-----------------------
Start of variable list:
-----------------------
Sample_ID:
NASH_PEG2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE126204
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 16:04:09 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/Scripts/02_FASTQC
Current job ID : 7055565
Current job name : Step_02_NASH_PEG2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055565.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:27 .
drwxrwxrwt. 21 root     root      4.0K Jun 24 16:19 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:27 NASH_PEG2_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 954M Jun 24 16:19 SRR8543823_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 1.1G Jun 24 16:27 SRR8543823_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8543823_1.fastq <==
@SRR8543823.1 1/1
GCCCGGCTGAAGCTGAAGGTTCTGTANTTTCATGGCCAGTCCCATGTTACCANCAATCTTCAGTTTNCCTTGAA
+
AAFFFJJJJJJJJJJJJJJJFJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJFJJJJJ#JJJJJFJ
@SRR8543823.2 2/1
GTAGAAGTAAAATAATAAATGTAATGGTAGCTGTTGGTGGGCTAATATTTATTAATACTAGAGTAGNTCCTCCGAT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJFJJJFJFFJJFFJJJFJJJJJJJJFJJJJJJJJJJJJJJ#JJJFJJJJF
@SRR8543823.3 3/1
CATAGGCGATGATGATTGATGGTTGCCGCTTTTGGAAGACCTGTGGTTCCCGAAGTATAAATGTATNCTGCTGGCG
+
AAFFFJJJJFJJFJJJJJJJJJFJJJJJJAFJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJF#JJJJJJJJJ
@SRR8543823.4 4/1
GGAGGGTGAATACGTAGGCTTGAATTAATGCTACTGCAAATTCTAGAATTGTGAGTAGAAGTAAAANAATAAATGT
+
AAAFFFJJFJFFJJ-FJFJ<JFJJJJFJFJJJJJJJJJJJFJJJJJJFJJJJJJJFJJJJFJJJJF#<JJJJJJJF
@SRR8543823.5 5/1
CCCACATCCCCATTCAGATTCCTTTCTGCAACCTAACAGGTTTAGCCAAAGTGAGTGCACTAGCCTNGTCTGGCCT
+
AAFFFJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJ#JJJJJAAJJ

==> SRR8543823_2.fastq <==
@SRR8543823.1 1/2
TGACTGCANAATCACNATGNNNGACTCAGANNTGCTGNNTTNGANGACTGNAANAATGNACCCTCNGTNNGCNNTC
+
AAFFFJJJ#JJJJJJ#JJJ###JJJJJFJ<##JFJJJ##FF#JF#FJFJJ#FJ#JJJJ#JJJJJJ#FF##FF##JF
@SRR8543823.2 2/2
AATACTTANTATTATTGAANNAATTAGCCTNNTTATTNNACNAANGGCATTAGNAGTCNGGCTTANAGNTAANNTT
+
AAFFFJJJ#JJJJJJJJJJ##FJJJJJJJJ##JJJJJ##JJ#FJ#FFJJJJJJ#JJJJ#JFJJJJ#JJ#JJJ##JJ
@SRR8543823.3 3/2
GATGCCGTNTCCGTCTTTTNNGTAAGCAGAANTTCTANNACNAANGGTGTGGANACAANACTGGANAANGTANNCG
+
AAFFFJJF#JJJJ7JJJFJ##JJJJJJJJJF#AFJJJ##JJ#AJ#JJJJJF<F#FFJJ#FJJFFF#7F#FAF##JJ
@SRR8543823.4 4/2
CTACTCTANTATTAATAAATNTTAGCCCACCNACAGCNNCCNTTNCATTTATTNTTTTNCTTCTANTCNCAANNCT
+
AA-FFJJJ#JJFJJJJJJJF#AJJJJJJJJJ#JJJJJ##JF#<J#FJJFJJJF#FJJJ#JJJJJF#JJ#JJJ##JA
@SRR8543823.5 5/2
GGGGAATANCATAGAGGGAANCCTGGCCCAAGCTTGGNGCTNCANTTCAGTGANAGCANGAAGGCNAGNCTANNCT
+
AAFFFJJJ#JJJJF<AJFFJ#JJJJJJJJJJJJFJJJ#JJJ#JJ#JFJJA-FJ#FJJJ#JFFJJJ#<J#FJJ##J-

Starting FASTQC command


Processing SRR8543823_1.fastq

Printing command:
fastqc --outdir SRR8543823_1.fastq

Analysis complete for SRR8543823_1.fastq

Processing SRR8543823_2.fastq

Printing command:
fastqc --outdir SRR8543823_2.fastq

Analysis complete for SRR8543823_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 8.6G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:31 .
drwxrwxrwt. 18 root     root      4.0K Jun 24 16:41 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:43 NASH_PEG2_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 4.3G Jun 24 16:19 SRR8543823_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 4.3G Jun 24 16:27 SRR8543823_2.fastq
==========================================================
Finished on : Mon Jun 24 16:43:09 EDT 2019
0 hours, 39 minutes and 2 seconds elapsed.
==========================================================