-----------------------
Start of variable list:
-----------------------
Sample_ID:
MANFHet_2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE123116
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Jul 12 13:11:36 EDT 2019
Running on node : scc-bc3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/02_FASTQC
Current job ID : 7678229
Current job name : Step_02_MANFHet_2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7678229.1.b

Loading required modules...


List files in scratch directory:

total 9.0G
drwx------   3 varsha97 waxmanlab 4.0K Jul 12 13:30 .
drwxrwxrwt. 23 root     root      4.0K Jul 12 13:26 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 12 13:30 MANFHet_2_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 4.3G Jul 12 13:20 SRR8261643_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 4.8G Jul 12 13:30 SRR8261643_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261643_1.fastq <==
@SRR8261643.1 1/1
NGAGAATTGTCATGGGTATGTCAAAGAGAAATTTAAAGAAAGACTTTGATTCTTGATGAGTTATCCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTG
+
#AAFFFJ<AAFFFJFJ7FFJJFJJJJJA<JJ<FAAJJJJFJJJFJJ-<FJJFFFFJJJJJ--FFJFAJJFJJJJJJFJJJFA-AJJFJJ<AFJFFJ7--FFJFAFJJ--FAFAJJJFJFFFJFJJFFFJJJJAA7FJJJJAJJ-AAFJJF
@SRR8261643.2 2/1
NTTGCAGACCTTCCGCACCTCAGCGGAGTCGACACGGCGGCCCCCAACAGGCCTGAGGATGTTCCGAACCGAAGCCGACTTCTGAAACGGACGCTTGAGGAGGCTCTTCACGGGGAGCACCGTCTGCGGTGAGGACGGCTGCGGTTGCAC
+
#AAFFFJFJJJJJJJJJJJJJJJJJFFJAJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJJJJJAJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJ7FFJFJJJJJJFJJ<JJJJJJJAFAJJJJFA<JJJJJJFJ<AJJJJJJFJJFJJJJJ
@SRR8261643.3 3/1
NGGGTTTCTCCCAAAGGCCTGAGGGAACAAGGAAGAGAGAGAAGCCAAATCTTTCTACAGGGAATGCAACCTGCAGCCCAGAGCCATGGTATAGCCTCCAAAGACCCTCACTGTCACTGGGCCCCACTGGGAGGAATAGTGGATCTCCTT
+
#AAFFJJJFFFFJJJJJJ<FJJJFFJJJFJJJJJJJJJJJJFFJJFAFJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJFJFJJJJJJJFJJJFAFJJAFAJJJJJJFJJJJJJJJJFFJJFJFFJJJFJA-FJJJJ<AFJJJJJFJJFJ
@SRR8261643.4 4/1
NAGGAATCAGAATGTCACAGTCAGCCTCCAAGATGCTTCCTTCATAGACCTTGGCTTTGGGGAAGCCCAGAATTGATCCATGTTGCAACTTGAAGTCTTCCAGTTCTTTTGGGTCAATCCCATCCGGATTCCATATACTCCCATCAGACT
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJAJJJJFJFJJJJJJJJJFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJAAJJJJJJJJJJJFFJJFJJJFJJJJJJJJJJJJJFJ7AJJJFA7FJFF<JFFFJJFJJJJJJJJJJJJJJJJJ
@SRR8261643.5 5/1
NCCTTCTCTTTGACAGCCGGGTGTTTGCGCACAAGCAGCCAACCCACGTGAGAGAAGAAGAAGCCACGGCGGGAATTGTGAGGGTCGGCGTGTGTTTCTGAGAACTTGTGGTGGGCGCGGTGATCTCGGGCCCATTCGTACACGTCATTC
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJ<JJJJJJFJJJFJ<JJJJAJJJJJJJJJJJJJJJJJJJJJJJJFA

==> SRR8261643_2.fastq <==
@SRR8261643.1 1/2
NATTGACCTAACCAATGCCAATCGCTGCCTTGAGCCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGAGTTCTCACCAGGACTCCAGGATCAGTCCTTCCTATCCATACAGCATCCAGTACGAAGTTCTGTGATCTTCT
+
#AAF--7AFF<F7FJ<<FFFF-<<JFFJF<F-<J-7A<FJJJJJ<FJ7-7<<F-A-7--7A7J<<<AAJ-7AF-7<7AF-A-F--<FFJJJJJAJ-FF-FF7F7-JJJF7<<AF-F-AFJ-FA7AF)-<-<---7-7F<<-<<F<<--77
@SRR8261643.2 2/2
NCAACCTGTGGATTACGGCCTCAATGATTCCATGTACCTGATCACCAAGCAGCTGCAGTTCCTGTGGGCGGTGCCTCTCATCCGCATTCTCTTCAGTGACATCCTGAGCAGGAAGCTGCTGGAGCATGCACAGCCGGCCCCCGTGCAACC
+
#A<AFF-7A7<F-FJFJJ-7FJ-FFJ7JFJJJAJ7AJJJJJJ7FAJJJJJFJJJJJFJFAJJ7-7-F7FJ7<J7FJF-FFFF7J<JJ7FAJ<-A7<-FAJF-FFFFJJFJFJ<<AF--)---7FFJA-7<--)7J))--<F)-<)-)7-A
@SRR8261643.3 3/2
NGGTTGAGAACTGCTGTTCTAGATGCTTCTCAATTGAATCTAGCTGCCAAACGAGATCCACTATTCCTCCCAGTGGGGCCCAGTGACAGTGAGGGTCTTTGGAGGCTATACCATGGCTCTGGGCTGCAGGTTGCATTCCCTTGAGAAAGA
+
#AA---FJ-FFJJJJ<F<---F-FAJAA<JJFFAJFF<AAF-<AA7<JJJJ-FFJJ7JJJJJ7FAF<JFJFFJJJ-AAJJAAF7A<JJJJJJJJAAJJ<FJJFFJJFJ<AJJ-FJJF<7AAF<<AA<A))--<AAFJF7<--)--<F<7<
@SRR8261643.4 4/2
NTTGGAAACCCATCAGTCAAGGAGGCATCCACGGGCGCATCTCCGCTACTGGGCGGGGTGTCTTCCATGGAATTGAAAACTTCATCAATGAGGCTTCTTACATGAGCATTTTAGGAATGACACCAGGCTTTGGCGATAAGACATTTGTTG
+
#A-AA--AA<-FFJJJFJF7FJJFJ<AJJJJJA<FFFJJJFJFA<JJF<A7--7A<<JFFJJJJF-AFJFAFFJJJFF<J<-FJF-FFJJJJFAFJJJJJAFFFJ<FF7JJF<<F<JJJFJJJFJ<<J7JJ<FF)AAJF--<7<<F<F<7
@SRR8261643.5 5/2
NCGGAGCTTCCTTATCATTGCCAACACCATGGCGTTCCAGAATGACGTGTACGAATGGGCCCGAGATCACCGCGCCCACCACAAGTTCTCAGAAACACACGCCGACCCTCACAATTCCCGCCGTGGCTTCTTCTTCTCTCACGTGGGTTG
+
#AAFF-FJFJJJJJJJJJJAJJJJJJJJJJJFJJJJJJJJJFJFJJAJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJAFFJJJJJJJJJJ7JJJJJFAJJJJJJJJJJJJJJFJJJJJJJFJFF<FAA<FA)

Starting FASTQC command


Processing SRR8261643_1.fastq

Printing command:
fastqc --outdir SRR8261643_1.fastq

Analysis complete for SRR8261643_1.fastq

Processing SRR8261643_2.fastq

Printing command:
fastqc --outdir SRR8261643_2.fastq

Analysis complete for SRR8261643_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 41G
drwx------   3 varsha97 waxmanlab 4.0K Jul 12 13:37 .
drwxrwxrwt. 23 root     root      4.0K Jul 12 13:26 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 12 14:00 MANFHet_2_FASTQC
-rw-r--r--   1 varsha97 waxmanlab  21G Jul 12 13:20 SRR8261643_1.fastq
-rw-r--r--   1 varsha97 waxmanlab  21G Jul 12 13:30 SRR8261643_2.fastq
==========================================================
Finished on : Fri Jul 12 14:00:15 EDT 2019
0 hours, 48 minutes and 39 seconds elapsed.
==========================================================