-----------------------
Start of variable list:
-----------------------
Sample_ID:
MANFHet_4
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE123116_fullpipeline_run
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul 17 16:36:41 EDT 2019
Running on node : scc-kb8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/Scripts/02_FASTQC
Current job ID : 7774444
Current job name : Step_02_MANFHet_4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7774444.1.linga

Loading required modules...


List files in scratch directory:

total 12G
drwx------   3 varsha97 waxmanlab 4.0K Jul 17 16:48 .
drwxrwxrwt. 10 root     root      4.0K Jul 17 16:36 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 16:48 MANFHet_4_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 5.4G Jul 17 16:43 SRR8261645_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 6.0G Jul 17 16:48 SRR8261645_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261645_1.fastq <==
@SRR8261645.1 1/1
NTGCTGATGCTCAAATTCTTCCTTCTCTGCAGTCTGGTTCTTATCCAGCCAGCTGATGATTTCATTGCACTTGTCAAGAATCTTCTGTTTGTCCTCATCATTGATCTTGCCTTGAAGTTTCTCATCTTCCACAGTTGCTTTCATGTTGAA
+
#AAFAJJFFJJJJJJJFJJJFJJFJ7A-FFJJFJJJA--F<<JJJJJ7FJJJJ7FJFJJF<FJJJJ-AAJJJJFAJJAFFJJJFJJJJJJJJFJJJJJFJJJ-7FJJJJJJAJFJ-<7AFFF-<-AJFJJJFFJ7JFFJJFJAAFJJJJF
@SRR8261645.2 2/1
NTTAGAGAAGGTAACATTCAAACCCACTCTGACATTCTAAATAATACATTCTACAGATGCCTGTAAGAGGCAGCTGGCCTGGGAAGCAACACTTAGAAGGGAAGCCAAGAATAGTAGGGGCATCTACCCATCTCCCAGAAGCCATTCTGT
+
#AAFFJJJJJJJJFJJJJFJFJJJJJJFFJFF<JJ7JJFJJJJJJJJJJJJJJJJJJFJJJFJJFJJJJ<JJJJJJ<AJJAAJJJJJJJJJJJJJJJFJJJJJJJJFFJJJFJJJJJAJJJFAF7JJJJJJJFAFJJJJJJJJJJAFFJJ
@SRR8261645.3 3/1
NGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAA
+
#<AAFFJJJJJJAJAA<JF<FFFJJAJFJJJJ<FJFFJJJJJJJJJJJJJFJJFJJJJ--7FJFJJJJJJJ<JJJJJJJJJF<JFJJJJJJFJF7JJ7JJFFJJJA<JJJJAJF<<FJJFJJJ<AJFF<JJFJJJJJFJJJJFA<FJJFJ
@SRR8261645.4 4/1
NGCCCTGACACCTTTTGAGCTCCTGGAGGACCGTAGTCCTGGAACTGGGAGGCATAGCACTGTGGCGGGAACCCAGTCTTGGCGTTCTCCCCTGAGCTCCTGGTAGATGGTGGCTGGGGAGGTGGCAGGTGTCTCAGTGGCTGGCCCAGG
+
#AAFFAFAJFJFJJJJJJFJJJJJJAFJAFJJJJJJJFJJJJJJJJJJFJFJJJFJJJJJJFJJJJFJJ<FFAJJJJFAFJFFJJJJJJJJJFFJJJJJJJJJJJJFJJ<FJ-A-7AFJJJJ<J7FJFJ7JFJFJJFJJFFJJJ<AA7AF
@SRR8261645.5 5/1
NCACGTTTGTTTACACACACAGAGACACACAGCCTTGTCTCCCACCAGACACAGGCCTCGAAGGAGCAGCTGACAGGCAAGGCAGCTCGAGGGTGGTGCTTTCGCTCATCGGTCTATTTCTCCGAACACAATATCCTGGGTACCTATGAT
+
#AAFFJJJJFFJFJF<FJ<JFJJJJJJJJJFJJA<7FF--FAFJJJJFJFJJFJFAA-<<AAJJJJJJFJ<AF<FJA7FAF7FFJJJJJFFJJ-F<-AA<A<AJ7-F<7J<A7F-A7JFJJJFJJJJJJJJAFFFFFF7<<J<JJJFJJJ

==> SRR8261645_2.fastq <==
@SRR8261645.1 1/2
NAGAGGGATAAGGTTTCCTCCAAGAACTCACTGGAGTCCTATGCCTTCAACATGAAAGCAACTGTGGAAGATGAGAAACTTCAAGGCAAGATCAATGATGAGGACAAACAGAAGATTCTTGACAAGTGCAATGAAATCATCAGCTGGCTT
+
#A-7A-AAFF<JFF7-F--AJAJJF77-A<A-<FJJAF7<AAFJF7---AJJ7AFFJFJJAJAAJJFJJFAFAJJJJJFFFFAJJAJAJFJJJJJJJJJJFFJJAFFFFJFJFJJ---F-FAJFJ---<FF<JAAFJJJ7FF7F777<F-
@SRR8261645.2 2/2
NTTTGAATACTAAAATTTCCTTACTAGTCGTAAAGTTATTGATGGTTGTGTTTCTATTGTTTAAGCTGTTCAGCTACAGAATGGCTTCTGGGAGATGGGTAGATGCCCCTACTATTCTTGGCTTCCCTTCTAAGTGTTGCTTCCCAGGCC
+
#AA-FJJFJJ<JFJFJJJF<FAF<AJFFJJA-FFJ-FJJJJAJ<JA<FFJ<AJJJJ-7<<JFFJFJFJJJJJF7AJJAF<JFFJFJJJJJAJFJ<AJJJFJFJJ7FF7<-JJJJJJJFJJAJJJJFJAJ)AAJ--7-AFAFFFFAF7<<<
@SRR8261645.3 3/2
NGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGGAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTTCCTCCA
+
#A<AFFJFAJAJJF-FJJJJJJJ-FJ<JA-AFFJJJFFJFF-AA7FFJJF-<<AFJFJFJFJFJJJFFJJJJFAF-FFJFA7F7<--FAF-AAJJFJJJFJ-7FAJJ<FF<F-FFFAAFFFA7-F<<-<-7<A-A-<77AF-<-<FJ-)7
@SRR8261645.4 4/2
NTGGAAACGTATGAAGAGCCTCATGGGCGGGACCTGTCCTTTGATGCCTGACAAGACCATCAGTGCGAACATGGCCCCCGATGAATTCACCCAAAAATCTATGAGAGGCCTGGGCCAGCCACTGAGACACCTGCCACCTCCCCAGCCACC
+
#AA-AFFJFA<AJFFJJJFF-AJ7<AJFFFJJJJ7<JJJJJJJJJJJJFJFJJJJ<FJJJJJJ<JFAJJJFJJ-FFJJJJF-7FJAFJJJJAFJJJJJFJJF-FJFF7F7<JJ-F-<-A-F<AFAFFJJJA7)AA7JF77))-)<<FFJ-
@SRR8261645.5 5/2
NGGTGGCAGATGACGTGGCCATCATAGGTACGCAGGATATTGTGTTCGGAGAAATAGACCGATGAGCGAAAGCACCACCCTCGAGCTGCCTTGCCTGTCAGCTGCTCCTTCGAGGCCTGTGTCGGGTGGGAGACAAGGCTGTGTGTCTCT
+
#A-A--AAF7-<-<F-JJFJJ7----7A-F<---7F--7-A---7<<FJ-A7AFJJJJ7JJ<F<FFFJ--<A-7F-AA<77777A<-----F-7-7<<FFJFJJJJJ7FF-AJJF--F-----))A7-7)-77)--A<<-))7-7----7

Starting FASTQC command


Processing SRR8261645_1.fastq

Printing command:
fastqc --outdir SRR8261645_1.fastq

Analysis complete for SRR8261645_1.fastq

Processing SRR8261645_2.fastq

Printing command:
fastqc --outdir SRR8261645_2.fastq

Analysis complete for SRR8261645_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 51G
drwx------   3 varsha97 waxmanlab 4.0K Jul 17 16:57 .
drwxrwxrwt. 15 root     root      4.0K Jul 17 17:05 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 17:46 MANFHet_4_FASTQC
-rw-r--r--   1 varsha97 waxmanlab  26G Jul 17 16:43 SRR8261645_1.fastq
-rw-r--r--   1 varsha97 waxmanlab  26G Jul 17 16:48 SRR8261645_2.fastq
==========================================================
Finished on : Wed Jul 17 17:46:25 EDT 2019
1 hours, 9 minutes and 44 seconds elapsed.
==========================================================