=101
GGAATCTGTTTGTAGATAATGAGAAGAGTAGGCAGTNNNNNNAGATNTCTAGAGGTTTAAGNNNNNNNNTAGTTGAAAATGCACAAGTGTGTGCCCAAGCA
+SRR1177970.1 1 length=101
?<@;D=ABCF<DA4,,,2<A:3<<A>CG#########################################################################
@SRR1177970.2 2 length=101
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCNNNNANNNNNNNNNNNNNNNN
+SRR1177970.2 2 length=101
#####################################################################################################
@SRR1177970.3 3 length=101
GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACNNANNNNNNNNNNNNNNNN
+SRR1177970.3 3 length=101
#####################################################################################################
@SRR1177970.4 4 length=101
CAGGATCTANACTGCTGACATCCAGGCTGAGAGGNNNNNNNNNNNNNNCATNGNCCNNNNNNNNNNNNNNNNTCGTTGGGTTTGGAAAATACTTGCTTCTC
+SRR1177970.4 4 length=101
@;=B1=BDD#3<CC;22C::FF+2+2+28H819D###################################################################
@SRR1177970.5 5 length=101
CATCAGCACCCAGCTGGACAGTGTGCTGCAATAGNNNNNNNNNNNNNNGCCCAGGCGGTNNNNNNNNNNNACCTTCACTGTGGTGGACTTGTCTACGTGAA
+SRR1177970.5 5 length=101
B@CFFFABFHDFHIIIJFIIJ3CCHH>HHGICHH##############--7<FHGEGHB###########,,8?BDCCCACDC3<BBDDCC34>CDBDDD@

Starting FASTQC command


Processing SRR1177970_R1.fastq

Printing command:
fastqc --outdir SRR1177970_R1.fastq

Analysis complete for SRR1177970_R1.fastq

Processing SRR1177970_R2.fastq

Printing command:
fastqc --outdir SRR1177970_R2.fastq

Analysis complete for SRR1177970_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 11G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 14 17:23 .
drwxrwxrwt. 53 root   root       164K Jun 14 17:31 ..
-rw-r--r--   1 kkarri montilab-p 5.1G Jun 14 17:16 SRR1177970_R1.fastq
-rw-r--r--   1 kkarri montilab-p 5.1G Jun 14 17:17 SRR1177970_R2.fastq
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 14 17:31 TA_IP3_FASTQC
==========================================================
Finished on : Wed Jun 14 17:31:42 EDT 2017
0 hours, 15 minutes and 35 seconds elapsed.
==========================================================