-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M14
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/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_New/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 14:16:03 EST 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/02_FASTQC
Current job ID : 24486
Current job name : Step_02_G123_M14
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/24486.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 14:16 .
drwxrwxrwt. 24 root   root       20K Dec  7 14:16 ..
-rw-r-----   1 kkarri waxmanlab 671M Dec  7 14:16 G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 684M Dec  7 14:16 G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 14:16 G123_M14_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1459:2038 1:Y:0:CCGTCC
NTCACATTTACCCCTTAATATCCGCACTGCACTTCCACCAGTGTCGCTCC
+
#=<AB=1EF1>E;FGGGGG11@E/:ECG1>BFGGGGBFGGGE==1/<=</
@HWI-D00311:109:C8TK0ANXX:8:1101:1432:2064 1:N:0:CCGTCC
NTATTTCAATCACTTGCTCTTAGCAAAACCATGAGACTGGAGGCTATACC
+
#<<ABGGGGFCGGGGGGGG1DFBGGEG@FGG>C>DGGEGGG1/FFGGFG>
@HWI-D00311:109:C8TK0ANXX:8:1101:1387:2209 1:N:0:CCGTCC
CTTCGAGCCGTGCCTTGTCATCCGCAGAAACGGGCAATACAATGGGAATA
+
BC@BCGB=C//=FD1FGFGF@CFE@CCC@GD=CFD<FGGGFCF11E1<11
@HWI-D00311:109:C8TK0ANXX:8:1101:1319:2233 1:N:0:CCGTCC
CTAAACTTTCAGTCTTGAAGTTTTAAGTTCAGTTAATTTATCAGAACTAA
+
ABBABE1=@FGG1EB>FGG;EB1CBGG1FDGDFGEEE11ECC:1=FG11=
@HWI-D00311:109:C8TK0ANXX:8:1101:1668:2196 1:N:0:CCGTCC
CTGCCATACTGCTCTCCCAGCCTGGCCCCAGAACAGGTGGTTAGCACAAG
+
BBBB?FCGFG>GFEGGGGGGFGGGGGGGGGGGGGGGGFGGGGGGGGGEG>

==> G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1459:2038 2:Y:0:CCGTCC
CTGAAATCAGACCCTCAGCTGCAGTTTGAGAGAAGTTTCTGGGGAAGGTA
+
=B30:;EDC?>EFB;FG1@=;=B1==FCG@FCFF11<EEF<11/=FC/1?
@HWI-D00311:109:C8TK0ANXX:8:1101:1432:2064 2:N:0:CCGTCC
CTCATATTTGGGTTCAATTTCTTTTTTTATTTTTATTTTTTAAGTATCAA
+
CBBCCGGGGGGGFGGGGGGGGGGGGEG/FFGGGGGGGGGGG>DDGGGG>D
@HWI-D00311:109:C8TK0ANXX:8:1101:1387:2209 2:N:0:CCGTCC
CTTAGCCATCCCTGAAGAATGCCTCACGTGGAATATGACACTTATGCCTC
+
BBCCCGEFGGGGGFGGGGGFFCGFFGGGBF</FFGG>DFGG1@FGGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1319:2233 2:N:0:CCGTCC
CTGAAAACAGGCCATGGTCCTAGAGTCTGAACTTGCTACTTTGGTTCTTT
+
A@<ABGGGG1>@FFF1@FGDGEFFG:EFGEGG@GGF1FG1<F11FFGCCF
@HWI-D00311:109:C8TK0ANXX:8:1101:1668:2196 2:N:0:CCGTCC
CTTTTTAGTGGTCAGCCTGGCTGGATGGTGGCCTTGTGAGCTGGTGTGCA
+
B@AABGGGFGGGGGGFGGGGGGBCGEEDGGGGGGGGGGCGGGD@F>GFGG

Starting FASTQC command


Processing G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq

Printing command:
fastqc --outdir G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq

Analysis complete for G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq

Processing G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq

Printing command:
fastqc --outdir G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq

Analysis complete for G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.6G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 14:16 .
drwxrwxrwt. 15 root   root       20K Dec  7 14:18 ..
-rw-r-----   1 kkarri waxmanlab 2.3G Dec  7 14:16 G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R1.fastq
-rw-r-----   1 kkarri waxmanlab 2.3G Dec  7 14:16 G123-pool-CCGTCC_CCGTCC_BC8TK0ANXX_L008_001.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 14:19 G123_M14_FASTQC
==========================================================
Finished on : Fri Dec  7 14:19:07 EST 2018
0 hours, 3 minutes and 4 seconds elapsed.
==========================================================