-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE77729_PB_ENV
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 10:59:35 EDT 2019
Running on node : scc-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/02_FASTQC
Current job ID : 5784541
Current job name : Step_02_WT1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5784541.1.linga

Loading required modules...


List files in scratch directory:

total 5.5G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 11:01 .
drwxrwxrwt. 65 root   root       92K Apr 30 10:59 ..
-rw-r--r--   1 kkarri waxmanlab 2.7G Apr 30 11:00 SRR3157436_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.8G Apr 30 11:01 SRR3157436_R2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 11:01 WT1_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR3157436_R1.fastq <==
@SRR3157436.69301298 69301298/1
CATGGGACTAAAANCTGAGTCACAGTAAGTGAGCAGCTCGTGCAGTGTCAC
+
CCCFFFFFHHHHH#3AFHIIIJJJJIIIIGGIIGHBHIIJDEGHIHIIGGI
@SRR3157436.69301299 69301299/1
GGGCCATAAGAAAGTTATCATAGTCTGTCTTAGGTATAGTAAATGTATTGA
+
C@@FFFFFGHGHHICEGIJGFHHGIJJGIIGCHGHHIIGCHGCGGFHIJFI
@SRR3157436.69301300 69301300/1
CCACCTCCAGGCGCTTCATGTCTATCAACTGAGCCCGGACATTGCTCTGCA
+
?<?DDFDFBF?FHEEFG4?ECFEHIIIGIE@DD?FBD<DHBEHICHAEAFH
@SRR3157436.69301301 69301301/1
GTCTGTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATA
+
C@CFFFFFHHHHFBFGIBIHGEHGIIHGIGIIJJJJJJGHIHIIIJJIBGD
@SRR3157436.69301302 69301302/1
TGTGGATTAGCATTATTTGTTTGATAATAAGTTTAACTAGTCAGTGTTGGA
+
B@@DDFFFHHHGHJJJJIIHIJJIJJIJJIJIIIIHHHGIHIJJGHJJJHH

==> SRR3157436_R2.fastq <==
@SRR3157436.1 1/2
GACCGGGACAGCCCAGTGTTCTGGTACGCTCCGGAATGTTTAATCCAGTGT
+
@@CFFFFFHHHHHJJJIJIJJJJIGEIIJIJJJJJJJJJIJJIIJJIJJJJ
@SRR3157436.2 2/2
CTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATG
+
CCCFFFDFHFDHHJJGIGGIJJJJJJJJJJJGIJIIIJGIIGGIJJJDG@B
@SRR3157436.3 3/2
TTTGATAACACTTATGGGCAAGTGTCAGAAGACCTGAGGCGCAGAATTGAG
+
@@@DDDADHHHFHGGGHIIIECEHHGGHHGIIGGHEHGBD8DGHIIIIGHE
@SRR3157436.4 4/2
GCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATT
+
@CCFFFFFHBDDHIGHIIIIHGCHIIIIGGIIIIIGFGIIIGHGGIIIGIB
@SRR3157436.5 5/2
TGTAGCCATCATTATATTTCCTTCAATCCTATTCCCATCCTCAAAACGCCT
+
@CBFFFFFHFHHGJJIJJJJJIJIJJIJIIIHIJJJIIIGIIIIGIGIIIF

Starting FASTQC command


Processing SRR3157436_R1.fastq

Printing command:
fastqc --outdir SRR3157436_R1.fastq

Analysis complete for SRR3157436_R1.fastq

Processing SRR3157436_R2.fastq

Printing command:
fastqc --outdir SRR3157436_R2.fastq

Analysis complete for SRR3157436_R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 18G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 11:05 .
drwxrwxrwt. 47 root   root       92K Apr 30 11:13 ..
-rw-r--r--   1 kkarri waxmanlab 9.0G Apr 30 11:00 SRR3157436_R1.fastq
-rw-r--r--   1 kkarri waxmanlab 8.9G Apr 30 11:01 SRR3157436_R2.fastq
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 11:20 WT1_FASTQC
==========================================================
Finished on : Tue Apr 30 11:20:23 EDT 2019
0 hours, 20 minutes and 48 seconds elapsed.
==========================================================