-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M3
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-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/02_FASTQC
Current job ID : 471776
Current job name : Step_02_G123_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/471776.1.linga

Loading required modules...


List files in scratch directory:

total 1.6G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:30 .
drwxrwxrwt. 32 root   root      128K Dec 21 10:30 ..
-rw-r-----   1 kkarri waxmanlab 780M Dec 21 10:30 G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 795M Dec 21 10:30 G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:30 G123_M3_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1325:2065 1:N:0:TTAGGC
NTCCCATGTGATGCTGCTGTCCTTCTCCGATGGAGAGTCTGTTGAAGGGA
+
#<=ABGGGGEFG1F@@FGGCGGGG>CGGGGG/>CFGF1>CFBDF@1CDGB
@HWI-D00311:109:C8TK0ANXX:8:1101:1467:2118 1:N:0:TTAGGC
CTCATCAATAGGTTCTCCAATGACATTCATGATTCTGCCCAAGGTCTCAG
+
BBBCBGGGGGGG;CDGGGGGGGGGGGGDDGGGGGGGGGGGGGBGGDFCGF
@HWI-D00311:109:C8TK0ANXX:8:1101:1312:2197 1:Y:0:TTAGGC
ATACGGATTGGAAGTTCTATTGGCAGAACGACTCGATTATCAACTTCTAG
+
=B@0A</?FE>DF>1;E1==11:E19011=9<EGG01=/<11F111=G:>
@HWI-D00311:109:C8TK0ANXX:8:1101:1536:2019 1:N:0:TTAGGC
NGCACGATTAGCTTTCCCTGGTCAGCATGATTAACTTTCTAATGCTCAAT
+
#<=:AFBGGGFG>FCGGGGCGFGGGFGGGGGEGGDGGGGGGGGGG@GGGE
@HWI-D00311:109:C8TK0ANXX:8:1101:1560:2116 1:N:0:TTAGGC
TGCTTGAGCAAAGGGGATGCCCAGGAAGACATTTACCATGCGGTCTGTGT
+
<?B00111=CF@11;;E/CDCF>DFDGGD:EDGGGGGGG1EEEEECFE1C

==> G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq <==
@HWI-D00311:109:C8TK0ANXX:8:1101:1325:2065 2:N:0:TTAGGC
CGAATTGAACTTTAACCAGCTAAGGAAATGTAAAGGAAAAAACGACCCAT
+
CCCCCGGGGGGGGFGGGGGGGGGGECGGEGGGGGGGGGGGGGGFGGGGGE
@HWI-D00311:109:C8TK0ANXX:8:1101:1467:2118 2:N:0:TTAGGC
CTGGTTTTGGAGGTGGCCCAGCATTTGGGGGAGAGCACGGTCAGAACTAT
+
BCBBBGGGGGGB<FGGGGGGGGG@GGGEGGGGGDGGGGGGGGG>GFF>FC
@HWI-D00311:109:C8TK0ANXX:8:1101:1312:2197 2:Y:0:TTAGGC
ATGATACTGAAGCTACGAATATACTGACTATGAAGACATATGCTTTGATT
+
AB?@BB1CF1FGCFFGD/0;F1<1<=:CD1:<1E:FG1:::FGEF111:1
@HWI-D00311:109:C8TK0ANXX:8:1101:1536:2019 2:N:0:TTAGGC
GTGAATAAAGCTTTATGCTCCCTGCTCTTCATTTTAAATATTAGTGAGTG
+
BBBBBGGGGGGGGGGGFGGGGGGGG>BGGGGFGGGGGGGGGGGGGGGG@C
@HWI-D00311:109:C8TK0ANXX:8:1101:1560:2116 2:N:0:TTAGGC
CACTGTCATTGGACCCAAAGTCACTCAGCCTGAAGTGGATACCCCCCTGG
+
B=:ABGGG>D;1F1BF0CF1FGCDFGBEGGGGBGGEDG@CGGGGFEB/E0

Starting FASTQC command


Processing G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq

Printing command:
fastqc --outdir G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq

Analysis complete for G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq

Processing G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq

Printing command:
fastqc --outdir G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq

Analysis complete for G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 5.3G
drwx------   3 kkarri waxmanlab 4.0K Dec 21 10:31 .
drwxrwxrwt. 32 root   root      128K Dec 21 10:35 ..
-rw-r-----   1 kkarri waxmanlab 2.7G Dec 21 10:30 G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R1.fastq
-rw-r-----   1 kkarri waxmanlab 2.7G Dec 21 10:30 G123-pool-TTAGGC_TTAGGC_BC8TK0ANXX_L008_001.R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 21 10:36 G123_M3_FASTQC
==========================================================
Finished on : Fri Dec 21 10:36:09 EST 2018
0 hours, 5 minutes and 43 seconds elapsed.
==========================================================