-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M4
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G167
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jul 14 19:56:12 EDT 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/02_FASTQC
Current job ID : 6936714
Current job name : Step_02_G167_M4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936714.1.linga

Loading required modules...


List files in scratch directory:

total 2.3G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:56 .
drwxrwxrwt. 81 root   root      112K Jul 14 19:56 ..
-rwxr-xr-x   1 kkarri waxmanlab 1.1G Jul 14 19:56 4_S26_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.2G Jul 14 19:56 4_S26_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 19:56 G167_M4_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> 4_S26_R1_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1448:1226 1:N:0:AAGTCCAA+TACTCATA
CAGGAATGGCCTGTTGAAATGCACAGCTGGTAATATGGCCTTACGAATGCCACCAATAACCCCTGTGGCAGCAGCTGCTTCTGTGCCTGTCTCAGCCACATCCAGCACAGCCTTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJF7
@J00170:103:HMYG2BBXX:4:1101:2037:1226 1:N:0:AAGTCCAA+TACTCATA
CACTGGTCCAAAGATCTCCTCCTTGGCAATGGTCATGCCGTCTTTTACGTCCCCGAACACGGTGGGCTGGATAAAGTAGCCACGGTCCGCGGCAGCGCCCCCACCACACAGCAGCTTCGCCCCTTCTTGTTGTCCCGATTTGATGTAGCCG
+
AAFFFJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJFJFJFJJJJJJJJJJJJJJJJFJJJJJJ<JJJJJJJJJJFJJFJFJJJJJJJJFJJJJFFFJJ7--F-AFFFJJFFF
@J00170:103:HMYG2BBXX:4:1101:2483:1226 1:N:0:AAGTCCAA+TACTCATA
CACAGTCTTGGCTTCAGTACTCAAAAGTCACAGTCTTGATCCGCAGGTACTCATTCAGGGCCGCCTCTCCCAGGTCTTTGCCAAATCCAGACTGCTTGAATCCTCCAAAAGGTGCGGCCACATCGGTCTTGTTGTATGTGTTGACAAACAC
+
AAFFFFJJJJJJJJJJJJJJJJJJJJJFJFJFFFFJJJJJJJJJJJFJJFFJJFFJJJFJFJFJJJJJJJJAJF<JJJFFJFAAFJJFAFFFAJJFFAJJFJJJJFA7AF7AJ7FF7JJFJJFF7FJJJJJJ<FFJ<7<<AAA-<FFFFFF
@J00170:103:HMYG2BBXX:4:1101:2767:1226 1:N:0:AAGTCCAA+TACTCATA
GCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGACTTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTAAAGATCGGAAGAGCACACGTCT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJJJJJJFJF
@J00170:103:HMYG2BBXX:4:1101:3356:1226 1:N:0:AAGTCCAA+TACTCATA
CATTCTTCCACTTTGTGTCTACTTTCCTTTTACCGTTGATTTGCAGAGGCTAAGGAGGACTTCTAGTCACTAATGGTCTACTTTGAACAGGTGACCAGTGTAGTGTTACCTAGTGGTTTGTGACTTTAGTAGATCGGAAGAGCACACGTCT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJFJJJJFFJFJJJJJJJJJJJ

==> 4_S26_R2_001.fastq <==
@J00170:103:HMYG2BBXX:4:1101:1448:1226 2:N:0:AAGTCCAA+TACTCATA
ACAAGGCTGTGCTGGATGTGGCTGAGACAGGCACAGAAGCAGCTGCTGCCACAGGGGTTATTGGTGGCATTCGTAAGGCCATATTACCAGCTGTGCATTTCAANAGGCCATTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTA
+
AAAFFJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJFJJJFJJJJJJJJFJJJJJJJJJJJFJJJJJJJJJJJJFJJ7JJJJJ#JJJJJFJJJJJFJJJJJJJJJJJJJJJJJJFFJJJJJFFAJ<-AAJJ
@J00170:103:HMYG2BBXX:4:1101:2037:1226 2:N:0:AAGTCCAA+TACTCATA
ATGAAACTCAGTTTAAGAAGATCCTCGGCTACATCAAATCGGGACAACAAGAAGGGGCGAAGCTGCTGTGTGGTGGGGGCGCTGCCGCGGACCGTGGCTACTTTATCCAGCCCACCGTGTTCGGGGACGTAAAAGACGGCATGACCATTGC
+
AAFFFJJJJJJFJ7FFJJJJJJJJJJJFF<JJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJFAJFAJJJJJJJJJJJJJJJJJJJJJJJFFFJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJ7)<F7A<FJJ
@J00170:103:HMYG2BBXX:4:1101:2483:1226 2:N:0:AAGTCCAA+TACTCATA
GTATGTCAGTGACNAACTGCAGGCGGGCACTGTGTTTGTCAACACATACAACAAGACCGATGTGGCCGCACCTTTTGGAGGATTCAAGCAGTCTGGATTTGGCAAAGACCTGGGAGAGGCGGCCCTGAATGAGTACCTGCGGATCAAGACT
+
AAAAFJJJJJJJJ#JJJJJJJJJJJFFJJJ7FJFJFJJJJJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJJJJAJJJJ7FJFFJ-AJAAAJJJF-AA-AJFFJJ<FFJJJJJJFJ<FJJJFFF)<FFFJAAFJFA-A--<)<<-7<A<
@J00170:103:HMYG2BBXX:4:1101:2767:1226 2:N:0:AAGTCCAA+TACTCATA
TTAATGGCAACTTNAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCAGATCGGAAGAGCGTCGTGTA
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJFJ<F<AAJFFJJ7<A-<77F
@J00170:103:HMYG2BBXX:4:1101:3356:1226 2:N:0:AAGTCCAA+TACTCATA
ACTAAAGTCACAANCCACTAGGTAACACTACACTGGTCACCTGTTCAAAGTAGACCATTAGTGACTAGAAGTCCTCCTTAGCCTCTGCAAATCAACGGTAAAAGGAAAGTAGACACAAAGTGGAAGAATGAGATCGGAAGAGCGTCGTGTA
+
AAFFFJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<F

Starting FASTQC command


Processing 4_S26_R1_001.fastq

Printing command:
fastqc --outdir 4_S26_R1_001.fastq

Analysis complete for 4_S26_R1_001.fastq

Processing 4_S26_R2_001.fastq

Printing command:
fastqc --outdir 4_S26_R2_001.fastq

Analysis complete for 4_S26_R2_001.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 11G
drwx------   3 kkarri waxmanlab 4.0K Jul 14 19:58 .
drwxrwxrwt. 81 root   root      112K Jul 14 19:56 ..
-rwxr-xr-x   1 kkarri waxmanlab 5.3G Jul 14 19:56 4_S26_R1_001.fastq
-rwxr-xr-x   1 kkarri waxmanlab 5.3G Jul 14 19:56 4_S26_R2_001.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:05 G167_M4_FASTQC
==========================================================
Finished on : Sat Jul 14 20:05:25 EDT 2018
0 hours, 9 minutes and 13 seconds elapsed.
==========================================================