-----------------------
Start of variable list:
-----------------------
Sample_ID:
Yg_WT3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE123117
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 15:49:00 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/02_FASTQC
Current job ID : 7055528
Current job name : Step_02_Yg_WT3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055528.1.linga

Loading required modules...


List files in scratch directory:

total 4.3G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:13 .
drwxrwxrwt. 22 root     root      4.0K Jun 24 16:06 ..
-rw-r--r--   1 varsha97 waxmanlab 2.1G Jun 24 15:56 SRR8261615_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.3G Jun 24 16:13 SRR8261615_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:13 Yg_WT3_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261615_1.fastq <==
@SRR8261615.1 1/1
NCATGATGTCTGTCCTGAAGTTCTTGGTGGCTAGGAGGTGCCCAGAGAAGGACAACGTGGGGGTACCTCAGAGTGGGTAGAGATGCCACAGGCTGCATTGGAAGTGAGGGTCTTCAGGGTGTGCCTTCAACAGATCGGAAGAGCACACGT
+
#A<AFJJJJFFJJ<FJJJJJJJJJJJJJJJJJJJFJJJJJJJJJAAJJJJJJJJJJJJJJJJJJJJFJJJJAJJJJJJJ7JJJJJJFJJJ7JJJJJFFJJJJJJJJJJJJJJJJJFA7F-FFJJ7<FJJFFFAFFJJJAFAJJJJJJAAF
@SRR8261615.2 2/1
NTCCTATTAGATTGATTGAAGGGGGTAGAGCTAGATTAGCTAGACTTGCTATCAGTCATCATGTGGCTATAAGTGGGAAGACCATTTGAAGTCCTCGGGCCATGATTATAGTACGGCTGTGGATCCGTTCGTAGTTGGAGTTTGCTAGGC
+
#AAAFJJJJJFJJFJJJFJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJFJFAJJJJJJJJJJFJAJFJJJFFJJJAJJJJJJJJF
@SRR8261615.3 3/1
NCCCACGGAAGCTGCGCCTGCCAGGAGCATCGTATTTGAAATCTGAAGGCGCAGAGTCTTCTAAAAGCAAGTCTGTGTCTGAGCTGGTGGTTAGAAGCTCTACCTCACTGTCGGCCTCATCCACACATAGGTCTTCAGAGATGGGCAGTG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJ
@SRR8261615.4 4/1
NGGCAGCCATGAAGTCATTCTAAATTTGTTGAAGCATACGATACTGATATTACTTCTCGTTTTGAAGCAAAGGCCTCTCAAATTATAAAGATCATGATGAGAACAGCTGTTAGTGAAATAAATGATCCTATAGAAGAGAGATCGGAAGAG
+
#AAFFJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJFJJ7A-FJF<AFJJJJJJJJJJJJJJFJFJFJJJJFFJAAJJJ<
@SRR8261615.5 5/1
NCTGTGGCTGAAAGGAAGTTGAGGCTGCAGATTCATCATCATCATATTCATCAGAATCATCTTGTTGTTTCTTTTTCTGACTCTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCTCGTATGCCGTCTTCTGCT
+
#AAFFJJJJJ<JFJJJJJJJJFJJFJJJJJJFAJFJJJFJJJJJJJJ<JJJJJJJF<JFFFFJJJJJJJJJJJJJJFJFAJFJJJFJJJJJJJJFJJJJJJFJJAFJJJJJJJJJAJJFJJJJFFFAFA7<FAFFJFFFJJ7AAJFAAFF

==> SRR8261615_2.fastq <==
@SRR8261615.1 1/2
NTTGAAGGCACACACTGAAGACCCTCACTTCCAATACACCCTGTGGAATCTCTACCCACTCTGAGGTACCGCCACGTTGTCCTTCTCTGGGCACCTCCTAGCCACCAAGAACTTCAGGACAGACATCATGGAGATCGGAAGGGCGTCGTG
+
#-A7FJ7<JJJJ---<7FJAF<---7--F7-7<---<---7<J7A---<-AJF7JJ-7-<-F--<F--<A--A-<<F<A<-AJJJFFF<F<7<A-F-7AFFF)FF)7<FJF7A<AJFJ77A)<FFJ--<7F---<-FF777))7))<-))
@SRR8261615.2 2/2
NTTCATAGGAGCAACAATACTACTAATCGCACATGGCCTCACATCATCACTCCTATTCTGCCTAGCAAACTCCAACTACGAACGGATCCACAGCCGTACTATAATCATGGCCCGAGGACCTCAAATGGTCTTCCCACTGATAGCCACATG
+
#<-AFFJJFFJA<F-FFJJJFF7F7JJJJJJJJFFFFJJJAJFA7JFJ-A7<F<AF7JJAJJJJ<-AJJJJJJAJA-AA--7AFJJ7A-AFF-A-AFA-FA-FJFJF---AFJ)AF<)<)-<7F<A-<FF<FAFJAF-)-<A<AFJJJJ7
@SRR8261615.3 3/2
NCCCCTTTCCCCCGCGCGGCTCTCTGTGAACCGGGTTCTCGGCCGCTCCCGCCACTGCCCCTCTCTGAAGACCTATGTGTGGATGAGGCCCACAGTGAGGTAGAGCTTCTAACCACCAGCCCAGACACAGCCTTGCTTTTCAAAAACTCT
+
#<AAF<JJJFA<<---7F-A77--7--7<-<--7A----<<JAJ7---A--7A-AF-7AJ7777--77-7-7F---777FAF7-7--A7A-7AFJ-<A-A-7-----7AA<F-----7)-)7))-)7A--)77F)A---<---7----7-
@SRR8261615.4 4/2
NTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCATGATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGAGAAGTAATATCAGTATCGTATGCTTCAACAAATTTAGAATGACTTCATGGCTGCCCAGATCGGAAGAG
+
#AAFFJFJJJJJJJJFFJJJJJJJJFJFJJJFJFJJJFJJJJJJJJAFJJJJJJJJJJJJFJFFJJ7FJF7AJJJJFJFJAJJFJJJJJJJJJJJJJJ-AFFJJJFFFFAJJJJFJJJAAAJJFJ<FJJJ<FFF7)7<<))7F-7AFAA-
@SRR8261615.5 5/2
NGAGAGTCAGAAAAAGAAACAACAAGATGATTCTGATGAATATGATGATGATGAATCTGCAGCCTCAACTTCCTTTCAGCCACAGCAGATCGGAAGAGCGACGGTAGGGAAAGAGTGTAGGATAGGGTGTAGATCTCGGTGGTCGCCGTA
+
#AAA<A-A<AJFJJFJFFJJFJJJJFJFAA<---FFFJAAJJJAJFJJJFAJFJJ<A-7FJJ-FAAF-FA<<JJFJ<AFF-FJFAJJJF<JAFFJFFAFA-AF<<<<JJJJJA-7-7-<FJA-<F<F7A)<-<<<FJJJ-))<AFJJJ<F

Starting FASTQC command


Processing SRR8261615_1.fastq

Printing command:
fastqc --outdir SRR8261615_1.fastq

Analysis complete for SRR8261615_1.fastq

Processing SRR8261615_2.fastq

Printing command:
fastqc --outdir SRR8261615_2.fastq

Analysis complete for SRR8261615_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 20G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:18 .
drwxrwxrwt. 16 root     root      4.0K Jun 24 16:43 ..
-rw-r--r--   1 varsha97 waxmanlab 9.7G Jun 24 15:56 SRR8261615_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 9.7G Jun 24 16:13 SRR8261615_2.fastq
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:43 Yg_WT3_FASTQC
==========================================================
Finished on : Mon Jun 24 16:43:48 EDT 2019
0 hours, 54 minutes and 48 seconds elapsed.
==========================================================