-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M15
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G123
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec 21 10:30:26 EST 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC
Current job ID : 471788
Current job name : Step_02_G123_M15
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/471788.1.linga

Loading required modules...


List files in scratch directory:

total 1.5G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:30 .
drwxrwxrwt. 35 root   root      112K Dec 21 10:30 ..
-rw-r-----   1 kkarri waxmanlab 747M Dec 21 10:30 G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 761M Dec 21 10:30 G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:30 G123_M15_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1398:2081 1:Y:0:GTCCGC
CTACCTTACAAAAGCCATTTGGGATTCTACTCATTCCTCTAGTTTTTTTT
+
AB@:ACD11EF>C1C11;;B>GG01:1:E1111:C1:1:1>:1?11:/</
@HWI-D00311:109:C8TK0ANXX:8:1101:1456:2214 1:N:0:GTCCGC
TGCTGCAGATGATGCCAAAAGTGGTCCAGAAGTCTGAATCGTTGAATGTA
+
BBBCCDGFGGGGGCGGGGGBBG>FGGGGG>FGGG>FGGGGG0F1FFEFGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1619:2018 1:N:0:GTCCGC
NCCTACTCACCTGGATCCTCAGCTGCTCAGGAACTGGCTGCTGGTCGCTG
+
#<=ABCE>GGGGFGGGGGGGGGGGGGEGCFGGGGGGGGGBGFGGFFGGF<
@HWI-D00311:109:C8TK0ANXX:8:1101:1693:2054 1:Y:0:GTCCGC
NGGGTCCTCTGGGTCCACCCACTCTGTTCCTTTCATGGCTTCAGCAGCCT
+
#:3<:0?FF>@DDGGGGGEGGC1EFGFB@FG111E@FDBGGGGEBFE@:C
@HWI-D00311:109:C8TK0ANXX:8:1101:1742:2058 1:N:0:GTCCGC
NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
#<<A<FG<<CG/EG<9ECG</9<C>9/;//:/:////::CG;>/://:/:

==> G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1398:2081 2:Y:0:GTCCGC
GGTATATTAGAAAAGAAAAACAACAGATTAAACCATAGCTAGGAGGGAAG
+
A@AB0F>11@1;;1=@F1;0CBB00C11=FF111011:1=1E>1BF/FB/
@HWI-D00311:109:C8TK0ANXX:8:1101:1456:2214 2:N:0:GTCCGC
GCCTAGTAGTAAGGGTGGGTGTCATCATATTTATAAAGAGTGGCCTCAAC
+
CCCCCGGGGGGGGGGFGGGGGBGGGGGCGGGGGGGGGDFGGGGGGGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1619:2018 2:N:0:GTCCGC
GAGAAGTGCTGCTCACCACTGCCAAGGCCATCCCTGTGCAGGTGGACGGT
+
33<ABGGGFGDGG@GGGGGGGGGGG@G>FGGGGGGGGEEGFDCGGGGG//
@HWI-D00311:109:C8TK0ANXX:8:1101:1693:2054 2:Y:0:GTCCGC
CAGAAGCCAAACCCAGACCTGAAGCAGCAGCTAACTGGACACTCAAAGCG
+
A>@BBGGGGBGGEBGFG@@GGGGGEEDGGGGFGGGGGGGGGG=FGGGG1<
@HWI-D00311:109:C8TK0ANXX:8:1101:1742:2058 2:N:0:GTCCGC
GACAGTTCCAAAAAACTTTTAAATCCGTAGGAGATTCAAAGAGGATTCTC
+
3=3A0;=1?FGGG0=/11111>F111/00//=1011:=FG1110>1111:

Starting FASTQC command


Processing G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq

Printing command:
fastqc --outdir G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq

Analysis complete for G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq

Processing G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq

Printing command:
fastqc --outdir G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq

Analysis complete for G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 5.1G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:31 .
drwxrwxrwt. 35 root   root      112K Dec 21 10:34 ..
-rw-r-----   1 kkarri waxmanlab 2.6G Dec 21 10:30 G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R1.fastq
-rw-r-----   1 kkarri waxmanlab 2.6G Dec 21 10:30 G123-pool-GTCCGC_GTCCGC_BC8TK0ANXX_L008_001.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:35 G123_M15_FASTQC
==========================================================
Finished on : Fri Dec 21 10:35:24 EST 2018
0 hours, 4 minutes and 58 seconds elapsed.
==========================================================