-----------------------
Start of variable list:
-----------------------
Sample_ID:
O_YgHet_1
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 15:49:10 EDT 2019
Running on node : scc-kb8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/02_FASTQC
Current job ID : 7055546
Current job name : Step_02_O_YgHet_1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055546.1.linga

Loading required modules...


List files in scratch directory:

total 4.4G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:09 .
drwxrwxrwt. 21 root     root      4.0K Jun 24 15:56 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:09 O_YgHet_1_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 2.1G Jun 24 15:58 SRR8261633_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.4G Jun 24 16:09 SRR8261633_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261633_1.fastq <==
@SRR8261633.1 1/1
NGTAAATGTGGGGGGTCAAAAGGCGGGCGATTTCAGGGCGCATGCGGTGCTGGTAATTCAGACGGACAAAGGGGATGTTCACTTTTACCAGCCGTTCAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTAT
+
#A-AFFAJFFJJJJJFJJJJJJJJJJFJJJJA<FFJJJJJJJ<J<JJJJJJJJFJJJJJJJFJJJJJJJJJJFJAFAJJJJJJFFFJJJJJJJJJF<FJJJJJJFJJJJ77FFA-FAFFJJJJJJJFFJFFJJJJJA<A-A7<7<JJJJJ
@SRR8261633.2 2/1
NGAGATACTGGGAAAAGGCAATCAGGACTAGGCCTTTGAAATGTTGTTCTCCCAAATCATTATACCGATGGGCGATCTCACTCTTGTGTGCTTCTCGGCGAAACACACCCCTAGAAAAAGCAGAGCCGGAGACGAAGAGGAGGAGGAGAA
+
#AAFFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJF<JJJJJJJJJFFJAJJJJJJJFAFJJJJJJJJJJJF<AFFFFFJJJFJAFFJJJJJJJJJFJ<AJJJJJJJJJJAAAA
@SRR8261633.3 3/1
NTGGGCTCCACCCGGACCTCAAAACTGGGCAGCACGTATTCCTTCACCTCAAACTCTGCGGAGAAGATCTGCTTCGGCGCATGTTCGTAAAAGGCTCGGATCTTCCACTGCCCCATGTTGACAGATCGGAAGAGCACACGTCTGAACTCC
+
#AAFFJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFF<JJJJJJJJJJJJJJJJJJJJJJJ
@SRR8261633.4 4/1
NCCCGCTTCTCTGCCAGGTCCTTCTCTTTCTGTAGCTGCCGGCTCCTCTCTATCCAGGCTGCAGTATCATCCAGCCAGGGGTCATCCTCCCCCAGTGTCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATATCGT
+
#AAAFJFJJJFJJ<FJJJ<J<JJFFAFFF<<JJJJFJFJ<J<FJ--7F7JJJJJJJJJJFJJJJJAJ<FFFFJJJJJJF<7F7FFFFFFFJJ7JFAJJJJ<FFFAJFFJJFAAJJFJFJF7AJJ-F7FJJJFAAFFAJFAJFFJ--<77A
@SRR8261633.5 5/1
NTCGTGATCACTTCCTCTTCACTATCAAACGGAACAACACACGTCACTGGACCAAAGATCTCTTCCGTCATGCAGCGGGACTCATCCTTAATGTCTGTTATCACCGTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCT
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJF

==> SRR8261633_2.fastq <==
@SRR8261633.1 1/2
NTGAACGGCTGGTACAAGTGAACATCCCCTTTGTCCGTCTGAATTACCAGCACCGCATGCGCCCTGAAATCGCCCGCCTTTTGACCCCCCACATTTACCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTAGATCT
+
#AAA<FAAAFFFJJ--FF7FJFJFFJFFJJAAF--7FJFFJFJJAAF7A-7F-A-AFJ-FAAJ-<J<J<JFFJ<A-7A7FAJFFF7-FFJ<J<<AJJ<FF7J<FJAA<FFFJ7<)-A<F7F-A<JFAJFA7<AAF-AFAFFFA<-77<<F
@SRR8261633.2 2/2
NGGTAACCTTTCTCCTCCTCCTCTTCGTCTCCGGCTCTGCTTTTTCTAGGGGTGTGTTTCGCCGAGAAGCACACAAGAGTGAGATCGCCCATCGGTATAATGATTTGGGAGAACAACATTTCAAAGGCCTAGTCCTGATTGCCTTTTCCC
+
#AAAF<-FFJAJ777A7J<-7FJAFFJJJJ7F-FF-AAJJF-<A<JJFJFFFAAAJJJJJJJA<A--<<-<AJAFFF-AFFFJF7JFJFF7A7FJFFFJ-<<FAFAF<<JAFAFFJA7AFJF-<<77A7FF)<FJJJF-A-<F<77<-F<
@SRR8261633.3 3/2
NTCAACATGGGGCAGTGGAAGATCCGAGCCTTTTACGAACATGCGCCGAAGCAGATCTTCTCCGCAGAGTTTGAGGTGAAGGAATACGTGCTGCCCAGTTTTGAGGTCCGGGTGGAGCCCACAGATCGGAAGAGCGTCGTGTAGGGAAAG
+
#AAAFFJFJJJFJJJJJFJJJJJFJJJJJJJJFFJJJAJJJJFJFJJJJJJJJ-AFJJJJFJFF<AAFJ-7FJJJJJJJJAJFJJJJJJJJJJJFJFAFFJJFJJJFJFJJJ7F-AFJFJJJJ7FJJ-<FAFAFAA)7FF7-FF-AAFJ-
@SRR8261633.4 4/2
NAGACACTGGGGGAGGATGACCCCTGGCTGGATGATACTGCAGCCTGGATAGAGAGGAGCCGGCAGCTACAGAAAGAGAAGGACCTGGCAGAGAAGCGGGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCATGTGTAGAT
+
#<A-FFJJJJJFFJFFF7JAFJJJJAJJJAFJ7F<-FFJJJFJJF-7<JAFJJJFJJJJJJJFJFJJJFFFJFAFJFFAFJJJFJJJFAJJFJAJFFFJJFAF7J<AJFFAFA-))--)AFAFJAFJJFJ7<F<<---7)--<FA7<<--
@SRR8261633.5 5/2
NACGGTGATAACAGACATTAAGGATGAGTCCCGCTGCATGACGGAAGAGATCTTTGGTCCAGTGACGTGTGTTGTTCCGTTTGATAGTGAAGAGGAAGTGATCACGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTG
+
#AAAFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJFJJJJJJJFJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFJJJJJJJJJJJJJJJJJJJJJJAFFJJJJJJJJJ

Starting FASTQC command


Processing SRR8261633_1.fastq

Printing command:
fastqc --outdir SRR8261633_1.fastq

Analysis complete for SRR8261633_1.fastq

Processing SRR8261633_2.fastq

Printing command:
fastqc --outdir SRR8261633_2.fastq

Analysis complete for SRR8261633_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 20G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:12 .
drwxrwxrwt. 16 root     root      4.0K Jun 24 16:42 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:42 O_YgHet_1_FASTQC
-rw-r--r--   1 varsha97 waxmanlab  10G Jun 24 15:58 SRR8261633_1.fastq
-rw-r--r--   1 varsha97 waxmanlab  10G Jun 24 16:09 SRR8261633_2.fastq
==========================================================
Finished on : Mon Jun 24 16:42:44 EDT 2019
0 hours, 53 minutes and 34 seconds elapsed.
==========================================================