-----------------------
Start of variable list:
-----------------------
Sample_ID:
8wk_ASNase3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE122243
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue May  7 20:31:15 EDT 2019
Running on node : scc-kb7
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/02_FASTQC
Current job ID : 5983572
Current job name : Step_02_8wk_ASNase3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5983572.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   3 kkarri waxmanlab 4.0K May  7 20:33 .
drwxrwxrwt. 44 root   root      168K May  7 20:31 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  7 20:33 8wk_ASNase3_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.0G May  7 20:33 SRR8168088.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

@SRR8168088.1 1/1
NCTTTCTGAACAAAGGCTGGAGTTGTCCAATTGCAGTTCTTCTTCGCATAGAAATGCAATTGGAATATTTACAAATCATAATCAACAGAGCCCCAGGGGCN
+
#<<BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR8168088.2 2/1
NAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTC
+
#<<BBFFFFFFFFFFFFFFFFFFFFFFFBFFFBFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFF<F/BFBFFFF<<FFFFFFFFFFFFFF
@SRR8168088.3 3/1
NTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAATGTTATGTTTACTCCTACGAATATGATGGCGAAGTGGGCTTTTGCTCATGTGTCATCTAGN
+
#<<BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR8168088.4 4/1
TAAAGAAGGAGCTCCTACAGAGAATAAGAACATTCCTTGCTCAGCATGCCAGCCTTTAAGGGTGAATTAGAATGTGTTGGTCTGTGGATTTATTTCTGAAN
+
B/<<BFBFFF<BFFFFFFF/<F<FFFFFBF//FFFFFFFFFFF<BFFFBFFFFF<FBFFFB</<BFF//</FFB<FFF</<<</<FBF<FFFFBBF<F/FF
@SRR8168088.5 5/1
GTTTAAAGAAATTTGTGTTCCTTAGGGTGTTGATTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGN
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFBFFFFFBFFFFFFB<//<BFFFFFFFFBFF

Starting FASTQC command


Processing SRR8168088.fastq

Printing command:
fastqc --outdir SRR8168088.fastq

Analysis complete for SRR8168088.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 8.8G
drwx------   3 kkarri waxmanlab 4.0K May  7 20:34 .
drwxrwxrwt. 44 root   root      168K May  7 20:31 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  7 20:40 8wk_ASNase3_FASTQC
-rw-r--r--   1 kkarri waxmanlab 8.8G May  7 20:33 SRR8168088.fastq
==========================================================
Finished on : Tue May  7 20:40:13 EDT 2019
0 hours, 8 minutes and 58 seconds elapsed.
==========================================================