-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M11
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-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC
Current job ID : 471784
Current job name : Step_02_G123_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/471784.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:30 .
drwxrwxrwt. 36 root   root      124K Dec 21 10:30 ..
-rw-r-----   1 kkarri waxmanlab 641M Dec 21 10:30 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 664M Dec 21 10:30 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:30 G123_M11_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1472:2053 1:N:0:GGCTAC
NTACCTATTTTTATTCTACAGCTTAAATATTTCCTTTTCAGTTTAGCTGA
+
#<<<A=FGGGGGGCDFGEGF>D1FDGGGG>DEGGGGCDFGGGGCFDFE1F
@HWI-D00311:109:C8TK0ANXX:8:1101:1373:2117 1:N:0:GGCTAC
CTGTGCCAGCTTCATTCATGTCTAGGGTGGCCTTGTGGAAGGCCTGAGAG
+
?BBBBGGGGGGGGGGGGGGG>1>FFGGGGGFDCBGGGGG1@/=F@0:CFD
@HWI-D00311:109:C8TK0ANXX:8:1101:1333:2146 1:Y:0:GCCTAC
CCCACTAATCAGGCAGAGCGGCTGTATAAAGTCTGCACTTGTCCACACCT
+
A?=0011E1>D1;>F/@FF><E/EEF>FGEG1C1E1FEC1E1C1@DGEFB
@HWI-D00311:109:C8TK0ANXX:8:1101:1371:2239 1:N:0:GGCTAC
AACAAACACAATTTTCCCTTGCTTGATGACGTGGCTGACTACCTCCCGGG
+
BCCCCEGGGEFG>GGGGGGGBGGGGGFGGGGGGGGGGGGGGCGFGGGDD/
@HWI-D00311:109:C8TK0ANXX:8:1101:1334:2250 1:Y:0:GGCTAC
CCGTCTGTAACAGTAACTACCGAATGGGCCTACAATAGCCCAGTGGAGAT
+
<AB0<FF1FE1EF11E@CE1=//90=<<C0C1:EFGG><GF:=>1=101<

==> G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1472:2053 2:N:0:GGCTAC
CTTCGTTTAAAAAGAAAATGTAACTATTTTCTATATCTCTCAAAAACAAA
+
B>BABGEGGGGGGGD@DFFEFDGGGGGGGGGGGGGGGGGEGGGCFGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1373:2117 2:N:0:GGCTAC
AAGAGAGGAGTATGAAAATCTGTCTCTTGCCCCCTACCTTGGGATATAGC
+
3@3:AGG/FDGGE>;FFBFGGGGGGGD<@@F1FCBBBGGGFC@FGGGG>1
@HWI-D00311:109:C8TK0ANXX:8:1101:1333:2146 2:Y:0:GCCTAC
GTTTCTGGTCTTAATAGTCCTGTAAGAGCAAGATTTACTGAAATTTACTT
+
BC@B@>?1;1;FEGFG1>FFGECEGG>1@FGF:CC>DG@@FGCDE@GG@>
@HWI-D00311:109:C8TK0ANXX:8:1101:1371:2239 2:N:0:GGCTAC
TGACCACCATCAACCATGACAACCTACAACAACAAAGGACCAAAGCCTGA
+
B>ABCGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1334:2250 2:Y:0:GGCTAC
CACGAGGCTGGCAGCCTGAACCAAGCAGGCCCTGGACTGAACTGTCCCCG
+
33:0A//=?C//=<C0=:EFCGGGG0=1:<//:00=1C0EF@1:=1>10/

Starting FASTQC command


Processing G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq

Printing command:
fastqc --outdir G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq

Analysis complete for G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq

Processing G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq

Printing command:
fastqc --outdir G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq

Analysis complete for G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.4G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:31 .
drwxrwxrwt. 37 root   root      124K Dec 21 10:34 ..
-rw-r-----   1 kkarri waxmanlab 2.2G Dec 21 10:30 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq
-rw-r-----   1 kkarri waxmanlab 2.2G Dec 21 10:30 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:34 G123_M11_FASTQC
==========================================================
Finished on : Fri Dec 21 10:34:52 EST 2018
0 hours, 4 minutes and 26 seconds elapsed.
==========================================================