-----------------------
Start of variable list:
-----------------------
Sample_ID:
Yg_WT5
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 : 7055530
Current job name : Step_02_Yg_WT5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055530.1.linga

Loading required modules...


List files in scratch directory:

total 4.3G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:09 .
drwxrwxrwt. 22 root     root      4.0K Jun 24 16:06 ..
-rw-r--r--   1 varsha97 waxmanlab 2.0G Jun 24 15:57 SRR8261617_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.3G Jun 24 16:09 SRR8261617_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:09 Yg_WT5_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261617_1.fastq <==
@SRR8261617.1 1/1
NGGCACATGCAATAAACCAGTTTGAACTGGCTTGGTGTCGATGTCCTCTGGTTTAACCAGAGGTTTTAAAGTAAAATGCTGTAAGATGTTGGTCAGGATTAGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCT
+
#AAFFFJJJJJJJJJJJFJJJFJJJJJJJJJJJJFJJJJJFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJFFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJF<F
@SRR8261617.2 2/1
NCGGTAATGCAACTTCTGAATCCCTTGAAAATATAAACATCCAGTCTAGCAGTCTGTCTTGAATGAAATCTGTAGATTTTCCTTTTACTGTCACGTGTAATTACCAAAAAAGATACTTCCCAAGCAGAGACATATTCAGCTTTCTTCTCA
+
#AAAF<JJJFFFJJFJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJFFJJFJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJA<AJFJJJJJJJFFJJJJJJFJF<FF--F-7AFAFJJJFFJJJJA<JJJJJJJJJJJJA
@SRR8261617.3 3/1
NCTCACTGGGGAGAAGAAGATGTTGGAAGTGTTGGACTGATGGACCAGCTCCCGGTATAGGCTGATGGCAAAGTCTCCCAGGTTTTGTAGCGATCTCATGGGAGGCTGGGGACTGATCCTTCTGGGAGGTGTCTGTCTCCTGAACATCCT
+
#<<AAFFJJJJJJFJJJJJFJJJJJJJJJJJJFJJJJJJJJFAJJFJJJJJJJJJAJFJJJJFJJJJJJJJJJJJJJJAAFJFFFFJJJJJJJFJFFJJJJJJJJFJJJJJ7A<JFJJJFJJJJJAFJFFFJJJJFFJJAFJJJJJJAA<
@SRR8261617.4 4/1
NAGGTTTCATATGACTAACAGAGGTAAAGAAGCCAGTGCTATTGAATTTACATTTAATTCCTCAAAATGCACACACTATAACATTTTAAATGCCTACAGCAGGGTTCATTTGTTTTTATCTTTTTAGCCCAATTGAACAAATTCTTCAGT
+
#AAFFJJFJFJJJFJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJFJJJJJFJJJJJJJJJJJJJJJJJJJJFJJJJJFJJFJJJJJJJFJ7JJJFJJFJ<JJJAJJJJJJF<AJJJJJJJJA<-AAFJJJAFFFJJJJFFFFFFJ
@SRR8261617.5 5/1
NATTAAAGTTCCTTTCCATAGAACTAGATTCTTCTGCATGGATACAGACTAAAGTCAGTTCCAAACACAGGAGCAGAAGCAGCGGCAGCAGCAGCTTCATTTTGGTAGGGAATAGAATTGTCCTCCTGTCAGGACCACGTCTTTCAGAGA
+
#AAFFJJFJFJJJJJJJJJJJJJJJJJFAJJJJJJJJJJJJJFFJJJJJJJ<JJJJJJJJJJJJFJJJJJJJJFFJJJJJJJJJJJFJJ<<FAJAJFFJJJAJJJJJJJJFJFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJFJJJ<

==> SRR8261617_2.fastq <==
@SRR8261617.1 1/2
NTCTAATCCTGACCAACATATTACAGCATTTTACTTTAAAACCTCTGGTTAAACCAGAGGACATCGACACCAAGCCAGTTAAAACTGGTTTATTGCATGTGCCTCGATCGGAAGAGCGTCGTGTAGTGAGAGAGTGTCTTCGCCTGTGTA
+
#AAAAAFJ-FJJJ--7-<F--FFAA-<F-FFJAJJJJ<FJFFJJFF-AJFFJJ--AAF<AJJJJAAFFFF-A-77A-77A-AFJJJ7FFFJFJJJJFJJJJJJJJJJJJJJJAJJJF)F7FAAFJJ-<---77<-<<--7<<AA7-<)F-
@SRR8261617.2 2/2
NCTAAGGGTTCTCTCCAGCAACCCAAGAACCAGAGCTCCAAGAGCCTGGGGAGTATGTTCTCCTTGTGGGAAATTTGGGAGGTTGGTAAGAAGAGAACTAATCTAAAAGCATCATCATGGCTCAGATCTAGGGAAGTTGAGAAGAAAGCT
+
#<--<FJFAJJAJJA-FAJJ<-FAFJJ-F<<FF-A7-<JJ--AFJFAFFFJJJ-FF7F<7AAA7FF-7<7F-<FA<7F<77AAJJJJJJF<--AFFJ<---7AAJ<7<FFJAJA---<FJJJJFFJ<----7777A--A-<<7<F-F---
@SRR8261617.3 3/2
NAAAATGACTCCCTCAATGTCATGGCGCCTACTGCTTCAGGCAGGACGGTGTTGCATGGTTCCCAGCTTTCTGGCTGAGGATGTTCAGGAGACAGACACCTCCCAGCAGGATCAGTCCCCAGCCTCCCATGAGATCGCCACAAAACCTGG
+
#A7-<A7J7-7F-----<-<-F<-7-A7FAJJ<J<J<---<-FF--7-7--AF--F<77FFJJ-F7---7----FJA<-A-7-AA-A-<A7-FFJFF7A<F-<<JJ)-AAA-77A77A7AF7-<7)-A-F)------7))-<F-<<<FF7
@SRR8261617.4 4/2
NCCAACATTTTAAAAAGGTTATAGCATTCTTGCAAGATTAAATAGGGATAATTTTGCTATCATTTTGGTGGTCACTATCCTCCACTCAGAGTCACTGAAGAATTTGTTCAATTGGGCTAAAAAGATAAGAACAAATGAACCCTGCTGTAG
+
#AA-<FJF--<JAFFJ<A-A7FJJJJJ<JJJF<-FJ-7JJJJJF7-F--F777<AF-A-F-A<<A<J-<F<A-A7FFF<AAJJJFAFJJJFAFFJJF-FAJ-FFJFFJJ<AJFFJ<J7FJ<JJ7-<---77<AJJFJJJ--7<A<-)--7
@SRR8261617.5 5/2
NTGAAAGACGTGGTCCTGACAGGAGGACAATTCTATTCCCTACCAAAATGAAGCTGCTGCTGCCGCTGCTTCTGCCCCTGTGTTTGGAACTGACTTTAGTCTGTATCCATGCAGAAGAATCTAGTTCTATGGAAAGGAACTTTAATGAGA
+
#-7-<AAAAFF---J<JJA7FFJAJ-FFJJ<JJFF<-<F<JJJ-AFF-A-FAJFJJJJJFJJJA7--A7<7AJJ7-7A-A-7FAFJJF7FF-AJ<<FJJ<-<-<J-7F7F<AFFF-A-A<<JAA-FJFF-A7-7<<7F<FAA-AAF777-

Starting FASTQC command


Processing SRR8261617_1.fastq

Printing command:
fastqc --outdir SRR8261617_1.fastq

Analysis complete for SRR8261617_1.fastq

Processing SRR8261617_2.fastq

Printing command:
fastqc --outdir SRR8261617_2.fastq

Analysis complete for SRR8261617_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 19G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:17 .
drwxrwxrwt. 15 root     root      4.0K Jun 24 16:43 ..
-rw-r--r--   1 varsha97 waxmanlab 9.4G Jun 24 15:57 SRR8261617_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 9.4G Jun 24 16:09 SRR8261617_2.fastq
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:44 Yg_WT5_FASTQC
==========================================================
Finished on : Mon Jun 24 16:44:39 EDT 2019
0 hours, 55 minutes and 39 seconds elapsed.
==========================================================