-----------------------
Start of variable list:
-----------------------
Sample_ID:
IPO-2
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-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/02_FASTQC
Current job ID : 7044703
Current job name : Step_02_IPO-2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7044703.1.linga

Loading required modules...


List files in scratch directory:

total 3.3G
drwx------  3 varsha97 waxmanlab 4.0K Jun 24 11:53 .
drwxrwxrwt. 9 root     root      4.0K Jun 24 11:48 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 11:53 IPO-2_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.5G Jun 24 11:51 SRR7518417_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 1.8G Jun 24 11:53 SRR7518417_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7518417_1.fastq <==
@SRR7518417.1 1/1
NGGGTCTTTCATGCTACCTGTGGGAGAATTTTCAGTGGAAAGTTCTTCAATTTTGTCATTTTCTACTATATCATCTTGATCCAGCATCTTTTTGGAAAATGGTAATTCTGTGTCCTCTGGGAGACTCTGGAAGCCCCAAGGATTATCAAA
+
#AAFFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJFJJJJFJJFJFJJJJJJJJJJJJJJJJJJFFJJJJJJJJJFJJFFJJJFAJAFJJJJJJJJJJJJJJJ<A<-FF<<JJJJAAJJF
@SRR7518417.2 2/1
NTTCTTTCCAGTTTAAAATAAAATTAATTATAAACATTAAGTATAAACATTATGCCAGAAGTTGAAGGCTGTGCTGAATATGGGATAAGATTACATCTTTCTCAATGAATGGAAGTCTTAGAAATGAACCACACTGTGTTAGAGACAGCA
+
#AAFFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJ7JAJJJJJJJJJJJJJJJJJJJJJJJJ<JAJJJFA<AJJJJJF7FJJJJJJAFJJJAF-FFAFFFJFJAF<JAJA<F
@SRR7518417.3 3/1
NCAGGTTTCAGGAAAATATTTTCGAATGGTCTCTGTAAGTGGATCATTCGATGATGGATCTTTACGTGGTGGCTCTTCAGGTCTTTTACTCAATGTTGTGCGTAAACTCCAAGAAATTTCAGGGGTAAATGCAAGATCAAATTCCACACG
+
#AAFFFAJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJFJFFJJJJFJJJJJJJJJJJJJJJJFJJJJJJF<FFJJJFFFJJJJJJJJFFAJJAJJJJJJJ-7FJJJJ7FJFFF77JFJ7A
@SRR7518417.4 4/1
NCCAGCGCCTCTTCCTGACATCCACAGACTGATTGGATGCAATGCGCTGGACATCTCCCCAGTGCTGCAAGGATAGACTGAGGGGGGGTAGTTACGGTCTGTCCCATGATCTCGAAAACACTTAAAGACAGGAGAAAAGAAAGGAAGAGC
+
#<AAA-FAFJJ<JFJJF<-F<7<FFJJFJ<FJ-F--<7-AJJFAAA7<JJJFJAAJAJ<7<A<FJFJFJ-7777A<F<F-AAJJFJA<7A<--7-A7-7A-7--7<-77<<-A7-77-A<7---<JAFFAJFA)-AFFJJ--7--<--7-
@SRR7518417.5 5/1
NCCATCTGTACGTCCAGCATCGTCACTGGGATGAAGCTGCTTCTGTGTTAGGCTTTGAGCCAGATTCCCTGGCATAGCCTTCAACACATTTGTCTTTTCAGTTTACTCCCAACTCAACTGTATATTCTGAGGGCCTGATGCAGATAGATC
+
#AAA7FJFJJFJJJJJFJJJJJJJJJF<FJJJJ<7FAFJFJJFJJJJJJJFA77<FJJJ<F<F<AFFJJJJFF-F<A7<AJ<JJA-7-FAFFJFJJJJJ<<AFJA<<-7<77F<-AAF<F<AAFA-7-<AAJF-FFJJ<FF<-77-7FA<

==> SRR7518417_2.fastq <==
@SRR7518417.1 1/2
NGAACAAGAAAGGAAAATAGTAACTGTGGAAACCGAAGACCAGGCAGGTACAGAAAGCGTCTTGGAGAAGACAGACGAGTCTGGTTCCATGCAGTATCTGAAGAAGTTCTTTGATAATCCTTGGGGCTTCCAGAGTCTCCCAGAGGACAC
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJAFAJFFFFJJFJJJJJFJJJFJJFFJJFFJJJJJJJJ<7FFJJFJJAA<<FJJJJFJJJ<77A77))7<AFAFF<A<7A-)--7))<-7-7
@SRR7518417.2 2/2
NTTAATTTAAACAGTCAGTAGCTGGGATGTGCTGTCTCTAACACAGTGTGGTTCATTTCTAAGACTTCCATTCATTGAGAAAGATGTAATCTTATCCCATATTAAGCACAGCCTTCAACTTCTGGCATAATGTTTATACTTAATGTTTAT
+
#AAFFJJJJJJJJJFFJJJJJJJJJJJJJFJJJJJJJFJJJJJJJJJFJJJJJFJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJFJJJFFJJJ<AF-7FFFFJ-AF-FFJJ7JAJ7<JF7--<--7AFJJ<-<7-<7A-<<FF<<777A7
@SRR7518417.3 3/2
NTGGAACTGAGAAGGATGTCTATAGATATGTGGAGGACATGGGTTTAACAGCATTCACCAACTTGATGATCAAACTTCCTATAATTTGTTTTGACTATGGCATGGTTCCAATATCAGCACCTCGTGTGGAATTTGATCTTGCATTTACCC
+
#AAFFJFJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJ<JFJJJJJ-FJJJ7AFJJJJJJJJJFJJJJJJJJJJFJJFFJAJF-)FFFJA7FJ7FA-A-A))7AFFAJ-<-7<7A<<FJJJJA7FF
@SRR7518417.4 4/2
NTTCTCCTGTCTTTAAGTGTTTTCGAGATCATGGGACAGACCGTAACTACCCCCCCTGAGTCTAACCTTGCAGCACTGGGGAGATGTCAAGCGCATTGCATCCAATCAGTCTGTGGATGTAAGGAAGAGGCGCAGGGAGATCGGAAGAGC
+
#AAAFAAFJ--<<FJFFJJAFJJ<7-FJ7JFJJAJFFJFF<A7-FFF<JAFFFJAFF7J7-7-AF-AJJ7--<<AA7-JA---7F<F<-77AF-7FAF-F<-AFFA-AF--7A<7J7<JA-77<A-7<<7-<))))-))---AFAF7FF-
@SRR7518417.5 5/2
NTCTGCATCAGGCCCTCAGAATATACAGTTGAGTTGGGAGTAAACTGAAAAGACAAATGTGTTGAAGGCTATGCCAGGGAATCTGGCTCAAAGCCTAACACAGAAGCAGCTTCATCCCAGTGACGATGCTGGACGTACAGATGGAAGATC
+
#AAFFFFJ<JJFJJJFFJJJJJJJJJJJJJJJJJJJJFFFAFAJJJFFJ7FFJFJFJJJJ<JJJJ<FFAAAJJJJJJJJ<AAFJJJFJJJFJJFF-7-F<J<AF<<AAFFFJA<7--)FA7-A<F7FJJJJA-A<AF7<A7<7FFFFAF<

Starting FASTQC command


Processing SRR7518417_1.fastq

Printing command:
fastqc --outdir SRR7518417_1.fastq

Analysis complete for SRR7518417_1.fastq

Processing SRR7518417_2.fastq

Printing command:
fastqc --outdir SRR7518417_2.fastq

Analysis complete for SRR7518417_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 13G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 11:55 .
drwxrwxrwt. 10 root     root      4.0K Jun 24 12:02 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 12:03 IPO-2_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 6.2G Jun 24 11:51 SRR7518417_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 6.2G Jun 24 11:53 SRR7518417_2.fastq
==========================================================
Finished on : Mon Jun 24 12:03:22 EDT 2019
0 hours, 14 minutes and 33 seconds elapsed.
==========================================================