-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M2
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 10:30:25 EST 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC
Current job ID : 471775
Current job name : Step_02_G123_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/471775.1.linga

Loading required modules...


List files in scratch directory:

total 1.5G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:30 .
drwxrwxrwt. 40 root   root       92K Dec 21 10:30 ..
-rw-r-----   1 kkarri waxmanlab 722M Dec 21 10:30 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 748M Dec 21 10:30 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:30 G123_M2_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1395:2195 1:N:0:CGATGT
CTGCGCAGGTGGCTGAGCTCATCCTGCAGCTCAGTGGTGCGGCTCAGGGC
+
CCCCCGGGGGGGGGEGGGGGDGGGGCGGGGFFGGGGGGGGGGGGGGGGBG
@HWI-D00311:109:C8TK0ANXX:8:1101:1515:2106 1:N:0:CGATGT
CAGCTGGCGATCACCAGGCAGAACTGGAAACCCAGATGTCTCTGAAGAAG
+
BA@B@G>FAG<0/=CCFGDGGGCGGCCDCDDG/F0::CD1D=EDEC1=@1
@HWI-D00311:109:C8TK0ANXX:8:1101:1653:2159 1:N:0:CGATGT
GGTATACAGAATGCAAGGTGAAAGTCAGGCTACTGCCAGAATCCATCCTA
+
BBBCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG:FG
@HWI-D00311:109:C8TK0ANXX:8:1101:1594:2224 1:N:0:CGATGT
GCAGGTTCCAGAGGTGGACAGGCTGGGGGCCATGTGTCACGGTGGGACTC
+
ABB?BGGGGGGCGFEGGE1F0:FBDBDGFCCGG>GGGGG1FF:FGDGBEB
@HWI-D00311:109:C8TK0ANXX:8:1101:1774:2030 1:N:0:CGATGT
NTCCACTTTACAAGTTGTCCTTGTTGGCCCCGTGCTGCTAGCTCATGGGC
+
#=<ABGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

==> G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1395:2195 2:N:0:CGATGT
GAAAGATGTCCCTCCAGTCCCTACTCTGGCTGACATTGCCTGGATTGCTG
+
ABBBBGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1515:2106 2:N:0:CGATGT
GAAGAAGCTGCCCAAAAAGTTAAACACTATTACCGCTTTTGGGTCCTGCC
+
BBB?BG>CCC@0FGGG@>>GG1<FD>BEF>DGGGCGGGEFGGGGFGEDEG
@HWI-D00311:109:C8TK0ANXX:8:1101:1653:2159 2:N:0:CGATGT
GCCAAGTGAAATGTATAGGCTGATTCACCTTCTGCTCCAATTTGGAAACC
+
BBBBCGFGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
@HWI-D00311:109:C8TK0ANXX:8:1101:1594:2224 2:N:0:CGATGT
CACTTCTCAGGAGAGGGCTGGCATGTGCTTTCTCTTGGAATTGGTGTGAG
+
3<:AAFG>11>C>0;F//@F/FG1>1=EFE>11<1<>B1EGF1:1=0==1
@HWI-D00311:109:C8TK0ANXX:8:1101:1774:2030 2:N:0:CGATGT
CAAACACTCTCTGGGCACTCTGCACCTACACTAGTTTAGGAGGAACTATC
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGG

Starting FASTQC command


Processing G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq

Printing command:
fastqc --outdir G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq

Analysis complete for G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq

Processing G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq

Printing command:
fastqc --outdir G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq

Analysis complete for G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 5.0G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:31 .
drwxrwxrwt. 40 root   root       92K Dec 21 10:35 ..
-rw-r-----   1 kkarri waxmanlab 2.5G Dec 21 10:30 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq
-rw-r-----   1 kkarri waxmanlab 2.5G Dec 21 10:30 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:35 G123_M2_FASTQC
==========================================================
Finished on : Fri Dec 21 10:35:44 EST 2018
0 hours, 5 minutes and 19 seconds elapsed.
==========================================================