-----------------------
Start of variable list:
-----------------------
Sample_ID:
MANFHet_1
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-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/Scripts/02_FASTQC
Current job ID : 7774441
Current job name : Step_02_MANFHet_1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7774441.1.linga

Loading required modules...


List files in scratch directory:

total 9.7G
drwx------  3 varsha97 waxmanlab 4.0K Jul 17 16:47 .
drwxrwxrwt. 6 root     root      4.0K Jul 17 16:36 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul 17 16:47 MANFHet_1_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 4.6G Jul 17 16:42 SRR8261642_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 5.1G Jul 17 16:47 SRR8261642_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261642_1.fastq <==
@SRR8261642.1 1/1
NGCCATTTGGGTTTTGCTTTTACTGCAGGAGGGGACTGTGGGGTGCCACTTGCTGGCAGGGACTTTAGGGGCTGAGAGTCCACAGGAGGAGGAGTGGGAGGGGGTGGAAACTGACTGGCTATCTGCTTCACAAGATCGGAAGAGCACACG
+
#AAFAFFJJJJFF<<JJJJJJJJJJJJJJJ<JJJ-7AF-FFJJFAJJJF<<JJ7AFFJFFAJJ<AJFJJJFJFFFJA<AAFJJJJJJJJFJJFJAAFJJJJJJJ<J7F7JJAFF-<FJJJJFJJFJJJJJJJJFF-FJJJJJ<A-AJJJF
@SRR8261642.2 2/1
NACAGCATGTGTCATCATTTGTTCTGATGCCATGGGCTGACCTCTCAGCTTCAACAGAATTCCTATATACTGGGCCTATTTTTCTCTGGTTTCAGATCAGCCAGTTTGCAGAAAGCCACTCTGTGCATCCCGAGTCTACCTTGTCAGTTA
+
#AAFFFJFJJJJJJAJJFJJJJJJJJJFJJJJF<FJJ7FJFJFJFJF-AJJJJFJJFFJ<JFJJJAJJJJJJJJJJAAFAFFFJJJJFAAFFJJFJJJJJJJJJJJJJJJFJJJJJAAAFJFF7-AFFJJJJJ-<<FJFJJJJAJJJJJA
@SRR8261642.3 3/1
NCAGGAATCTCCAAAGTCCGACCCAGGTTATTTAGGGGGTCGAGGTTGTAGACTAACTCTTCTCTGTGGATGGCTCCTTCCTTCTCAATTTGGAGAATCTTAGACACAGCATCCCCTAAATCAAAAACCCCTCGAGCCACCACCTTCAGG
+
#AAFFFJAJJJJJJJFJJJJJJJJJJJFFFAJFJJJJJJ<FJJJJJJJJJJJJJFJJJJJJAJJJJJF<AFJJ<JJFJFJAJJJJJJFFFJFAFFJJFJJJJFJ<FJFJJJJ7J<JA7AFJJJJJJJJJJFAJFJJJJJJJJ<J<AAFFF
@SRR8261642.4 4/1
NACCTTTCTCCCCCTGGAAAGCCAAGCCCCAGATGATGGGTCTTCCCACAAAAACGGCCTTGGCTCCTAGGGCCAGAGCTTTGAGAACATCAGTACCTTTCCTTACTCCCCCATCCAGGAAGACTTAGATCGGAAGAGCACACGTCTGAA
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@SRR8261642.5 5/1
NTTTAAGTTGGTGGCAAGGGGCATCATCGAGGTGTGCAGGTTGTCCACATTCTCCTTGATCGTGGTCTGCATGCGCTGGATGTATGGGGTCAGCTGGAGCTTCATTTCCTGGGTCTGTGTGTTGATCTGATCTTGCAGGTCCACGGCATA
+
#AAFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJFJJJJJJJJJJJJJJJJFF7FJFJJJJJJJJJJJJJJJJFJJJJJFFFFJJFJJFJFJJJJAFJJJFFJA

==> SRR8261642_2.fastq <==
@SRR8261642.1 1/2
NGTGAGGCAGATAGCCAGTCAGTTTCCACCCCCTCCCACTCCTCCTCCTGTGGACTCTCAGCCCCTAAAGGCCCTGCCAGCAAGTGGCACCCCACAGTCCCCTCCTGCAGTAAAAGCAAAACCCAAATGGCAAGATCGGAAGAGCGTCGT
+
#AA-7--A777<AFF-FA<AAF<7-<FAJFJ7JJJJJJJFJJJJJFJJJAA-F<F-F7FF-AJFJ-FF-7-7AFJF7JFJJJJJJFJJJJJJJJJAFA7FJFA-FFJF-FAFFJFJFJJJJJJJJJ-7777<J)-<FA7---<-A)<A<)
@SRR8261642.2 2/2
NACAATATCAAGTCAGATACATTCTGTCAGGAGCTGGTAACTGACAAGGTAGACTCGGGATGCACAGAGTGGCTTTCTGCAAACTGGCTGATCTGAAACCAGAGAAAAATAGGCCCAGTATATAGGAATTCTGTTGAAGCTGAGAGGTCA
+
#AAA7AJJJFJJFF<FJ<FAF-F<-77FAJJJF-7FAFFFFAAFFJJFJ-FF<J7AJJJJJJJJJJJJ-AFJFJFFA-AFJJJJJJJJFJFJJ<-AFJJFJJJJAFJF<FJJ--AJFF<FFJ--7FJA<A7AJJJ-AJF-7-AAFFA-77
@SRR8261642.3 3/2
NTGCCAGCAGGTTCTGCCCGGCCTGTGGCCTTCTCTGTGGTACCCACAGCTGCTGCCAACGTGCCCCTGAAGGTGGTGGCTCGAGGGGTTTTTGATTTAGGGGATGCTGTGTCTAAGATTCTCAAAATTGAGAAGGAAGGACCCATCCAC
+
#A-AFF-A<7F<FJJJJJJ<FJ7AFJJJAJJJJ<JFFJJJJF<7AJJFFJJ<FJJJJFJJJJFJJJF<JJJJJFJFFAAAF-77FAJJJJAJAJ<JA<JJJJJJAJJJFJA7AFFJ--F-7<F-<AJJAFJAFF7<-AFF7-<<<FFF-F
@SRR8261642.4 4/2
NAGTCTTCCTGGATGGGGGAGTAAGGAAAGGTACTGATGTTCTCAAAGCTCTGGCCCTAGGAGCCAAGGCCGTTTTTGTGGGAAGACCCATCATCTGGGGCTTGGCTTTCCAGGGGGAGAAAGGTTAGATCGGAAGAGCGTCGTGTAGGG
+
#AAFFJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJFJJFJJJJJJJFJJJJJJJJJJJJJJ7AJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFJAJJJJJJJJJJJJJJJJFAAFFFJJJFJ
@SRR8261642.5 5/2
NCTGAAGCCCTATGCCGTGGACCTGCAAGATCAGATCAACACACAGACCCAGGAAATGAAGCTCCAGCTGACCCCATACATCCAGCGCATGCAGACCACGATCAAGGAGAATGTGGACAACCTGCACACCTCGATGATGCCCCTTGCCAC
+
#AAFFJJJJJJJJJJJJJJJJJJFJJJJJFFJJJJFJJJJJJJJAFJJ<JJJJFJJJJJJJJJJJJJJJAFJJJJJJJJJJJJJFJFJJJJJJJJJJJJJFJJJJJJJJJJJJJJFJJAAJJJJJJJJJJJFJJJAA<FAFJJJF-AJFF

Starting FASTQC command


Processing SRR8261642_1.fastq

Printing command:
fastqc --outdir SRR8261642_1.fastq

Analysis complete for SRR8261642_1.fastq

Processing SRR8261642_2.fastq

Printing command:
fastqc --outdir SRR8261642_2.fastq

Analysis complete for SRR8261642_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 45G
drwx------  3 varsha97 waxmanlab 4.0K Jul 17 16:54 .
drwxrwxrwt. 9 root     root      4.0K Jul 17 17:05 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul 17 17:24 MANFHet_1_FASTQC
-rw-r--r--  1 varsha97 waxmanlab  23G Jul 17 16:42 SRR8261642_1.fastq
-rw-r--r--  1 varsha97 waxmanlab  23G Jul 17 16:47 SRR8261642_2.fastq
==========================================================
Finished on : Wed Jul 17 17:24:45 EDT 2019
0 hours, 48 minutes and 4 seconds elapsed.
==========================================================