-----------------------
Start of variable list:
-----------------------
Sample_ID:
NASH_PEG3
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 16:17:19 EDT 2019
Running on node : scc-ka5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/Scripts/02_FASTQC
Current job ID : 7055566
Current job name : Step_02_NASH_PEG3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055566.1.linga

Loading required modules...


List files in scratch directory:

total 2.4G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:35 .
drwxrwxrwt. 18 root     root      4.0K Jun 24 16:15 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:35 NASH_PEG3_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.1G Jun 24 16:26 SRR8543824_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 1.3G Jun 24 16:35 SRR8543824_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8543824_1.fastq <==
@SRR8543824.1 1/1
TCTGAAAGTATTGAGTGAACAGGCTCNGCATATCCGGTCCGTCTGCCTGTCTNTTAACCAAAGCTCNTTCCAGGCT
+
AAFFFJJJ<JJ<FJJJJJJJJJJJAJ#JJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJJJJJ#JJJJJJJJF
@SRR8543824.2 2/1
GTCGTTTGTTGGGATTATATATGAATNAAAGCATAGGTCTTCATAGTCAGTANATTCGTAGCTTCANTATCATTGG
+
AAFFFJJJJJJJJJAJJJJJJJJJJJ#JJJJJJJJJJFJJJJJJJJFJJJFF#JJJJJJJJJJJJJ#JJJJJJJJJ
@SRR8543824.3 3/1
GCCAGTATAGTAACCAGGTGTAACCTAACCCATCTTCATTGGCAGAGGTCCAAGAAGTTGAAGCTGNGTTCTTACT
+
AAFFFFJJJJJJJJJJJJ-FFJJJJJJJJJJJAF<JJJJJJJJJJJJJJJJ7JFFJJF7JFFJJAJ#FFJJJJJJ<
@SRR8543824.4 4/1
CTTGTCCATGCCAAACCTATTCAGAAGCCTGCGGGCCAGCAGCAGGCCAGTGCAATAGGCTGCAGCNTAATTTGTC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJFJJJJJJ
@SRR8543824.5 5/1
CATGTCGGCTCCGAGTCGGGCCTGTGCCGCCTGCACCTCTTTGCCCAGCCTGGCCCGTGTCTCCTCNGCCACTGG
+
AAFFFJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJ#JJJJJJJJ

==> SRR8543824_2.fastq <==
@SRR8543824.1 1/2
GGAAGGACNGCAGCANAGANNNGCACTGTTNNTAGGCNNTANTCNGCCATNATNAAGCNGCTCGCNATNNTCNNAC
+
A-<FFFFF#FJJJJJ#JJJ###JJJJJJFJ##JJJJJ##JJ#JJ#JJJJJ#JJ#JJJJ#JJJJJJ#JJ##JJ##JJ
@SRR8543824.2 2/2
ATTAACCGNTAAAACNATANNNCACCAATGNNACTGANNCTNCGNATATANTGNCTATNAAGACCNATNNTTNNAT
+
AAFFFJJJ#JJJJJJ#JJJ###JJJJJJJJ##JJJJJ##JJ#JJ#JJJJJ#JJ#JJJJ#JJJJJJ#JJ##JJ##JJ
@SRR8543824.3 3/2
AGTAAAATNACAAGCTATTNNCACCAGCATNNTCTATNNCTNATNTAGTTNGTNCAGCNTTTCATNGTNNTTNNTC
+
AAFF<JFJ#FJJJJJFJJF##JFJJAJJJF##JJJJJ##JJ#JJ#JJJJJ#JJ#JJFJ#JJFJFJ#JF##JJ##-7
@SRR8543824.4 4/2
AGAGGGTANAACTGACTACNNTGCTCGAAANNGATTGNNGANCCNGGACANGANTAAGNACAACANACNCAANNAT
+
AA<<FJJJ#JJJJFJJJJJ##JJJFJJJJJ##JJJJJ##JF#JJ#JJJJJ#JJ#JJJJ#JJJJJJ#JJ#JJJ##JJ
@SRR8543824.5 5/2
GACGCTGTNTGACCAGGTCNNGGAAGAGCTNNAGAGCNNCCNAGNCACACNAGNACTGNCGGCACNGANGGANNAC
+
AA<FFJJJ#JJJJJFJFJJ##JJJJJFJJJ##JJJJJ##JJ#FJ#FJJJJ#JJ#JJJJ#JFJFJJ#JJ#JJA##AF

Starting FASTQC command


Processing SRR8543824_1.fastq

Printing command:
fastqc --outdir SRR8543824_1.fastq

Analysis complete for SRR8543824_1.fastq

Processing SRR8543824_2.fastq

Printing command:
fastqc --outdir SRR8543824_2.fastq

Analysis complete for SRR8543824_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 9.6G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:37 .
drwxrwxrwt. 10 root     root      4.0K Jun 24 16:45 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:45 NASH_PEG3_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 4.8G Jun 24 16:26 SRR8543824_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 4.8G Jun 24 16:35 SRR8543824_2.fastq
==========================================================
Finished on : Mon Jun 24 16:45:25 EDT 2019
0 hours, 28 minutes and 6 seconds elapsed.
==========================================================