-----------------------
Start of variable list:
-----------------------
Sample_ID:
IPO-1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE117066
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 11:48:49 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/02_FASTQC
Current job ID : 7044702
Current job name : Step_02_IPO-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7044702.1.linga

Loading required modules...


List files in scratch directory:

total 2.8G
drwx------  3 varsha97 waxmanlab 4.0K Jun 24 11:51 .
drwxrwxrwt. 6 root     root      4.0K Jun 24 11:48 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 11:51 IPO-1_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.3G Jun 24 11:49 SRR7518416_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 1.5G Jun 24 11:51 SRR7518416_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7518416_1.fastq <==
@SRR7518416.1 1/1
NTGTGGTTCAGTAGCACCTCCTTGACAGCCTTGTAGCCATGCAGGACCAAGATGCGCCTCTGACCCAGGTGCAGTGTGAACACTGGCCCGAAGCGCTTTGCCAACTTGGTTAAAGACTTGGGAGATCGGAAGAGCATACGTCTGAACTCC
+
#A-AFF7FJFFJJJJFJFJJ<FJ-FFJFFFJFAJJFJ<JFJJJJJJ--F-7FFJFFFJ<AFJFJFJ<AJJJ<AJ-FAAFJAJFF7F7A-A7A-A<AAJ7---7F7-7F-<FJFA7<--7<AA<7AA7<FJA)<A-7-A<--7-7<A<<--
@SRR7518416.2 2/1
NGAGGATTTGAACTGGAGCAGAGAGACCCATCAGTCCCCAACGCTTCTGGTCGCCGCAGCATCTTGAATCACGCTGTTTCTTTTCCACGCCGCTTTGTTCCCGCTGTACCCCATACGTGAAAACCACATTCTCCCGAAACTAAAAAATCG
+
#AAAFJFJFFJJAFF-AF<AJ7FFAJJA<-FFJ<FF--7FJ-A--7-FFJA-FA-AAAFJFJF<<FJFFFF--7-7-77777FF--<<----77<-<A----7-7-A--7<--7---7-7F<---7-A<A-<<-<-7A--7A-7--7---
@SRR7518416.3 3/1
NTCTTGTTTTGTACAGCAGTCAGCCAGTTCACCATAGTTTTCACGGAGGTTTGGAATGGCACACAACTTATCTCCAAAAAGAGTGTGAAGGGATTTGTCACAGTTGGCGGCAGACTCATCGGCAACACACGTCTTTGCAAAGTCTGTTAC
+
#AAFFJFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJAJJ<FJFJJJJJJJJJJJJJJJJJJ<FFAJJJJJJJJAJFJJJJJJFFJJJJFJJJFJJJJJJJJJJJJJ7JJJJA<JJJJJJJJJFFJJF<F7FJFJJJJJJF
@SRR7518416.4 4/1
NGGATAATAATAAAGACAACACCTTATTGTGCTGAGATGAAGAACACACAGCTCAGTCCCTCACACGATGCAAATGCTCAGGAGACATTGACCATATTTTATGTAGCAGATGCCAAATCTCAGAGGGACCCTTAGATAGCAATGGCTCGG
+
#AA<AJJJJJJJJJJJJJJJJ<JJJJJJJJFAFAJJJJJJJJJJJJFJFJFA77FJFF-AAJJJJJJJFFF7<F-AA7<JF<JFAFJJAAJA-<<FJJJFJJFJJ777-FA--<-7-7<--A-7-A7<F)))7<7FA-<7<A-<-7--)-
@SRR7518416.5 5/1
NTCATGAGTGTCTTCAAGTTATAGTTTCCAGAGATGGACAGTCTGGGGATATGGATCTGAGCATCGCTTCTGCGCCTGTTTAGCAGGAACTGAGAGATGAGCTCCTTGTTGAGAGTTTGCTCCAGATGCTGCATCTTCCCATCATCGGGC
+
#AAAFJJJJJJJJJJJJFAFJJJJJJJJJJJJJJJJJJJJJFJFFFFJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJFJJJFJ<JAFAAJJJJJJFFFJFJ--77AFAFJF<FJFJJ<----FAA<<A7-

==> SRR7518416_2.fastq <==
@SRR7518416.1 1/2
NCCAAGTCTTTAACCAAGTTGGCAAAGCGCTTCGGGCCAGTGTTCACACTGCACCTGGGTCAGAGGCGCATCGTGGTCCTGCATGGCTACAAGGCTGTCAAGGAGGTGCTACTGAACAACAAAGAACGGAAGAGAAATGTGAAGGGAAAG
+
#AAAFFJFJJJJJJFJJJFJJJJJJFFJJJJJJJJJFJJFJJJJJFJJFJFFJAJJ<AFFAFFFF<<<<J<AJFAF<-AAAFJF<F7AAFJJF--<<-7<--<AF)AA<<--AFJ<FAJ<7AA----77<F-<-------7--<-7----
@SRR7518416.2 2/2
NGGAAAATGAAAGGACTGGCGTTCATTCAAGACCCTGACGGCTACTGGATTGAGATTCTGAATCCTAACAAAATAGCAACGATTATTTAGTTTCGGGAGAATGTGCCTTTGAGGTATGGGGGAAAGCGGGAACAAAGCGGCGTGGAAAAG
+
#AAAFAJJAJJFJJJJJJJ<F-F-<<FFAJAFF7<7AJA<<-7A-FFF7FFJJJAJJ<<FA---7AJF<<FJA-A-77F7JJAFFFJA7FFJF--F--A-7-FAF-)---77A<-AAA<F)-<)7--7))-77<FJA--)))))-7-<--
@SRR7518416.3 3/2
NTTTGGGAGAACAACATTTCAAAGGCCTAGTCCTGATTGCCTTTTCCCAGTATCTCCAGAAATGCTCATACGATGAGCATGCCAAATTAGTGCAGGAAGTAACAGACTTTGCAAAGACGTGTGTTGCCGATGAGTCTGCCGCCAACTGTG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJ<JJJJJJJJJFJJJJAJJJJJJJFJFFJJAAFJJJF<J7JAF<<F)7<AFAF--<F-)--)-7)AAFF
@SRR7518416.4 4/2
NTCTTCCTCCATTCTAGATATGTACCCAGATGAATATATTGCACAGACCTCTGGCTTCCCCTTTACATCTGCAGCCAGAGATTCCGAGCCATTGCTACCTAAGGGTCCCTCTGAGACTAGGCATACGCTAAATAAAATATGGTCAATGTC
+
#AAAFJJJJJAFJJFFJFJJJJJJFJFJAFJFJJFFJJFFJJJJF7J7JFAJJJF<A7<AJ7JJ<AJF7FF7F--7AAJFA<AAAA7<7<FAF7<AJ-A-<-77A-)--)<A<<FAA77-7)-----7<<-7A-7-AFF-------7---
@SRR7518416.5 5/2
NGCAAATGGAAACAGCCATTCGATCCTGAGAACACTGAGGAAGCTGAGTTCCATGTGGACGAGTCCACCACAGTGAAGGTGCCCATGATGACCCTCTCGGGCATGCTTGATGTGCATCATTGCAGCATGCTGTCCAGCTGGGTGCTGCTG
+
#AAFFJAJF<JJJJJJFJJJJFF-<J<FF7JJJJJJJJFJJJJFJFJJJJFJJFJJJFJFJJ-FAAJJFJJJJJAFJFJFJFFAJJJFJJJJJ-<A7-J<JFJAJ<A7F-FFFJ7F7A<A7A--7)<FA)7<F))7-)7))-7<)7))7<

Starting FASTQC command


Processing SRR7518416_1.fastq

Printing command:
fastqc --outdir SRR7518416_1.fastq

Analysis complete for SRR7518416_1.fastq

Processing SRR7518416_2.fastq

Printing command:
fastqc --outdir SRR7518416_2.fastq

Analysis complete for SRR7518416_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 11G
drwx------  3 varsha97 waxmanlab 4.0K Jun 24 11:52 .
drwxrwxrwt. 6 root     root      4.0K Jun 24 11:48 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 11:59 IPO-1_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 5.1G Jun 24 11:49 SRR7518416_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 5.1G Jun 24 11:51 SRR7518416_2.fastq
==========================================================
Finished on : Mon Jun 24 11:59:12 EDT 2019
0 hours, 10 minutes and 23 seconds elapsed.
==========================================================