-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M9
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G170
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Sep  4 09:01:56 EDT 2019
Running on node : scc-tk3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/02_FASTQC
Current job ID : 9135342
Current job name : Step_02_G170_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9135342.1.linga

Loading required modules...


List files in scratch directory:

total 5.7G
drwx------  3 kkarri waxmanlab 4.0K Sep  4 09:13 .
drwxrwxrwt. 9 root   root      4.0K Sep  4 09:01 ..
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep  4 09:13 G170_M9_FASTQC
-rw-r--r--  1 kkarri waxmanlab 2.7G Sep  4 09:07 G170_M9_R1.fastq.gz
-rw-r--r--  1 kkarri waxmanlab 3.0G Sep  4 09:13 G170_M9_R2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G170_M9_R1.fastq <==
@K00124:462:H3HCGBBXX:2:1101:7121:1766 1:N:0:TTAGGCAT+AGATCTCG
TGCTGGAAGCAGCCAAGCATCAGTATAAAGACACAGATAAGACAGGCCAGGCACAGAGGCAGGCTGACAAGTAGTTGGAAAAGCAATCGCTTCCAGGGTGGGTAGTAGAACCCCTCAGCCCGGGTGCTGGGGCTGATGAGCCGGATGCGC
+
AAFFFJAFJFFJFJJJJFAJJJJJAJ<FJJ-<-<---FF-FFFFAJ-77FJFAJFJJJAJFFFJA<-AJ7FJJA-AJAF7J-FAA-7A7JFF-F--FA-F---7AJFF7-7--7FA-F<<<<<J-A-<A7F<7A--7<--7-AFA)<<)7
@K00124:462:H3HCGBBXX:2:1101:8440:1766 1:N:0:TTAGGCAT+AGATCTCG
CTGTGTCAAAGATGGCCTGGGGTTCTGGGTGAAACTTGGCTTGGGTTTGAACTGGGGCCTTGGTGGGTCCCGACTGCCTGGATTTTGTGTCTTTAGCTTCTGCTCCTACCAAGGGCTGGACAGCCTCTTTCTGTGTATCAGCACCATGGG
+
A<<FFJFJFFJFJFJ<AF-FJJJJAJFJJJF------FFAF<AJJJ-7<<FJFJA<F<FFFJ<-<-777----77A--77F-7F-A---A<-A---7<<JJ<JF-77-A---F-7777A-A------7F<-7F--7--7-7--7))-7)F
@K00124:462:H3HCGBBXX:2:1101:9820:1766 1:N:0:TTAGGCAT+AGATCTCG
AGATTACCTAAACATTTTTTAAAAACTGGAACCTGCAAATAAAATAATCTGATAAAGTCTCTATTAACACTTATAAAGAATCATGAGGCTCTTGCCATTTTTCTTGCGAAACCTTCAGCCAGTTGTTCAAAGATCGGAAGAGCACATGTG
+
AAFFFFJFJJJJJJJJJJJJJJJJA-FJJJF7FFJ-AJJ-FFJAJFJF-AFJFFFJJJ-A-F<7FFAA<7<FAFAA-77-AFFJJJFA<FJA-77AAJJFJ<JJJ-A77---7AFF-AAFA<JJFJFA--77AF7F<----<-7)7-7A<
@K00124:462:H3HCGBBXX:2:1101:15463:1766 1:N:0:TTAGGCAT+AGATCTCG
CGCCTTCTTCTTCTTCTTAGGTTTTTCTTCTTGAATTATAGGGGGGTTTGTAGCTTCTCGTTGTAGATAGCTAATAAAATCATTTAATTCACGGTCACCTTCATACTTCTTTGGAGTTAGCTTCTTGTTGGCTTGTGAGAAGTAGATGGT
+
AAFFFJJJJJJJJJJJJJ<JJAFAAFJJJF7FA<F--FJJJJJJJ7FJJJJJJJJFJF-JFFJJJJJAFAAJFF<<JFFJJJJJFF<F<-F7AF-AAJJFJJFJAAAJJJF-7AAA7J<AFAA-7J-AJ<FFF---A-A---F7-7AFA<
@K00124:462:H3HCGBBXX:2:1101:17026:1766 1:N:0:TTAGGCAT+AGATCTCG
GGCCCACCCCGACGTCGGGGATCATCCAGGTAGTTGCGTACTGGGTTGGGCTCCAGCACCCCTTCCCGCTGGTTGCGCTCATATTCTGCAATCTTCTCCATCTCCTCATTCATCTTCTCGATATTCTGCCTGCGCCGTAGATCGGAAGAG
+
AAFFFFJAJJJJJJJJJJJJJJJJJJFFJJ-FJJJFJJJ-FJJJJJJFJJAAJJ<FJJJFA<JJJ-AJA7AFJJJ-J---A<<JFJ-<-7-<-7FJFJJFJJAJAJJFA<--FFFFFF<<7<7FFJ-A-7JFF------A-A<A<A----

==> G170_M9_R2.fastq <==
@K00124:462:H3HCGBBXX:2:1101:7121:1766 2:N:0:TTAGGCAT+AGATCTCG
CTCACCTGGGGAGGCTGTGGAGGAGCTACGTCGCCAGTTCAGGGGCATCTGGCGCACCAGCTCCTTCACCCTGGCTGCGGAGTTCTACTACCCACCCTGGAAGCGATTGCTTTTCTAACTACTTGTCAGCCTGCCTCTGTGCTTGGCCTG
+
AA--AFFJJAF7<J<JJJFA<FA<FA-<-7FF7J7FFFJ-<<A7JJ----<<A<<<--7AA--7-A-FF-7-77-7FA---777-7-<7---77F-A<77---7A<AFJ<A<-F7-A-77<-FF7-<--777)-A7))------7-7)7)
@K00124:462:H3HCGBBXX:2:1101:8440:1766 2:N:0:TTAGGCAT+AGATCTCG
CCGCAAGCTTCCATCAAGCCGGCTGGAGGTGGGAAGGGGCTGGTCCCCGTGGACTTGGAAGTGGCGTACACTGCAGTCCGTCTTGGTGTAGCCAAGAGTTCGGAGAAGCAGGCTGCCACGGTAGCGGCTGGGTCGTCCTACGACGCCTTT
+
A-A-A-A-7-<--<<<-F--A<7--A7---7A-77AJ-A--7J--7--7-777--AAFA--<7F-A------7--7--777---7--<-------77-7---7-A--7<-77-77---------)-)7-A)A)))))-)--<--7)-))-
@K00124:462:H3HCGBBXX:2:1101:9820:1766 2:N:0:TTAGGCAT+AGATCTCG
TTGAACAACTGGCTGAAGCCTTTGGAAGAAAAATTGCGAGAGCGTCATGATTCTTTATAAGTGTTAATAGAGACTTTCTGAGATTATTTTGTTTGCAGTTTTCAGTTTTTAAAAAATGTTTTGGTAATGTAGATCGGAAGAGCGTCGTGT
+
AAFAFFJJJJJF-F<A<FF-<<---<-FFFFA-F-FA-FF-7-7A7--F-FJFFJJJFF-<7-<--7<A--7-7AFF-7-7--<JAJJ<FFJFJJ-7-7J---77AAJAA<-----7<-<--7------77F----)7-)---)7AF<)-
@K00124:462:H3HCGBBXX:2:1101:15463:1766 2:N:0:TTAGGCAT+AGATCTCG
TTTTCCTACCATCTTCTTCTCACCAGCCAACAAGAAGCTAACTCCAAAGAAGTATGAAGGTGGCCGTGAATTAAATGATTTTATTAGCTATCTACAACGAGAAGCTACAAATCCCCCTATAATTCAAGAAGAAAAACCTACGAAGCAGAA
+
AAA-AA7AFJJJFF-AJFF-7F7FAJ<AFJ<J7J7FJJJJJJF7F<A<F-FJJA-AAJJFFF7J<JFJ-<<J<-7AF-AFJ<7AJ-7A--A-7<<FFFJ77---A-A7<AF--7-77-7<A-A<<--7-7-------A7--<--<)7A--
@K00124:462:H3HCGBBXX:2:1101:17026:1766 2:N:0:TTAGGCAT+AGATCTCG
GCGGCGCAGGCAGAATATCGAGAAGATGAATGAGGAGATGGAGAAGATTGCCGAATATGAGTGCCATCAGCGGGAAGGGGTGATGGAGCCCAACCCAGTACGCAACTTCCTGGATGATCCCCGACGTCGGGGTGGGCCAGATCGGAAGAG
+
AAFFFJJJJJJJFJ-FJFJFAFJ<<F<J7-FJ<F-7FFJJJAJ-7A-A-<FJJJJJJJJJF--7-F-A-77FAF7<A-<AJ77<F-7FA-FF<FJJJFJF<A7<7FJJJ<F7<77<A--JFAF<AA)7-J<JF-)))A-F)77<<-<)-7

Starting FASTQC command


Processing G170_M9_R1.fastq

Printing command:
fastqc --outdir G170_M9_R1.fastq

Analysis complete for G170_M9_R1.fastq

Processing G170_M9_R2.fastq

Printing command:
fastqc --outdir G170_M9_R2.fastq

Analysis complete for G170_M9_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 28G
drwx------  3 kkarri waxmanlab 4.0K Sep  4 09:18 .
drwxrwxrwt. 9 root   root      4.0K Sep  4 09:01 ..
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep  4 09:33 G170_M9_FASTQC
-rw-r--r--  1 kkarri waxmanlab  14G Sep  4 09:07 G170_M9_R1.fastq
-rw-r--r--  1 kkarri waxmanlab  14G Sep  4 09:13 G170_M9_R2.fastq
==========================================================
Finished on : Wed Sep  4 09:33:02 EDT 2019
0 hours, 31 minutes and 6 seconds elapsed.
==========================================================